Data from Palsson Lab								Data from Hatzimanikatis Lab		
SimPheny ID	abbreviation	new since iJR904	officialName	equation	subSystem	proteinClass	geneAssociation	reaction notes	model notes	standard Gibbs free energy change	uncertainty in Gibbs energy	reaction equation
19848	12DGR120tipp	Yes	"1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)"	12dgr120[p] --> 12dgr120[c]	"Transport, Inner Membrane"			AMF	"not sure if the lipid actually is part of the membrane during the enzymatic reaction, then, no uptake would be needed and it would remain on the outer face of the inner membrane or alternatively, there is some type of reuptake to inner membrane or cytosol

AMF

LplT is a transporter for a similar molecule with 1-acyl chain and a phosphate group"	0	0	[c] : 12dgr120[p] --> 12dgr120[c] 
19849	12DGR140tipp	Yes	"1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:0)"	12dgr140[p] --> 12dgr140[c]	"Transport, Inner Membrane"			AMF	"not sure if the lipid actually is part of the membrane during the enzymatic reaction, then, no uptake would be needed and it would remain on the outer face of the inner membrane or alternatively, there is some type of reuptake to inner membrane or cytosol

AMF"	0	0	[c] : 12dgr140[p] --> 12dgr140[c] 
19847	12DGR141tipp	Yes	"1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:1)"	12dgr141[p] --> 12dgr141[c]	"Transport, Inner Membrane"			AMF	"not sure if the lipid actually is part of the membrane during the enzymatic reaction, then, no uptake would be needed and it would remain on the outer face of the inner membrane or alternatively, there is some type of reuptake to inner membrane or cytosol

AMF"	0	0	[c] : 12dgr141[p] --> 12dgr141[c] 
19850	12DGR160tipp	Yes	"1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:0)"	12dgr160[p] --> 12dgr160[c]	"Transport, Inner Membrane"			AMF	"not sure if the lipid actually is part of the membrane during the enzymatic reaction, then, no uptake would be needed and it would remain on the outer face of the inner membrane or alternatively, there is some type of reuptake to inner membrane or cytosol

AMF"	0	0	[c] : 12dgr160[p] --> 12dgr160[c] 
19543	12DGR161tipp	Yes	"1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:1)"	12dgr161[p] --> 12dgr161[c]	"Transport, Inner Membrane"			AMF	"needed for the reuptake of the product from the EptB enzyme

not sure if the lipid actually is part of the membrane during the enzymatic reaction, then, no uptake would be needed and it would remain on the outer face of the inner membrane or alternatively, there is some type of reuptake to inner membrane or cytosol

AMF"	0	0	[c] : 12dgr161[p] --> 12dgr161[c] 
19851	12DGR180tipp	Yes	"1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:0)"	12dgr180[p] --> 12dgr180[c]	"Transport, Inner Membrane"			AMF	"not sure if the lipid actually is part of the membrane during the enzymatic reaction, then, no uptake would be needed and it would remain on the outer face of the inner membrane or alternatively, there is some type of reuptake to inner membrane or cytosol

AMF"	0	0	[c] : 12dgr180[p] --> 12dgr180[c] 
19544	12DGR181tipp	Yes	"1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:1)"	12dgr181[p] --> 12dgr181[c]	"Transport, Inner Membrane"			AMF	"needed for the reuptake of the product from the EptB enzyme

not sure if the lipid actually is part of the membrane during the enzymatic reaction, then, no uptake would be needed and it would remain on the outer face of the inner membrane or alternatively, there is some type of reuptake to inner membrane or cytosol

AMF"	0	0	[c] : 12dgr181[p] --> 12dgr181[c] 
20018	12PPDRtex	Yes	"(R)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)"	12ppd-R[e] <==> 12ppd-R[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : 12ppd-R[e] <==> 12ppd-R[p] 
20019	12PPDRtpp	Yes	"(R)-Propane-1,2-diol facilitated transport (periplasm)"	12ppd-R[p] <==> 12ppd-R[c]	"Transport, Inner Membrane"			JLR	"JLR- reference implies that 12PPD leaves via facilitated diffusion based on rate of exit
AMF"	0	0	[c] : 12ppd-R[p] <==> 12ppd-R[c] 
9017	12PPDStex	Yes	"(S)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)"	12ppd-S[e] <==> 12ppd-S[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : 12ppd-S[e] <==> 12ppd-S[p] 
8972	12PPDStpp	Yes	"(S)-Propane-1,2-diol facilitated transport (periplasm)"	12ppd-S[p] <==> 12ppd-S[c]	"Transport, Inner Membrane"			JLR	JLR- reference implies that 12PPD leaves via facilitated diffusion based on rate of exit	0	0	[c] : 12ppd-S[p] <==> 12ppd-S[c] 
13771	14GLUCANabcpp	Yes	"1,4-alpha-D-glucan transport via ABC system (periplasm)"	14glucan[p] + atp[c] + h2o[c] --> 14glucan[c] + adp[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b4034  and  b4033  and  b4032  and  b4035 )	JLR	"added to incorporate the metabolism of glucan, the glucan structure was assigned to the malthp formula and is variable

assumed transport the same as maltodextrins"	-7.01673	1.48181	[c] : 14glucan[p] + atp[c] + h2o[c] --> 14glucan[c] + adp[c] + h[c] + pi[c] 
13772	14GLUCANtexi	Yes	"1,4-alpha-D-glucan transport via diffusion (extracellular to periplasm) irreversible"	14glucan[e] --> 14glucan[p]	"Transport, Outer Membrane"		b4036		"added to incorporate the metabolism of glucan, the glucan structure was assigned to the malthp formula and is variable

assumed transport the same as maltodextrins"	0	0	[c] : 14glucan[e] --> 14glucan[p] 
12415	23CAMPtex	Yes	23cAMP transport via diffusion (extracellular to periplasm)	23camp[e] <==> 23camp[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : 23camp[e] <==> 23camp[p] 
12416	23CCMPtex	Yes	23cCMP transport via diffusion (extracellular to periplasm)	23ccmp[e] <==> 23ccmp[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : 23ccmp[e] <==> 23ccmp[p] 
12418	23CGMPtex	Yes	23cGMP transport via diffusion (extracellular to periplasm)	23cgmp[e] <==> 23cgmp[p]	"Transport, Outer Membrane"				"assumed diffusion
"	0	0	[c] : 23cgmp[e] <==> 23cgmp[p] 
12417	23CUMPtex	Yes	23cUMP transport via diffusion (extracellular to periplasm)	23cump[e] <==> 23cump[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : 23cump[e] <==> 23cump[p] 
10587	23DAPPAt2rpp	Yes	"2,3-diaminopropionate proton-linked transporter"	23dappa[p] + h[p] <==> 23dappa[c] + h[c]	Update			MKA - rxn assumed	"Assumed transport since DAPAL is a proven reaction
AMF"	0	0	[c] : 23dappa[p] + h[p] <==> 23dappa[c] + h[c] 
11508	23DAPPAtex	Yes	"2,3-diaminopropionate transport via diffusion"	23dappa[e] <==> 23dappa[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : 23dappa[e] <==> 23dappa[p] 
12412	23PDE2pp	Yes	"2',3'-cyclic-nucleotide phosphodiesterase (UMP) (periplasm)"	[p] : 23cump + h2o --> 3ump + h	Update	3.1.4.16	b4213	AMF	"PMID: 3005231
cpdB is a periplasmic enzyme that has two distinct bifunctional sites for the 23 cyclic phophatidase and the nucleotidase

these substrates were not give specifically in the paper, but were on KEGG as such and can all be sources of pi according to biolog data.

there could be more substrates
AMF"	-8.05534	7.15885	[p] : 23cump[p] + h2o[p] --> 3ump[p] 
12413	23PDE4pp	Yes	"2',3'-cyclic-nucleotide phosphodiesterase (CMP) (periplasm)"	[p] : 23ccmp + h2o --> 3cmp + h	Update	3.1.4.16	b4213	AMF	"PMID: 3005231
cpdB is a periplasmic enzyme that has two distinct bifunctional sites for the 23 cyclic phophatidase and the nucleotidase

these substrates were not give specifically in the paper, but were on KEGG as such and can all be sources of pi according to biolog data.

there could be more substrates
AMF"	-8.05534	7.15885	[p] : 23ccmp[p] + h2o[p] --> 3cmp[p] 
12411	23PDE7pp	Yes	"2',3'-cyclic-nucleotide phosphodiesterase (AMP) (periplasm)"	[p] : 23camp + h2o --> 3amp + h	Update	3.1.4.16	b4213	AMF	"PMID: 3005231
cpdB is a periplasmic enzyme that has two distinct bifunctional sites for the 23 cyclic phophatidase and the nucleotidase

these substrates were not give specifically in the paper, but were on KEGG as such and can all be sources of pi according to biolog data.

there could be more substrates
AMF"	-8.05534	7.15885	[p] : 23camp[p] + h2o[p] --> 3amp[p] 
12414	23PDE9pp	Yes	"2',3'-cyclic-nucleotide phosphodiesterase (GMP) (periplasm)"	[p] : 23cgmp + h2o --> 3gmp + h	Update	3.1.4.16	b4213	AMF	"PMID: 3005231
cpdB is a periplasmic enzyme that has two distinct bifunctional sites for the 23 cyclic phophatidase and the nucleotidase

these substrates were not give specifically in the paper, but were on KEGG as such and can all be sources of pi according to biolog data.

there could be more substrates
AMF"	-8.05534	7.15885	[p] : 23cgmp[p] + h2o[p] --> 3gmp[p] 
9020	26DAHtex	Yes	"meso-2,6-Diaminoheptanedioate transport via diffusion (extracellular to periplasm)"	26dap-M[e] <==> 26dap-M[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : 26dap-M[e] <==> 26dap-M[p] 
19925	2AGPA120tipp	Yes	2-Acyl-sn-glycero-3-phosphatidate (n-C12:0) transporter via facilitated diffusion (periplasm)	2ddecg3p[p] --> 2ddecg3p[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2ddecg3p[p] --> 2ddecg3p[c] 
19926	2AGPA140tipp	Yes	2-Acyl-sn-glycero-3-phosphatidate (n-C14:0) transporter via facilitated diffusion (periplasm)	2tdecg3p[p] --> 2tdecg3p[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2tdecg3p[p] --> 2tdecg3p[c] 
19929	2AGPA141tipp	Yes	2-Acyl-sn-glycero-3-phosphatidate (n-C14:1) transporter via facilitated diffusion (periplasm)	2tdec7eg3p[p] --> 2tdec7eg3p[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2tdec7eg3p[p] --> 2tdec7eg3p[c] 
19927	2AGPA160tipp	Yes	2-Acyl-sn-glycero-3-phosphatidate (n-C16:0) transporter via facilitated diffusion (periplasm)	2hdecg3p[p] --> 2hdecg3p[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2hdecg3p[p] --> 2hdecg3p[c] 
19930	2AGPA161tipp	Yes	2-Acyl-sn-glycero-3-phosphatidate (n-C16:1) transporter via facilitated diffusion (periplasm)	2hdec9eg3p[p] --> 2hdec9eg3p[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2hdec9eg3p[p] --> 2hdec9eg3p[c] 
19928	2AGPA180tipp	Yes	2-Acyl-sn-glycero-3-phosphatidate (n-C18:0) transporter via facilitated diffusion (periplasm)	2odecg3p[p] --> 2odecg3p[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2odecg3p[p] --> 2odecg3p[c] 
19931	2AGPA181tipp	Yes	2-Acyl-sn-glycero-3-phosphatidate (n-C18:1) transporter via facilitated diffusion (periplasm)	2odec11eg3p[p] --> 2odec11eg3p[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2odec11eg3p[p] --> 2odec11eg3p[c] 		
19918	2AGPE120tipp	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0) transporter via facilitated diffusion (periplasm)	2agpe120[p] --> 2agpe120[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpe120[p] --> 2agpe120[c] 		
19919	2AGPE140tipp	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0) transporter via facilitated diffusion (periplasm)	2agpe140[p] --> 2agpe140[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpe140[p] --> 2agpe140[c] 		
19922	2AGPE141tipp	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1) transporter via facilitated diffusion (periplasm)	2agpe141[p] --> 2agpe141[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpe141[p] --> 2agpe141[c] 		
19920	2AGPE160tipp	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0) transporter via facilitated diffusion (periplasm)	2agpe160[p] --> 2agpe160[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpe160[p] --> 2agpe160[c] 		
19923	2AGPE161tipp	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1) transporter via facilitated diffusion (periplasm)	2agpe161[p] --> 2agpe161[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpe161[p] --> 2agpe161[c] 		
19921	2AGPE180tipp	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0) transporter via facilitated diffusion (periplasm)	2agpe180[p] --> 2agpe180[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpe180[p] --> 2agpe180[c] 		
19924	2AGPE181tipp	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1) transporter via facilitated diffusion (periplasm)	2agpe181[p] --> 2agpe181[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpe181[p] --> 2agpe181[c] 		
19941	2AGPEAT120	Yes	2-acyl-glycerophospho-ethanolamine acyltransferase (n-C12:0)	[c] : 2agpe120 + atp + ddca --> amp + pe120 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpe120[c] + atp[c] + ddca[c] + h[c] --> amp[c] + pe120[c] + ppi[c] 		
19940	2AGPEAT140	Yes	2-acyl-glycerophospho-ethanolamine acyltransferase (n-C14:0)	[c] : 2agpe140 + atp + ttdca --> amp + pe140 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpe140[c] + atp[c] + h[c] + ttdca[c] --> amp[c] + pe140[c] + ppi[c] 		
19944	2AGPEAT141	Yes	2-acyl-glycerophospho-ethanolamine acyltransferase (n-C14:1)	[c] : 2agpe141 + atp + ttdcea --> amp + pe141 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-3.13098	4.25015	[c] : 2agpe141[c] + atp[c] + h[c] + ttdcea[c] --> amp[c] + pe141[c] + ppi[c] 		
19939	2AGPEAT160	Yes	2-acyl-glycerophospho-ethanolamine acyltransferase (n-C16:0)	[c] : 2agpe160 + atp + hdca --> amp + pe160 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpe160[c] + atp[c] + h[c] + hdca[c] --> amp[c] + pe160[c] + ppi[c] 		
19943	2AGPEAT161	Yes	2-acyl-glycerophospho-ethanolamine acyltransferase (n-C16:1)	[c] : 2agpe161 + atp + hdcea --> amp + pe161 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpe161[c] + atp[c] + h[c] + hdcea[c] --> amp[c] + pe161[c] + ppi[c] 		
19942	2AGPEAT180	Yes	2-acyl-glycerophospho-ethanolamine acyltransferase (n-C18:0)	[c] : 2agpe180 + atp + ocdca --> amp + pe180 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpe180[c] + atp[c] + h[c] + ocdca[c] --> amp[c] + pe180[c] + ppi[c] 		
19945	2AGPEAT181	Yes	2-acyl-glycerophospho-ethanolamine acyltransferase (n-C18:1)	[c] : 2agpe181 + atp + ocdcea --> amp + pe181 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpe181[c] + atp[c] + h[c] + ocdcea[c] --> amp[c] + pe181[c] + ppi[c] 		
19932	2AGPG120tipp	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0) transporter via facilitated diffusion (periplasm)	2agpg120[p] --> 2agpg120[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpg120[p] --> 2agpg120[c] 		
19933	2AGPG140tipp	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0) transporter via facilitated diffusion (periplasm)	2agpg140[p] --> 2agpg140[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpg140[p] --> 2agpg140[c] 		
19936	2AGPG141tipp	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1) transporter via facilitated diffusion (periplasm)	2agpg141[p] --> 2agpg141[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpg141[p] --> 2agpg141[c] 		
19934	2AGPG160tipp	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0) transporter via facilitated diffusion (periplasm)	2agpg160[p] --> 2agpg160[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpg160[p] --> 2agpg160[c] 		
19937	2AGPG161tipp	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1) transporter via facilitated diffusion (periplasm)	2agpg161[p] --> 2agpg161[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpg161[p] --> 2agpg161[c] 		
19935	2AGPG180tipp	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0) transporter via facilitated diffusion (periplasm)	2agpg180[p] --> 2agpg180[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpg180[p] --> 2agpg180[c] 		
19938	2AGPG181tipp	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1) transporter via facilitated diffusion (periplasm)	2agpg181[p] --> 2agpg181[c]	"Transport, Inner Membrane"		b2835	"AMF
PMID: 15661733"	"PMID: 15661733
LplT-Aas transport/acylation activity was independent of the proton motive force
shown to act on pe, assumed to transport pg, pa.

personal communication (Charles Rock) 'We think that Lpt1 is a facilitator like the glycerol facilitator and does not require membrane electrochemical gradient.  The transporter will move 2-acyl-GPC, which is not an E. coli lipid, so it is not very specific.  We do not know whether other specific lipids are transported by this system, but it might be that lysophospholipids in general are substrates.'
AMF"	0	0	[c] : 2agpg181[p] --> 2agpg181[c] 		
19948	2AGPGAT120	Yes	2-acyl-glycerophospho-glycerol acyltransferase (n-C12:0)	[c] : 2agpg120 + atp + ddca --> amp + pg120 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpg120[c] + atp[c] + ddca[c] + h[c] --> amp[c] + pg120[c] + ppi[c] 		
19949	2AGPGAT140	Yes	2-acyl-glycerophospho-glycerol acyltransferase (n-C14:0)	[c] : 2agpg140 + atp + ttdca --> amp + pg140 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpg140[c] + atp[c] + h[c] + ttdca[c] --> amp[c] + pg140[c] + ppi[c] 		
19950	2AGPGAT141	Yes	2-acyl-glycerophospho-glycerol acyltransferase (n-C14:1)	[c] : 2agpg141 + atp + ttdcea --> amp + pg141 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-3.13098	4.25015	[c] : 2agpg141[c] + atp[c] + h[c] + ttdcea[c] --> amp[c] + pg141[c] + ppi[c] 		
19951	2AGPGAT160	Yes	2-acyl-glycerophospho-glycerol acyltransferase (n-C16:0)	[c] : 2agpg160 + atp + hdca --> amp + pg160 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpg160[c] + atp[c] + h[c] + hdca[c] --> amp[c] + pg160[c] + ppi[c] 		
19952	2AGPGAT161	Yes	2-acyl-glycerophospho-glycerol acyltransferase (n-C16:1)	[c] : 2agpg161 + atp + hdcea --> amp + pg161 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpg161[c] + atp[c] + h[c] + hdcea[c] --> amp[c] + pg161[c] + ppi[c] 		
19953	2AGPGAT180	Yes	2-acyl-glycerophospho-glycerol acyltransferase (n-C18:0)	[c] : 2agpg180 + atp + ocdca --> amp + pg180 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpg180[c] + atp[c] + h[c] + ocdca[c] --> amp[c] + pg180[c] + ppi[c] 		
19954	2AGPGAT181	Yes	2-acyl-glycerophospho-glycerol acyltransferase (n-C18:1)	[c] : 2agpg181 + atp + ocdcea --> amp + pg181 + ppi	Glycerophospholipid Metabolism	2.3.1.40	b2836	AMF	"Aas proven to act on acyl-lysophosphoethanolamine and this is the substrate discussed for the enzyme, but most likely acts on other lipids as well a evident in the increased inorporation of exogenous lysophospholipids in the membrane with overexpression, such as exogenous 2-acyl-GP-choline that was argued to be a substrate for aas in PMID: 8300626
enzyme was also shown to function on the cytosolic side of the inner membrane
AMF"	-4.72457	3.42862	[c] : 2agpg181[c] + atp[c] + h[c] + ocdcea[c] --> amp[c] + pg181[c] + ppi[c] 		
2906	2DGLCNRx	No	2-dehydro-D-gluconate reductase (NADH)	[c] : 2dhglcn + h + nadh --> glcn + nad	Alternate Carbon Metabolism		b3553	"JLR
"	JLR- Ref says that nadph is preferred	-4.73639	4.5435	[c] : 2dhglcn[c] + h[c] + nadh[c] --> glcn[c] + nad[c] 		
2907	2DGLCNRy	No	2-dehydro-D-gluconate reductase (NADPH)	[c] : 2dhglcn + h + nadph --> glcn + nadp	Alternate Carbon Metabolism	1.1.1.215	b3553	JLR		-4.73639	4.5435	[c] : 2dhglcn[c] + h[c] + nadph[c] --> glcn[c] + nadp[c] 		
2486	2DGULRx	No	2-dehydro-L-gulonate reductase (NADH)	[c] : 2dhguln + h + nadh --> idon-L + nad	Alternate Carbon Metabolism		b3553	JLR	JLR- Ref says that nadph is preferred	-4.73639	4.5435	[c] : 2dhguln[c] + h[c] + nadh[c] --> idon-L[c] + nad[c] 		
2151	2DGULRy	No	2-dehydro-L-gulonate reductase (NADPH)	[c] : 2dhguln + h + nadph --> idon-L + nadp	Alternate Carbon Metabolism		b3553	JLR		-4.73639	4.5435	[c] : 2dhguln[c] + h[c] + nadph[c] --> idon-L[c] + nadp[c] 
12301	34dhpactex	Yes	dihydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)	34dhpac[e] <==> 34dhpac[p]	"Transport, Outer Membrane"			AMF	"PMID: 3309152 original paper source
PMID: 11729263 - review where it states that that tyroxdapp and 42a12booxpp are confirmed susbstrates and can be used in K-12 for nitrogen source only, not sure if they are transported inside the cell or not or if they can't be processed after transport"	0	0	[c] : 34dhpac[e] <==> 34dhpac[p] 
12419	3AMPtex	Yes	3AMP transport via diffusion (extracellular to periplasm)	3amp[e] <==> 3amp[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : 3amp[e] <==> 3amp[p] 
12420	3CMPtex	Yes	3CMP transport via diffusion (extracellular to periplasm)	3cmp[e] <==> 3cmp[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : 3cmp[e] <==> 3cmp[p] 
12422	3GMPtex	Yes	3GMP transport via diffusion (extracellular to periplasm)	3gmp[e] <==> 3gmp[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : 3gmp[e] <==> 3gmp[p] 
19171	3HAD100	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C10:0)	[c] : 3hdecACP --> h2o + tdec2eACP	Cell Envelope Biosynthesis	4.2.1.60	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hdecACP[c] --> h2o[c] + tdec2eACP[c] 
19172	3HAD120	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:0)	[c] : 3hddecACP --> h2o + tddec2eACP	Cell Envelope Biosynthesis	4.2.1.61	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hddecACP[c] --> h2o[c] + tddec2eACP[c] 
19212	3HAD121	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:1)	[c] : 3hcddec5eACP --> h2o + t3c5ddeceACP	Cell Envelope Biosynthesis	4.2.1.61	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hcddec5eACP[c] --> h2o[c] + t3c5ddeceACP[c] 
19173	3HAD140	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:0)	[c] : 3hmrsACP --> h2o + tmrs2eACP	Cell Envelope Biosynthesis	4.2.1.61	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hmrsACP[c] --> h2o[c] + tmrs2eACP[c] 
19213	3HAD141	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:1)	[c] : 3hcmrs7eACP --> h2o + t3c7mrseACP	Cell Envelope Biosynthesis	4.2.1.61	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hcmrs7eACP[c] --> h2o[c] + t3c7mrseACP[c] 
19174	3HAD160	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:0)	[c] : 3hpalmACP --> h2o + tpalm2eACP	Cell Envelope Biosynthesis	4.2.1.61	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hpalmACP[c] --> h2o[c] + tpalm2eACP[c] 
19214	3HAD161	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:1)	[c] : 3hcpalm9eACP --> h2o + t3c9palmeACP	Cell Envelope Biosynthesis	4.2.1.61	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hcpalm9eACP[c] --> h2o[c] + t3c9palmeACP[c] 
19322	3HAD180	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:0)	[c] : 3hoctaACP --> h2o + toctd2eACP	Cell Envelope Biosynthesis	4.2.1.61	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hoctaACP[c] --> h2o[c] + toctd2eACP[c] 
19215	3HAD181	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:1)	[c] : 3hcvac11eACP --> h2o + t3c11mrseACP	Cell Envelope Biosynthesis	4.2.1.61	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hcvac11eACP[c] --> h2o[c] + t3c11vaceACP[c] 
19168	3HAD40	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C4:0)	[c] : 3haACP --> but2eACP + h2o	Cell Envelope Biosynthesis	4.2.1.58	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3haACP[c] --> but2eACP[c] + h2o[c] 
19169	3HAD60	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C6:0)	[c] : 3hhexACP --> h2o + thex2eACP	Cell Envelope Biosynthesis	4.2.1.58	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hhexACP[c] --> h2o[c] + thex2eACP[c] 
19170	3HAD80	Yes	3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C8:0)	[c] : 3hoctACP --> h2o + toct2eACP	Cell Envelope Biosynthesis	4.2.1.58	( b0954  or  b0180 )	"AMF
EC number taken from KEGG, not sure or reversibility"	"FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0.278853	2.66722	[c] : 3hoctACP[c] --> h2o[c] + toct2eACP[c] 		
3212	3HCINNMH	No	3-hydroxycinnamate hydroxylase	[c] : 3hcinnm + h + nadh + o2 --> dhcinnm + h2o + nad	Alternate Carbon Metabolism		b0347	JLR- see PMID:9603882		-91.3033	6.53293	[c] : 3hcinnm[c] + h[c] + nadh[c] + o2[c] --> dhcinnm[c] + h2o[c] + nad[c] 		
2368	3HPPPNH	No	3-(3-hydroxy-phenyl)propionate hydroxylase	[c] : 3hpppn + h + nadh + o2 --> dhpppn + h2o + nad	Alternate Carbon Metabolism		b0347	JLR- see PMID 9603882		-91.3033	6.53293	[c] : 3hpppn[c] + h[c] + nadh[c] + o2[c] --> dhpppn[c] + h2o[c] + nad[c] 		
10552	3KGK	Yes	3-keto-L-gulonate kinase	[c] : 3dhguln + atp --> 3dhgulnp + adp + h	Update		b3580	"MKA
by ""cryptic"" gene in ecoli"	"LyxK is deemed cryptic because the promoter is cryptic, so the function of LyxK is assigned
AMF

promoter region interupted by insert in wt"	-4.65732	2.09859	[c] : 3dhguln[c] + atp[c] --> 3dhgulnp[c] + adp[c] 		
12409	3NTD2pp	Yes	3'-nucleotidase (UMP) (periplasm)	[p] : 3ump + h2o --> pi + uri	Update		b4213	"MKA
AMF"	"PMID: 3005231
cpdB is a periplasmic enzyme that has two distinct bifunctional sites for the 23 cyclic phophatidase and the nucleotidase

these substrates were not give specifically in the paper, but were on KEGG as such and can all be sources of pi according to biolog data.

there could be more substrates
AMF"	-3.54819	2.12947	[p] : 3ump[p] + h2o[p] --> h[p] + pi[p] + uri[p] 		
12407	3NTD4pp	Yes	3'-nucleotidase (CMP) (periplasm)	[p] : 3cmp + h2o --> cytd + pi	Update		b4213	"MKA
AMF"	"PMID: 3005231
cpdB is a periplasmic enzyme that has two distinct bifunctional sites for the 23 cyclic phophatidase and the nucleotidase

these substrates were not give specifically in the paper, but were on KEGG as such and can all be sources of pi according to biolog data.

there could be more substrates
AMF"	-3.54819	2.12947	[p] : 3cmp[p] + h2o[p] --> cytd[p] + h[p] + pi[p] 		
12406	3NTD7pp	Yes	3'-nucleotidase (AMP) (periplasm)	[p] : 3amp + h2o --> adn + pi	Update		b4213	"MKA
AMF"	"PMID: 3005231
cpdB is a periplasmic enzyme that has two distinct bifunctional sites for the 23 cyclic phophatidase and the nucleotidase

these substrates were not give specifically in the paper, but were on KEGG as such and can all be sources of pi according to biolog data.

there could be more substrates
AMF"	-3.54819	2.12947	[p] : 3amp[p] + h2o[p] --> adn[p] + h[p] + pi[p] 		
12410	3NTD9pp	Yes	3'-nucleotidase (GMP) (periplasm)	[p] : 3gmp + h2o --> gsn + pi	Update		b4213	"MKA
AMF"	"PMID: 3005231
cpdB is a periplasmic enzyme that has two distinct bifunctional sites for the 23 cyclic phophatidase and the nucleotidase

these substrates were not give specifically in the paper, but were on KEGG as such and can all be sources of pi according to biolog data.

there could be more substrates
AMF"	-3.54819	2.12947	[p] : 3gmp[p] + h2o[p] --> gsn[p] + h[p] + pi[p] 		
19164	3OAR100	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C10:0)	[c] : 3odecACP + h + nadph <==> 3hdecACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
AMF"	-4.73639	4.5435	[c] : 3odecACP[c] + h[c] + nadph[c] <==> 3hdecACP[c] + nadp[c] 		
19165	3OAR120	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:0)	[c] : 3oddecACP + h + nadph <==> 3hddecACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
AMF"	-4.73639	4.5435	[c] : 3oddecACP[c] + h[c] + nadph[c] <==> 3hddecACP[c] + nadp[c] 		
19208	3OAR121	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:1)	[c] : 3ocddec5eACP + h + nadph --> 3hcddec5eACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
FabG acts on both saturated and unsaturated FA, long and short chain
AMF"	-4.73639	4.5435	[c] : 3ocddec5eACP[c] + h[c] + nadph[c] --> 3hcddec5eACP[c] + nadp[c] 		
19166	3OAR140	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:0)	[c] : 3omrsACP + h + nadph <==> 3hmrsACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
FabG acts on both saturated and unsaturated FA, long and short chain
AMF"	-4.73639	4.5435	[c] : 3omrsACP[c] + h[c] + nadph[c] <==> 3hmrsACP[c] + nadp[c] 		
19209	3OAR141	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:1)	[c] : 3ocmrs7eACP + h + nadph --> 3hcmrs7eACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
FabG acts on both saturated and unsaturated FA, long and short chain
AMF"	-4.73639	4.5435	[c] : 3ocmrs7eACP[c] + h[c] + nadph[c] --> 3hcmrs7eACP[c] + nadp[c] 		
19167	3OAR160	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:0)	[c] : 3opalmACP + h + nadph <==> 3hpalmACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
FabG acts on both saturated and unsaturated FA, long and short chain
AMF"	-4.73639	4.5435	[c] : 3opalmACP[c] + h[c] + nadph[c] <==> 3hpalmACP[c] + nadp[c] 		
19210	3OAR161	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:1)	[c] : 3ocpalm9eACP + h + nadph --> 3hcpalm9eACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
FabG acts on both saturated and unsaturated FA, long and short chain
AMF"	-3.14281	5.1915	[c] : 3ocpalm9eACP[c] + h[c] + nadph[c] --> 3hcpalm9eACP[c] + nadp[c] 		
19321	3OAR180	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:0)	[c] : 3ooctdACP + h + nadph <==> 3hoctaACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
FabG acts on both saturated and unsaturated FA, long and short chain
AMF"	-4.73639	4.5435	[c] : 3ooctdACP[c] + h[c] + nadph[c] <==> 3hoctaACP[c] + nadp[c] 		
19211	3OAR181	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:1)	[c] : 3ocvac11eACP + h + nadph --> 3hcvac11eACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
FabG acts on both saturated and unsaturated FA, long and short chain
AMF"	-4.73639	4.5435	[c] : 3ocvac11eACP[c] + h[c] + nadph[c] --> 3hcvac11eACP[c] + nadp[c] 		
19161	3OAR40	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C4:0)	[c] : actACP + h + nadph <==> 3haACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
AMF"	-4.73639	4.5435	[c] : actACP[c] + h[c] + nadph[c] <==> 3haACP[c] + nadp[c] 		
19162	3OAR60	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C6:0)	[c] : 3ohexACP + h + nadph <==> 3hhexACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
AMF"	-4.73639	4.5435	[c] : 3ohexACP[c] + h[c] + nadph[c] <==> 3hhexACP[c] + nadp[c] 		
19163	3OAR80	Yes	3-oxoacyl-[acyl-carrier-protein] reductase (n-C8:0)	[c] : 3ooctACP + h + nadph <==> 3hoctACP + nadp	Cell Envelope Biosynthesis	1.1.1.100	b1093	AMF	"not sure of reversibility
AMF"	-4.73639	4.5435	[c] : 3ooctACP[c] + h[c] + nadph[c] <==> 3hoctACP[c] + nadp[c] 		
19157	3OAS100	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C10:0)	[c] : h + malACP + ocACP --> 3odecACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	( b2323  or  b1095 )	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : h[c] + malACP[c] + ocACP[c] --> 3odecACP[c] + ACP[c] + co2[c] 		
19158	3OAS120	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:0)	[c] : dcaACP + h + malACP --> 3oddecACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	( b2323  or  b1095 )	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : dcaACP[c] + h[c] + malACP[c] --> 3oddecACP[c] + ACP[c] + co2[c] 		
19204	3OAS121	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:1)	[c] : cdec3eACP + h + malACP --> 3ocddec5eACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	b2323	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : cdec3eACP[c] + h[c] + malACP[c] --> 3ocddec5eACP[c] + ACP[c] + co2[c] 		
19159	3OAS140	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:0)	[c] : ddcaACP + h + malACP --> 3omrsACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	( b2323  or  b1095 )	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : ddcaACP[c] + h[c] + malACP[c] --> 3omrsACP[c] + ACP[c] + co2[c] 		
19205	3OAS141	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:1)	[c] : cddec5eACP + h + malACP --> 3ocmrs7eACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	b2323	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : cddec5eACP[c] + h[c] + malACP[c] --> 3ocmrs7eACP[c] + ACP[c] + co2[c] 		
19160	3OAS160	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:0)	[c] : h + malACP + myrsACP --> 3opalmACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	( b2323  or  b1095 )	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : h[c] + malACP[c] + myrsACP[c] --> 3opalmACP[c] + ACP[c] + co2[c] 		
19224	3OAS161	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:1)	[c] : h + malACP + tdeACP --> 3ocpalm9eACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	b2323	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : h[c] + malACP[c] + tdeACP[c] --> 3ocpalm9eACP[c] + ACP[c] + co2[c] 		
19320	3OAS180	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:0)	[c] : h + malACP + palmACP --> 3ooctdACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	( b1095  or  b2323 )	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : h[c] + malACP[c] + palmACP[c] --> 3ooctdACP[c] + ACP[c] + co2[c] 		
19227	3OAS181	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:1)	[c] : h + hdeACP + malACP --> 3ocvac11eACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	b1095	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : h[c] + hdeACP[c] + malACP[c] --> 3ocvac11eACP[c] + ACP[c] + co2[c] 		
19155	3OAS60	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C6:0)	[c] : butACP + h + malACP --> 3ohexACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	( b2323  or  b1095 )	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : butACP[c] + h[c] + malACP[c] --> 3ohexACP[c] + ACP[c] + co2[c] 		
19156	3OAS80	Yes	3-oxoacyl-[acyl-carrier-protein] synthase (n-C8:0)	[c] : h + hexACP + malACP --> 3ooctACP + ACP + co2	Cell Envelope Biosynthesis	2.3.1.41	( b2323  or  b1095 )	AMF	"FabB acts on both unsaturated and saturated, short and long FA, but will not act on pamitoleoyl-ACP
FabF acts on saturated, short and long FA - does not synthesize short unsaturated FA and is needed to generate cis-vaccenate from palitoleoyl-ACP (3OAS181)
FabH does not elongate FA
see NH pg 615
AMF"	1.3349	4.20263	[c] : h[c] + hexACP[c] + malACP[c] --> 3ooctACP[c] + ACP[c] + co2[c] 		
12630	3PEPTabcpp	Yes	tripeptide (LalaDgluMdap) transport via ABC system (periplasm)	LalaDgluMdap[p] + atp[c] + h2o[c] --> LalaDgluMdap[c] + adp[c] + h[c] + pi[c]	Murein Recycling		( b1329  and  b1244  and  b1245  and  b1246  and  b1247 )		"MppA is specific for the murein tripeptide, OppA is a more general peptide transporter

OppA could transport many other peptides
PMID: 9495761"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + LalaDgluMdap[p] --> adp[c] + h[c] + LalaDgluMdap[c] + pi[c] 		
13204	3PEPTtex	Yes	LalaDgluMdap (tripeptide) transport via diffusion (extracellular to periplasm)	LalaDgluMdap[e] <==> LalaDgluMdap[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : LalaDgluMdap[e] <==> LalaDgluMdap[p] 		
12421	3UMPtex	Yes	3UMP transport via diffusion (extracellular to periplasm)	3ump[e] <==> 3ump[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : 3ump[e] <==> 3ump[p] 		
12235	42A12BOOXpp	Yes	"4-(2-Aminoethyl)-1,2-benzenediol:oxygen oxidoreductase(deaminating)(flavin-containing)"	[p] : dopa + h2o + o2 --> 34dhpac + h2o2 + nh4	Update	1.4.3.6	b1386	SAB	"PMID: 3309152 original paper source
PMID: 11729263 - review where it states that that tyroxdapp and 42a12booxpp are confirmed susbstrates and can be used in K-12 for nitrogen source only, not sure if they are transported inside the cell or not or if they can't be processed after transport"	-18.53	2.13874	[p] : dopa[p] + h2o[p] + o2[p] --> 34dhpac[p] + h2o2[p] + nh4[p] 		
12243	4HOXPACDtex	Yes	4-hydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)	4hoxpacd[e] <==> 4hoxpacd[p]	"Transport, Outer Membrane"				"PMID: 3309152 original paper source
PMID: 11729263 - review where it states that that tyroxdapp and 42a12booxpp are confirmed susbstrates and can be used in K-12 for nitrogen source only, not sure if they are transported inside the cell or not or if they can't be processed after transport"	0	0	[c] : 4hoxpacd[e] <==> 4hoxpacd[p] 		
3034	4HTHRS	No	4-Hydroxy-L-threonine synthase	[c] : h2o + phthr --> 4hthr + pi	Cofactor and Prosthetic Group Biosynthesis		b0004	JLR		-2.35942	1.9257	[c] : h2o[c] + phthr[c] --> 4hthr[c] + h[c] + pi[c] 		
12614	4PCP	Yes	"tetrapeptide L,D-carboxypeptidase"	[c] : LalaDgluMdapDala + h2o --> LalaDgluMdap + ala-D	Murein Recycling		b1192	AMF	"LdcA is a cytoplasmic LD-carboxypeptidase
four different similar susbstrates
PMID: 10428950"	-3.36489	3.34628	[c] : h2o[c] + LalaDgluMdapDala[c] --> ala-D[c] + LalaDgluMdap[c] 		
12615	4PCPpp	Yes	"tetrapeptide L,D-carboxypeptidase (periplasm)"	[p] : LalaDgluMdapDala + h2o --> LalaDgluMdap + ala-D	Murein Recycling			AMF	"the periplasmic enzyme is unknown
cytoplasmic is LdcA"	-3.36489	3.34628	[p] : h2o[p] + LalaDgluMdapDala[p] --> ala-D[p] + LalaDgluMdap[p] 		
12631	4PEPTabcpp	Yes	tetrapeptide (LalaDgluMdapDala) transport via ABC system (periplasm)	LalaDgluMdapDala[p] + atp[c] + h2o[c] --> LalaDgluMdapDala[c] + adp[c] + h[c] + pi[c]	Murein Recycling		( b1243  and  b1244  and  b1245  and  b1246  and  b1247 )	AMF	"MppA is specific for the murein tripeptide, OppA is a more general peptide transporter

OppA could transport many other peptides
PMID: 9495761"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + LalaDgluMdapDala[p] --> adp[c] + h[c] + LalaDgluMdapDala[c] + pi[c] 		
13205	4PEPTtex	Yes	LalaDgluMdapDala (pentapeptide) transport via diffusion (extracellular to periplasm)	LalaDgluMdapDala[e] <==> LalaDgluMdapDala[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : LalaDgluMdapDala[e] <==> LalaDgluMdapDala[p] 		
2148	5DGLCNR	No	5-dehydro-D-gluconate reductase	[c] : 5dglcn + h + nadph <==> glcn + nadp	Alternate Carbon Metabolism	1.1.1.69	b4266	JLR		-4.73639	4.5435	[c] : 5dglcn[c] + h[c] + nadph[c] <==> glcn[c] + nadp[c] 		
1244	A5PISO	No	arabinose-5-phosphate isomerase	[c] : ru5p-D <==> ara5p	Alternate Carbon Metabolism	5.3.1.13	b3197	tv		0.429448	2.63724	[c] : ru5p-D[c] <==> ara5p[c] 		
3363	AACPS1	No	acyl-[acyl-carrier-protein] synthetase (n-C14:0)	[c] : ACP + atp + ttdca --> amp + myrsACP + ppi	Cell Envelope Biosynthesis	6.2.1.20	b2836	JLR	"from ecocyc: Acyl-ACP synthetase functions to ligate free fatty acids, with lengths of C-8 to C-18, to ACP.
AMF"	-2.74083	4.99608	[c] : ACP[c] + atp[c] + h[c] + ttdca[c] --> amp[c] + myrsACP[c] + ppi[c] 		
3364	AACPS2	No	acyl-[acyl-carrier-protein] synthetase  (n-C14:1)	[c] : ACP + atp + ttdcea --> amp + ppi + tdeACP	Cell Envelope Biosynthesis	6.2.1.20	b2836	JLR	"from ecocyc: Acyl-ACP synthetase functions to ligate free fatty acids, with lengths of C-8 to C-18, to ACP.
AMF"	-2.74083	4.99608	[c] : ACP[c] + atp[c] + h[c] + ttdcea[c] --> amp[c] + ppi[c] + tdeACP[c] 		
3365	AACPS3	No	acyl-[acyl-carrier-protein] synthetase  (n-C16:0)	[c] : ACP + atp + hdca --> amp + palmACP + ppi	Cell Envelope Biosynthesis	6.2.1.20	b2836	JLR	"from ecocyc: Acyl-ACP synthetase functions to ligate free fatty acids, with lengths of C-8 to C-18, to ACP.
AMF"	-2.74083	4.99608	[c] : ACP[c] + atp[c] + h[c] + hdca[c] --> amp[c] + palmACP[c] + ppi[c] 		
3366	AACPS4	No	acyl-[acyl-carrier-protein] synthetase  (n-C16:1)	[c] : ACP + atp + hdcea --> amp + hdeACP + ppi	Cell Envelope Biosynthesis	6.2.1.20	b2836	JLR	"from ecocyc: Acyl-ACP synthetase functions to ligate free fatty acids, with lengths of C-8 to C-18, to ACP.
AMF"	-2.74083	4.99608	[c] : ACP[c] + atp[c] + h[c] + hdcea[c] --> amp[c] + hdeACP[c] + ppi[c] 		
3367	AACPS5	No	acyl-[acyl-carrier-protein] synthetase  (n-C18:1)	[c] : ACP + atp + ocdcea --> amp + octeACP + ppi	Cell Envelope Biosynthesis	6.2.1.20	b2836	JLR	"from ecocyc: Acyl-ACP synthetase functions to ligate free fatty acids, with lengths of C-8 to C-18, to ACP.
AMF"	-4.33442	5.59188	[c] : ACP[c] + atp[c] + h[c] + ocdcea[c] --> amp[c] + octeACP[c] + ppi[c] 		
19991	AACPS6	Yes	acyl-[acyl-carrier-protein] synthetase  (n-C18:0)	[c] : ACP + atp + ocdca --> amp + ocdcaACP + ppi	Cell Envelope Biosynthesis	6.2.1.20	b2836	AMF	"from ecocyc: Acyl-ACP synthetase functions to ligate free fatty acids, with lengths of C-8 to C-18, to ACP.
AMF"	-2.74083	4.99608	[c] : ACP[c] + atp[c] + h[c] + ocdca[c] --> amp[c] + ocdcaACP[c] + ppi[c] 		
19992	AACPS7	Yes	acyl-[acyl-carrier-protein] synthetase  (n-C12:0)	[c] : ACP + atp + ddca --> amp + ddcaACP + ppi	Cell Envelope Biosynthesis	6.2.1.20	b2836	AMF	"from ecocyc: Acyl-ACP synthetase functions to ligate free fatty acids, with lengths of C-8 to C-18, to ACP.
AMF"	-2.74083	4.99608	[c] : ACP[c] + atp[c] + ddca[c] + h[c] --> amp[c] + ddcaACP[c] + ppi[c] 		
19993	AACPS8	Yes	acyl-[acyl-carrier-protein] synthetase  (n-C10:0)	[c] : ACP + atp + dca --> amp + dcaACP + ppi	Cell Envelope Biosynthesis	6.2.1.20	b2836	AMF	"from ecocyc: Acyl-ACP synthetase functions to ligate free fatty acids, with lengths of C-8 to C-18, to ACP.
AMF"	-2.74083	4.99608	[c] : ACP[c] + atp[c] + dca[c] + h[c] --> amp[c] + dcaACP[c] + ppi[c] 		
19994	AACPS9	Yes	acyl-[acyl-carrier-protein] synthetase  (n-C8:0)	[c] : ACP + atp + octa --> amp + ocACP + ppi	Cell Envelope Biosynthesis	6.2.1.20	b2836	AMF	"from ecocyc: Acyl-ACP synthetase functions to ligate free fatty acids, with lengths of C-8 to C-18, to ACP.
AMF"	-2.74083	4.99608	[c] : ACP[c] + atp[c] + h[c] + octa[c] --> amp[c] + ocACP[c] + ppi[c] 		
11706	AACTOOR	Yes	Aminoacetone:oxygen oxidoreductase(deaminating)(flavin-containing)	[c] : aact + h2o + o2 --> h2o2 + mthgxl + nh4	Update			MM	"Not sure of the reaction, needed to degrade aact
AMF

TynA (periplasmic enzyme) can catalyze this reaction so that is the justification for entry"	-18.53	2.13874	[c] : aact[c] + h2o[c] + o2[c] --> h2o2[c] + mthgxl[c] + nh4[c] 		
2499	AADDGT	No	"dTDP-N-4-acetamido-4,6-dideoxy-D-galactose transferase"	[c] : dtdp4aaddg + unagamu --> dtdp + h + unagamuf	Cell Envelope Biosynthesis		b4481	JLR		27.8594	7.50865	[c] : dtdp4aaddg[c] + unagamu[c] --> dtdp[c] + unagamuf[c] 		
12339	AALDCDLs	Yes	Aminoacetaldehyde: CO2 ligase (spontaneous reaction)	[c] : aacald + co2 <==> 2amsa + h	Unassigned			"spontaneous reaction
AMF"	"spontaneous reaction
"	4.96805	1.79669	[c] : aacald[c] + co2[c] <==> 2amsa[c] + h[c] 		
14059	AAMYL	Yes	alpha-amylase	[c] : 14glucan --> malthx	Update		b1927	"AMF
reaction represents the conversion of glucan to a maltodexrin"	"added to incorporate the metabolism of glucan, the glucan structure was assigned to the malthp formula and is variable

assumed transport the same as maltodextrins"	0	0.5	[c] : 14glucan[c] --> malthx[c] 		
14060	AAMYLpp	Yes	alpha-amylase (periplasm)	[p] : 14glucan --> malthx	Update		b3571	"AMF
reaction represents the conversion of glucan to a maltodexrin"	"added to incorporate the metabolism of glucan, the glucan structure was assigned to the malthx formula and is variable

assumed transport the same as maltodextrins"	0	0.5	[p] : 14glucan[p] --> malthx[p] 		
3233	AB6PGH	No	Arbutin 6-phosphate glucohydrolase	[c] : arbt6p + h2o --> g6p + hqn	Alternate Carbon Metabolism	3.2.1.86	b2901	JLR (Kegg R05133)	JLR- confidence based on Hall and Xu review (http://www.molbiolevol.org/cgi/reprint/9/4/688.pdf)	-0.870043	4.45878	[c] : arbt6p[c] + h2o[c] --> g6p[c] + hqn[c] 		
374	ABTA	No	4-aminobutyrate transaminase	[c] : 4abut + akg --> glu-L + sucsal	Arginine and Proline Metabolism	2.6.1.19	( b2662  or  b1302 )		"PuuE - MKA
goaG induced by putrescine
PMID: 15590624 AMF

no notes on GabT"	2.42139	2.1337	[c] : 4abut[c] + akg[c] --> glu-L[c] + sucsal[c] 		
1267	ABUTD	No	Aminobutyraldehyde dehydrogenase	[c] : 4abutn + h2o + nad --> 4abut + (2) h + nadh	Arginine and Proline Metabolism	1.2.1.19	b1444	JLR	"characerized and proven to be this gene
PMID: 16023116
AMF "	-9.85991	4.39284	[c] : 4abutn[c] + h2o[c] + nad[c] --> 4abut[c] + (2) h[c] + nadh[c] 		
8964	ABUTt2pp	Yes	4-aminobutyrate transport in via proton symport (periplasm)	4abut[p] + h[p] --> 4abut[c] + h[c]	"Transport, Inner Membrane"		b2663			0	0	[c] : 4abut[p] + h[p] --> 4abut[c] + h[c] 		
9226	ABUTtex	Yes	4-aminobutyrate transport via diffusion (extracellular to periplasm)	4abut[e] <==> 4abut[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : 4abut[e] <==> 4abut[p] 		
2480	ACACCT	No	acetyl-CoA:acetoacetyl-CoA transferase	[c] : acac + accoa --> aacoa + ac	Alternate Carbon Metabolism		( b2221  and  b2222 )	JLR	"JLR- see NH21 for info on regulation

From ecocyc: The growth of E. coli on short-chain fatty acids (C3-C6) requires the activation of the acids to their respective thioesters. This activation is catalyzed by acetoacetyl-CoA transferase. [ Sramek75  ]
also, see PMID: 3025185
AMF"	0	0.5	[c] : acac[c] + accoa[c] --> aacoa[c] + ac[c] 		
1498	ACACT1r	No	acetyl-CoA C-acetyltransferase	[c] : (2) accoa <==> aacoa + coa	Membrane Lipid Metabolism	2.3.1.9	b2224	JLR- reversible form of ACACT1		5.82626	4.21018	[c] : (2) accoa[c] <==> aacoa[c] + coa[c] 		
8776	ACACt2pp	Yes	acetoacetate transport via proton symport  (periplasm)	acac[p] + h[p] <==> acac[c] + h[c]	Putative Transporters		b2223	"originally named AACTP
NCD"	"JLR-based on Saier's database
see PMID: 3025185 for realated SCFA metabolism
AMF"	0	0	[c] : acac[p] + h[p] <==> acac[c] + h[c] 					
9028	ACACtex	Yes	acetoacetate transport via diffusion (extracellular to periplasm)	acac[e] <==> acac[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : acac[e] <==> acac[p] 					
289	ACALD	Yes	acetaldehyde dehydrogenase (acetylating)	[c] : acald + coa + nad <==> accoa + h + nadh	Pyruvate Metabolism	1.2.1.10	( b1241  or  b0351 )		MhPF is based on sequence homology.	-4.00728	5.93943	[c] : acald[c] + coa[c] + nad[c] <==> accoa[c] + h[c] + nadh[c] 					
9029	ACALDtex	Yes	acetaldehyde transport via diffusion (extracellular to periplasm)	acald[e] <==> acald[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : acald[e] <==> acald[p] 					
8973	ACALDtpp	Yes	acetaldehyde reversible transport (periplasm)	acald[p] <==> acald[c]	"Transport, Inner Membrane"			NCD		0	0	[c] : acald[p] <==> acald[c] 					
13742	ACANTHAT	Yes	acetyl-CoA:anthranilate acetyltransferase	[c] : accoa + anth --> acanth + coa	Update	2.3.1.118	b1463	AMF	"from PMID: 10806332
AMF
not sure of physiological role, can also act on
4abz and others
"	2.4889	5.0972	[c] : accoa[c] + anth[c] --> acanth[c] + coa[c] 					
2453	ACBIPGT	No	Adenosyl cobinamide phosphate guanyltransferase	[c] : adocbip + gtp + h --> agdpcbi + ppi	Cofactor and Prosthetic Group Biosynthesis		b1993	"JLR (Kegg Rxn R05222)
EC 2.7.7.62"	PMID: 7592411	No energy	No energy	[c] : adocbip[c] + gtp[c] + h[c] --> agdpcbi[c] + ppi[c] 					
32	ACCOAC	Yes	acetyl-CoA carboxylase	[c] : accoa + atp + hco3 --> adp + h + malcoa + pi	Membrane Lipid Metabolism	6.4.1.2	( b0185  and  b2316  and  b3255  and  b3256 )	"A biotinyl-protein.
Step 1: biotin + ATP + HCO3 -> carboxy-biotin + ADP + Pi. 
Step 2: carboxy-biotin + ACCOA -> MALCOA
bacteria have separate enzymes for each step and a biotin-carrier protein; in yeast a single protein carries out all activities
NCD
"	"irreversible
NH pg.614
JLR
AMF"	-1.72537	2.11121	[c] : accoa[c] + atp[c] + hco3[c] --> adp[c] + h[c] + malcoa[c] + pi[c] 					
3258	ACCOAL	No	acetate-CoA ligase (ADP-forming)	[c] : atp + coa + ppa --> adp + pi + ppcoa	Alternate Carbon Metabolism	6.2.1.13	b0335	JLR- also acts on propanoate		-1.1641	4.51371	[c] : atp[c] + coa[c] + ppa[c] --> adp[c] + pi[c] + ppcoa[c] 					
13797	ACGAL1PPpp	Yes	N-acetyl-D-galactosamine 1-phosphatase (periplasm)	[p] : acgal1p + h2o --> acgal + pi	Update	3.1.3.10		AMF	"assumed probable reactions, may be carried out by the Agp reaction - almost assigned to Agp reaction

needed to degrade 1-phosphates from UDP- hydrolase activity of UshA which is known to produce these products

AMF"	-3.54819	2.12947	[p] : acgal1p[p] + h2o[p] --> acgal[p] + h[p] + pi[p] 					
13803	ACGAL1Ptex	Yes	N-acetyl-D-galactosamine 1-phosphate transport via diffusion (extracellular to periplasm)	acgal1p[e] <==> acgal1p[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : acgal1p[e] <==> acgal1p[p] 					
13805	ACGALtex	Yes	N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)	acgal[e] <==> acgal[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : acgal[e] <==> acgal[p] 					
13795	ACGAM1PPpp	Yes	N-acetyl-D-glucosamine 1-phosphatase (periplasm)	[p] : acgam1p + h2o --> acgam + pi	Update	3.1.3.10		AMF	"assumed probable reactions, may be carried out by the Agp reaction - almost assigned to Agp reaction

needed to degrade 1-phosphates from UDP- hydrolase activity of UshA which is known to produce these products

AMF"	-3.54819	2.12947	[p] : acgam1p[p] + h2o[p] --> acgam[p] + h[p] + pi[p] 					
13800	ACGAM1Ptex	Yes	N-acetyl-D-glucosamine 1-phosphate transport via diffusion (extracellular to periplasm)	acgam1p[e] <==> acgam1p[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : acgam1p[e] <==> acgam1p[p] 					
9377	ACGAMK	Yes	N-acetylglucosamine kinase	[c] : acgam + atp --> acgam6p + adp + h	Murein Recycling	2.7.1.59	b1119		"AMF
PMID: 15489439"	-4.65732	2.09859	[c] : acgam[c] + atp[c] --> acgam6p[c] + adp[c] 					
2498	ACGAMT	No	UDP-N-acetylglucosamine:undecaprenylphosphate N-acetylglucosamine -1-phosphate transferase	[c] : uacgam + udcpp --> ump + unaga	Cell Envelope Biosynthesis		b3784	JLR		0	0.5	[c] : uacgam[c] + udcpp[c] --> ump[c] + unaga[c] 					
8777	ACGAptspp	Yes	N-Acetyl-D-glucosamine transport via PEP:Pyr PTS  (periplasm)	acgam[p] + pep[c] --> acgam6p[c] + pyr[c]	"Transport, Inner Membrane"		( ( b2417  and  b1101  and  b2415  and  b2416 )  or  ( b0679  and  b2415  and  b2416 ) )	"on Saier page, TC#: 4.A.1.1.2"		-10.1729	3.20748	[c] : acgam[p] + pep[c] --> acgam6p[c] + pyr[c] 
9228	ACGAtex	Yes	N-Acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)	acgam[e] <==> acgam[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : acgam[e] <==> acgam[p] 
308	ACGK	No	acetylglutamate kinase	[c] : acglu + atp --> acg5p + adp	Arginine and Proline Metabolism	2.7.2.8	b3959			3.00718	2.24154	[c] : acglu[c] + atp[c] + h[c] --> acg5p[c] + adp[c] 
3466	ACGS	No	N-acetylglutamate synthase	[c] : accoa + glu-L --> acglu + coa + h	Arginine and Proline Metabolism	2.3.1.1	b2818			-2.48774	5.01459	[c] : accoa[c] + glu-L[c] --> acglu[c] + coa[c] + h[c] 
325	ACHBS	No	2-aceto-2-hydroxybutanoate synthase	[c] : 2obut + h + pyr --> 2ahbut + co2	"Valine, Leucine, and Isoleucine Metabolism"		( ( b3670  and  b3671 )  or  ( b3767  and  b3768  and  b3769 )  or  ( b0077  and  b0078 ) )	JLR- I think the EC is 4.1.3.18		-6.52706	3.14093	[c] : 2obut[c] + h[c] + pyr[c] --> 2ahbut[c] + co2[c] 
1196	ACKr	No	acetate kinase	[c] : ac + atp <==> actp + adp	Pyruvate Metabolism	2.7.2.1	( b3115  or  b2296  or  b1849 )	"JLR- This is the reversible form of ACK.  The reaction already exists in the database, but it is listed as ACK_do not use."		3.00718	2.24154	[c] : ac[c] + atp[c] + h[c] <==> actp[c] + adp[c] 
326	ACLS	No	acetolactate synthase	[c] : h + (2) pyr --> alac-S + co2	"Valine, Leucine, and Isoleucine Metabolism"	4.1.3.18	( ( b3670  and  b3671 )  or  ( b3767  and  b3768  and  b3769 )  or  ( b0077  and  b0078 ) )	"A flavoprotein. Requires thiamine diphosphate; also catalyses the formation of 2-aceto-2-hydroxybutanoate (see ACHBS).
Also EC 2.2.1.6 - NCD
"		-6.52706	3.14093	[c] : h[c] + (2) pyr[c] --> alac-S[c] + co2[c] 
6170	ACM6PH	Yes	N-acetylmuramate 6-phosphate hydrolase	[c] : acmum6p + h2o --> acgam6p + lac-D	Update			"JLR- reaction is assumed, not sure about it at all"	"Added because cell can grow on the carbon source.  Reaction is unknown, and assumed lac-D is by-product.

PUTATIVE"	-3.32755	3.07096	[c] : acmum6p[c] + h2o[c] --> acgam6p[c] + lac-D[c] 
3231	ACMAMUT	No	UDP-N-acetyl-D-mannosaminuronic acid transferase	[c] : uacmamu + unaga --> h + udp + unagamu	Cell Envelope Biosynthesis		b3794	JLR	JLR- putative enzyme assignment	-0.675884	3.38607	[c] : uacmamu[c] + unaga[c] --> udp[c] + unagamu[c] 
8778	ACMANAptspp	Yes	N-acetyl-D-mannosamine transport via PTS  (periplasm)	acmana[p] + pep[c] --> acmanap[c] + pyr[c]	"Transport, Inner Membrane"		( b1817  and  b1818  and  b1819  and  b2415  and  b2416 )	JLR		-10.1729	3.20748	[c] : acmana[p] + pep[c] --> acmanap[c] + pyr[c] 
9031	ACMANAtex	Yes	N-acetyl-D-mannosamine transport via diffusion (extracellular to periplasm)	acmana[e] <==> acmana[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : acmana[e] <==> acmana[p] 
8779	ACMUMptspp	Yes	N-acetylmuramate transport via PEP:Pyr PTS (periplasm)	acmum[p] + pep[c] --> acmum6p[c] + pyr[c]	Update		( b2417  and  b2429  and  b2415  and  b2416 )		This compound can serve as a carbon source reactions are missing.	-10.1729	3.20748	[c] : acmum[p] + pep[c] --> acmum6p[c] + pyr[c] 
9032	ACMUMtex	Yes	N-acetylmuramate transport via diffusion (extracellular to periplasm)	acmum[e] --> acmum[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : acmum[e] --> acmum[p] 
8780	ACNAMt2pp	Yes	N-acetylneuraminate proton symport (periplasm)	acnam[p] + h[p] --> acnam[c] + h[c]	"Transport, Inner Membrane"		b3224	JLR		0	0	[c] : acnam[p] + h[p] --> acnam[c] + h[c] 
9033	ACNAMtex	Yes	N-acetylneuraminate transport via diffusion (extracellular to periplasm)	acnam[e] <==> acnam[p]	"Transport, Outer Membrane"		( b4311  or  b0929  or  b2215 )		"This indicates that, in the absence of the porins OmpF and OmpC, the channel formed by nanC is the only way for Neu5Ac (acnam) to enter the bacteria. Glucose and GlcNAc probably enter by other weakly expressed general porins.
PMID: 15743943
AMF
"	0	0	[c] : acnam[e] <==> acnam[p] 
2947	ACNML	No	N-Acetylneuraminate lyase	[c] : acnam --> acmana + pyr	Alternate Carbon Metabolism	4.1.3.3	b3225	JLR		0.294857	5.20947	[c] : acnam[c] --> acmana[c] + pyr[c] 
5391	ACOAD1f	Yes	acyl-CoA dehydrogenase (butanoyl-CoA)	[c] : btcoa + fad --> b2coa + fadh2	Membrane Lipid Metabolism	1.3.99.2	b0221	"Assume NAD/NADH as acceptors
Lumped long-chain acyl-CoA dehydrogenase (EC 1.3.99.13)
This reaction is therefore equilivalent to trans-2-enoyl-CoA reductase (NAD) (EC 1.3.1.44)"	Another isozyme exists because a fadE mutant can still grow on FA under aerobic conditions see PMID 12535077	2.96898	7.05102	[c] : btcoa[c] + fad[c] --> b2coa[c] + fadh2[c] 					
5393	ACOAD2f	Yes	acyl-CoA dehydrogenase (hexanoyl-CoA)	[c] : fad + hxcoa --> fadh2 + hx2coa	Membrane Lipid Metabolism	1.3.99.3	b0221	"Assume NAD/NADH as acceptors
Lumped long-chain acyl-CoA dehydrogenase (EC 1.3.99.13)
This reaction is therefore equilivalent to trans-2-enoyl-CoA reductase (NAD) (EC 1.3.1.44)"	Another isozyme exists because a fadE mutant can still grow on FA under aerobic conditions see PMID 12535077	2.96898	7.05102	[c] : fad[c] + hxcoa[c] --> fadh2[c] + hx2coa[c] 					
5400	ACOAD3f	Yes	acyl-CoA dehydrogenase (octanoyl-CoA)	[c] : fad + occoa --> fadh2 + oc2coa	Membrane Lipid Metabolism	1.3.99.3	b0221	"Assume FAD/FADH2 as acceptors
Lumped long-chain acyl-CoA dehydrogenase (EC 1.3.99.13)
This reaction is therefore equilivalent to trans-2-enoyl-CoA reductase (NAD) (EC 1.3.1.44)"	Another isozyme exists because a fadE mutant can still grow on FA under aerobic conditions see PMID 12535077	2.96898	7.05102	[c] : fad[c] + occoa[c] --> fadh2[c] + oc2coa[c] 					
5401	ACOAD4f	Yes	acyl-CoA dehydrogenase (decanoyl-CoA)	[c] : dcacoa + fad --> dc2coa + fadh2	Membrane Lipid Metabolism	1.3.99.3	b0221	"Assume FAD/FADH2 as acceptors
Lumped long-chain acyl-CoA dehydrogenase (EC 1.3.99.13)
This reaction is therefore equilivalent to trans-2-enoyl-CoA reductase (NAD) (EC 1.3.1.44)"	Another isozyme exists because a fadE mutant can still grow on FA under aerobic conditions see PMID 12535077	2.96898	7.05102	[c] : dcacoa[c] + fad[c] --> dc2coa[c] + fadh2[c] 					
5405	ACOAD5f	Yes	acyl-CoA dehydrogenase (dodecanoyl-CoA)	[c] : ddcacoa + fad --> dd2coa + fadh2	Membrane Lipid Metabolism	1.3.99.3	b0221	"JC
Assume FAD/FADH2 as acceptors
Lumped long-chain acyl-CoA dehydrogenase (EC 1.3.99.3)"	Another isozyme exists because a fadE mutant can still grow on FA under aerobic conditions see PMID 12535077	2.96898	7.05102	[c] : ddcacoa[c] + fad[c] --> dd2coa[c] + fadh2[c] 					
5402	ACOAD6f	Yes	acyl-CoA dehydrogenase (tetradecanoyl-CoA)	[c] : fad + tdcoa --> fadh2 + td2coa	Membrane Lipid Metabolism	1.3.99.3	b0221	"Assume FAD/FADH2 as acceptors
Lumped long-chain acyl-CoA dehydrogenase (EC 1.3.99.13)
This reaction is therefore equilivalent to trans-2-enoyl-CoA reductase (NAD) (EC 1.3.1.44)"	Another isozyme exists because a fadE mutant can still grow on FA under aerobic conditions see PMID 12535077	2.96898	7.05102	[c] : fad[c] + tdcoa[c] --> fadh2[c] + td2coa[c] 					
5406	ACOAD7f	Yes	acyl-CoA dehydrogenase (hexadecanoyl-CoA)	[c] : fad + pmtcoa --> fadh2 + hdd2coa	Membrane Lipid Metabolism	1.3.99.3	b0221	"JC
Assume FAD/FADH2 as acceptors
Lumped long-chain acyl-CoA dehydrogenase (EC 1.3.99.3)"	Another isozyme exists because a fadE mutant can still grow on FA under aerobic conditions see PMID 12535077	2.96898	7.05102	[c] : fad[c] + pmtcoa[c] --> fadh2[c] + hdd2coa[c] 					
8134	ACOAD8f	Yes	acyl-CoA dehydrogenase (octadecanoyl-CoA)	[c] : fad + stcoa --> fadh2 + od2coa	Membrane Lipid Metabolism	1.3.99.3	b0221	"JLR
Assume FAD/FADH2 as acceptors
Lumped long-chain acyl-CoA dehydrogenase (EC 1.3.99.3)"	Another isozyme exists because a fadE mutant can still grow on FA under aerobic conditions see PMID 12535077	2.96898	7.05102	[c] : fad[c] + stcoa[c] --> fadh2[c] + od2coa[c] 					
3280	ACOATA	No	Acetyl-CoA ACP transacylase	[c] : ACP + accoa <==> acACP + coa	Membrane Lipid Metabolism	2.3.1.38	b1091	"tv
rxn is now charge balanced; removed h - NCD"		0	0.5	[c] : accoa[c] + ACP[c] <==> acACP[c] + coa[c] 					
3511	ACODA	No	acetylornithine deacetylase	[c] : acorn + h2o --> ac + orn	Arginine and Proline Metabolism	3.5.1.16	b3957			-3.36489	3.34628	[c] : acorn[c] + h2o[c] --> ac[c] + orn[c] 					
13531	ACOLIPAtex	Yes	arabinose modified core oligosaccharide lipid A transport via vector (periplasm to extracellular)	acolipa[p] --> acolipa[e]	Lipopolysaccharide Biosynthesis / Recycling			"AMF
not sure how it travels across the periplam or flipped to outer serface of the membrane"	"this reaction is needed to have the LPS lipid A derivative presented to the outer membrane surface - both moved across the periplasm and flipped across the outer membrane

not sure on the method of transport

this paper talks about the possibility of the transport PMID: 15576375

AMF"	0	0	[c] : acolipa[p] --> acolipa[e] 					
20119	ACONIs	Yes	aconitate isomerase (spontaneous)	[c] : acon-T <==> acon-C	Spontaneous Reaction	5.3.3.7		#N/A	#N/A	0	0.5	[c] : acon-T[c] <==> acon-C[c] 					
2407	ACONMT	No	Trans-aconitate methyltransferase	[c] : acon-T + amet --> aconm + ahcys	Unassigned		b1519	JLR		No energy	No energy	[c] : acon-T[c] + amet[c] --> aconm[c] + ahcys[c] 					
20120	ACONTa	Yes	"aconitase (half-reaction A, Citrate hydro-lyase)"	[c] : cit <==> acon-C + h2o	Citric Acid Cycle	4.2.1.3	( b1276  or  b0118 )	#N/A	#N/A	1.73013	3.37981	[c] : cit[c] <==> acon-C[c] + h2o[c] 					
20121	ACONTb	Yes	"aconitase (half-reaction B, Isocitrate hydro-lyase)"	[c] : acon-C + h2o <==> icit	Citric Acid Cycle	4.2.1.3	( b1276  or  b0118 )	#N/A	#N/A	-0.190448	3.32787	[c] : acon-C[c] + h2o[c] <==> icit[c] 					
302	ACOTA	No	acetylornithine transaminase	[c] : acorn + akg <==> acg5sa + glu-L	Arginine and Proline Metabolism	2.6.1.11	( b3359  or  b1748 )		"from ecocyc:
The transaminase is the gene product of astC and is the catabolic version of acetylornithine transaminase, the argD gene product. The astC enzyme shows a higher affinity for succinylornithine than for acetylornithine. [ Schneider98  , Fraley98  ,  Cunin86  ]
PMID: 9696779
PMID: 9696779
AMF"	2.42139	2.1337	[c] : acorn[c] + akg[c] <==> acg5sa[c] + glu-L[c] 					
3596	ACPS1	No	acyl-carrier protein synthase	[c] : apoACP + coa --> ACP + h + pap	Cofactor and Prosthetic Group Biosynthesis	2.7.8.7	( b2563  or  b3475 )	JLR	"JLR-  apoACP is the inactive form.

when acpS was deleted, it was lethal, so acpT (yhhU) can not support the physiological funtion that was confirmed in vivo
PMID: 10625633
despite this fact, the AspT association was made in the model since this gene may be able to preform the reaction under certain conditions"	No energy	No energy	[c] : apoACP[c] + coa[c] --> ACP[c] + pap[c] 					
291	ACS	No	acetyl-CoA synthetase	[c] : ac + atp + coa --> accoa + amp + ppi	Pyruvate Metabolism	6.2.1.1	b4069			-2.74083	4.99608	[c] : ac[c] + atp[c] + coa[c] + h[c] --> accoa[c] + amp[c] + ppi[c] 					
13993	ACSERtex	Yes	O-Acetyl-L-serine transport via diffusion (extracellular to periplasm)	acser[e] <==> acser[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : acser[e] <==> acser[p] 					
13992	ACSERtpp	Yes	O-Acetyl-L-serine export via facilitated transport	acser[c] --> acser[p]	"Transport, Inner Membrane"		( b2578  or  b1533 )	"AMF
PMID: 12562784"	"YfiK characterized in PMID: 12562784 

EamA characterized in PMID: 10844694
EamA substrate specificity and the energization of the efflux pump is unknown.
AMF"	0	0	[c] : acser[c] --> acser[p] 					
8974	ACt2rpp	Yes	acetate reversible transport via proton symport (periplasm)	ac[p] + h[p] <==> ac[c] + h[c]	"Transport, Inner Membrane"			NCD		0	0	[c] : ac[p] + h[p] <==> ac[c] + h[c] 					
8781	ACt4pp	Yes	Na+/Acetate symport (periplasm)	ac[p] + na1[p] --> ac[c] + na1[c]	Update		b4067	"JLR
2.A.21.7.2"	"Ref couldn't distinguish between a proton or a Na symporter, assumed Na based on sequence homology"	0	0	[c] : ac[p] + na1[p] --> ac[c] + na1[c] 					
9027	ACtex	Yes	Acetate transport via diffusion (extracellular to periplasm)	ac[e] <==> ac[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ac[e] <==> ac[p] 					
3513	ADA	No	Adenosine deaminase	[c] : adn + h + h2o --> ins + nh4	Nucleotide Salvage Pathway	3.5.4.4	b1623	Added EC- JLR		-5.6874	4.84135	[c] : adn[c] + h[c] + h2o[c] --> ins[c] + nh4[c] 					
3621	ADCL	No	4-aminobenzoate synthase	[c] : 4adcho --> 4abz + h + pyr	Cofactor and Prosthetic Group Biosynthesis		b1096	"Not in IUBMB. No EC
EC: 4.1.3.38 IT"		-36.613	10.8838	[c] : 4adcho[c] --> 4abz[c] + h[c] + pyr[c] 					
3619	ADCS	No	4-amino-4-deoxychorismate synthase	[c] : chor + gln-L --> 4adcho + glu-L	Cofactor and Prosthetic Group Biosynthesis		( b3360  and  b1812 )	Not in IUBMB. No EC		-6.68353	3.4036	[c] : chor[c] + gln-L[c] --> 4adcho[c] + glu-L[c] 					
3515	ADD	No	adenine deaminase	[c] : ade + h + h2o --> hxan + nh4	Nucleotide Salvage Pathway	3.5.4.2	b3665	note:  reaction also occures spontaneously - oxidative deaminination  (MKA)		-5.6874	4.84135	[c] : ade[c] + h[c] + h2o[c] --> hxan[c] + nh4[c] 					
8782	ADEt2rpp	Yes	adenine transport via proton symport (reversible) (periplasm)	ade[p] + h[p] <==> ade[c] + h[c]	"Transport, Inner Membrane"		b3654	JLR	JLR- not sure about the reaction 	0	0	[c] : ade[p] + h[p] <==> ade[c] + h[c] 					
9034	ADEtex	Yes	adenine transport via diffusion (extracellular to periplasm)	ade[e] <==> ade[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ade[e] <==> ade[p] 					
181	ADK1	No	adenylate kinase	[c] : amp + atp <==> (2) adp	Nucleotide Salvage Pathway	2.7.4.3	b0474	Inorganic triphosphate can also act as donor		0	0.5	[c] : amp[c] + atp[c] <==> (2) adp[c] 					
4682	ADK3	No	adentylate kinase (GTP)	[c] : amp + gtp <==> adp + gdp	Nucleotide Salvage Pathway		b0474	JLR		0	0.5	[c] : amp[c] + gtp[c] <==> adp[c] + gdp[c] 					
1080	ADK4	No	adentylate kinase (ITP)	[c] : amp + itp <==> adp + idp	Nucleotide Salvage Pathway		b0474	JLR		0	0.5	[c] : amp[c] + itp[c] <==> adp[c] + idp[c] 					
1217	ADMDCr	No	Adenosylmethionine decarboxylase	[c] : amet + h <==> ametam + co2	Arginine and Proline Metabolism	4.1.1.50	b0120	JLR- added reversible form of ADMDC		-4.96805	1.79669	[c] : amet[c] + h[c] <==> ametam[c] + co2[c] 					
2539	ADNCYC	No	adenylate cyclase	[c] : atp --> camp + ppi	Nucleotide Salvage Pathway	4.6.1.1	b3806	JLR		1.09851	7.6982	[c] : atp[c] --> camp[c] + ppi[c] 					
179	ADNK1	No	adenosine kinase	[c] : adn + atp --> adp + amp + h	Nucleotide Salvage Pathway	2.7.1.20	b0474	2-Aminoadenosine can also act as acceptor		-4.65732	2.09859	[c] : adn[c] + atp[c] --> adp[c] + amp[c] 					
8783	ADNt2pp	Yes	adenosine transport in via proton symport (periplasm)	adn[p] + h[p] --> adn[c] + h[c]	"Transport, Inner Membrane"		( b2964  or  b2393 )			0	0	[c] : adn[p] + h[p] --> adn[c] + h[c] 					
8784	ADNt2rpp	Yes	"adenosine transport in via proton symport, reversible (periplasm)"	adn[p] + h[p] <==> adn[c] + h[c]	"Transport, Inner Membrane"		b2406	JLR		0	0	[c] : adn[p] + h[p] <==> adn[c] + h[c] 					
9035	ADNtex	Yes	adenosine transport via diffusion (extracellular to periplasm)	adn[e] <==> adn[p]	"Transport, Outer Membrane"		b0411		"assumed passive diffusion through the outer peptidoglycan layer

Tsx is responsible for the permeation of ribo- and deoxy-nucleosides, across the outer membrane of E. coli"	0	0	[c] : adn[e] <==> adn[p] 					
1143	ADNUC	Yes	adenosine hydrolase	[c] : adn + h2o --> ade + rib-D	Update	3.2.2.8	b0030	"tv
D or L-ribose"		-2.26379	3.60328	[c] : adn[c] + h2o[c] --> ade[c] + rib-D[c] 					
2455	ADOCBIK	No	Adenosyl cobinamide kinase	[c] : adocbi + atp --> adocbip + adp + h	Cofactor and Prosthetic Group Biosynthesis		b1993	"JLR (Kegg Rxn R05221)
EC 2.7.1.156"	PMID: 7592411	No energy	No energy	[c] : adocbi[c] + atp[c] --> adocbip[c] + adp[c] + h[c] 					
9128	ADOCBLabcpp	Yes	Adenosylcobalamin transport via ABC system (periplasm)	adocbl[p] + atp[c] + h2o[c] --> adocbl[c] + adp[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b1711  and  b1709  and  b0158 )	"AMF
PMID: 342526"	"This form can also be transported across the outer membrane, but I am not sure if the adenylated form exists in the environment

PMID: 342526"	-7.01673	1.48181	[c] : adocbl[p] + atp[c] + h2o[c] --> adocbl[c] + adp[c] + h[c] + pi[c] 					
2454	ADOCBLS	No	Adenosylcobalamin 5'-phosphate synthase	[c] : agdpcbi + rdmbzi --> adocbl + gmp + h	Cofactor and Prosthetic Group Biosynthesis		b1992	"JLR (Kegg RXN R05223)
EC 2.7.8.26"	PMID: 7592411	No energy	No energy	[c] : agdpcbi[c] + rdmbzi[c] --> adocbl[c] + gmp[c] 					
9127	ADOCBLtonex	Yes	Adenosylcobalimin transport via ton system (extermal)	adocbl[e] + h[p] --> adocbl[p] + h[c]	"Transport, Outer Membrane"		( b3966  and  ( b1252  and  b3005  and  b3006 ) )	"AMF - PMID:8405078 and PMID: 10209752
assumption of 1 proton transported across the membrane
transport for B12 may be calcium dependant"	"PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR

B12 transport has been shown to be calcium dependent, but not represented in this reaction"	0	0	[c] : adocbl[e] + h[p] --> adocbl[p] + h[c] 					
2835	ADPRDP	Yes	ADPribose diphosphatase	[c] : adprib + h2o --> amp + (2) h + r5p	Update	3.6.1.13	b3397		"characterized in PMID: 12135348
AMF"	-8.66075	4.06632	[c] : adprib[c] + h2o[c] --> amp[c] + r5p[c] 					
178	ADPT	No	adenine phosphoribosyltransferase	[c] : ade + prpp --> amp + ppi	Nucleotide Salvage Pathway	2.4.2.7	b0469			-3.6643	3.87109	[c] : ade[c] + prpp[c] --> amp[c] + ppi[c] 					
2867	ADSK	No	adenylyl-sulfate kinase	[c] : aps + atp --> adp + h + paps	Cysteine Metabolism	2.7.1.25	b2750			-3.46855	2.28701	[c] : aps[c] + atp[c] --> adp[c] + paps[c] 					
1077	ADSL1r	No	adenylsuccinate lyase	[c] : dcamp <==> amp + fum	Purine and Pyrimidine Biosynthesis	4.3.2.2	b1131	JLR- added reversible form of ADSL1	"ADSL2r reversible in NH 569
ADSL1r assumed reversible
AMF
"	3.59749	3.50988	[c] : dcamp[c] <==> amp[c] + fum[c] 					
1309	ADSL2r	No	adenylosuccinate lyase	[c] : 25aics <==> aicar + fum	Purine and Pyrimidine Biosynthesis	4.3.2.2	b1131	JLR- added reversible form of ADSL2	"ADSL2r reversible in NH 569
ADSL1r assumed reversible
AMF
"	3.59749	3.50988	[c] : 25aics[c] <==> aicar[c] + fum[c] 					
3516	ADSS	No	adenylosuccinate synthase	[c] : asp-L + gtp + imp --> dcamp + gdp + (2) h + pi	Purine and Pyrimidine Biosynthesis	6.3.4.4	b4177			-2.65748	5.30304	[c] : asp-L[c] + gtp[c] + imp[c] --> dcamp[c] + gdp[c] + (2) h[c] + pi[c] 		
3518	AGDC	No	N-acetylglucosamine-6-phosphate deacetylase	[c] : acgam6p + h2o --> ac + gam6p	Alternate Carbon Metabolism	3.5.1.25	b0677	"acetylglucosamine phosphate deacetylase; 
acetylaminodeoxyglucosephosphate acetylhydrolase; 
2-acetamido-2-deoxy-D-glucose-6-phosphate amidohydrolase"		-3.36489	3.34628	[c] : acgam6p[c] + h2o[c] --> ac[c] + gam6p[c] 		
12535	AGM3PA	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase	[c] : anhgm3p + h2o --> LalaDgluMdap + anhgm	Murein Recycling		b0110	AMF	"AmpD is cylosolic
PMID: 15901686"	-3.36489	3.34628	[c] : anhgm3p[c] + h2o[c] --> anhgm[c] + LalaDgluMdap[c] 		
12534	AGM3PApp	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase (periplasm)	[p] : anhgm3p + h2o --> LalaDgluMdap + anhgm	Murein Recycling		( b2435  or  b4169  or  b2817 )	AMF	"AMF
AmiA,B,C all have amidase activity
see PMID: 11454209"	-3.36489	3.34628	[p] : anhgm3p[p] + h2o[p] --> anhgm[p] + LalaDgluMdap[p] 		
12637	AGM3PH	Yes	"N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide beta -1,4-N-acetylglucosaminidase"	[c] : anhgm3p + h2o --> acgam + anhm3p	Murein Recycling		b1107	AMF	"will also cleave the muropeptides as efficiently as the anhydrousmuropeptides, and the free form with no peptides

PMID: 10940025"	-3.32755	3.07096	[c] : anhgm3p[c] + h2o[c] --> acgam[c] + anhm3p[c] 		
12632	AGM3Pt2pp	Yes	GlcNAc-anhMurNAc tripeptide transport in via proton symport (periplasm)	anhgm3p[p] + h[p] --> anhgm3p[c] + h[c]	Murein Recycling		b0433	AMF	"AmpG permease is a single-component permease dependent on the proton motive force - the exact stoich is still unknown, simpost was assumed

the only §-N-acetylglucosaminidase in Escherichia coli is cytoplasmic which then makes it necessary to transport these inside

the disaccharide itself was readily transported and that the N-acetylmuramic acid moiety must be present in the 1,6-anhydro form - - other cmpds can be added

PMID: 12426329
AMF"	0	0	[c] : anhgm3p[p] + h[p] --> anhgm3p[c] + h[c] 		
13206	AGM3Ptex	Yes	GlcNAc-anhMurNAc tripeptide transport via diffusion (extracellular to periplasm)	anhgm3p[e] <==> anhgm3p[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : anhgm3p[e] <==> anhgm3p[p] 		
12537	AGM4PA	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase	[c] : anhgm4p + h2o --> LalaDgluMdapDala + anhgm	Murein Recycling		b0110	AMF	"AmpD is cylosolic
PMID: 15901686"	-3.36489	3.34628	[c] : anhgm4p[c] + h2o[c] --> anhgm[c] + LalaDgluMdapDala[c] 		
12536	AGM4PApp	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase (periplasm)	[p] : anhgm4p + h2o --> LalaDgluMdapDala + anhgm	Murein Recycling		( b2817  or  b2435  or  b4169 )	AMF	"AMF
AmiA,B,C all have amidase activity
see PMID: 11454209"	-3.36489	3.34628	[p] : anhgm4p[p] + h2o[p] --> anhgm[p] + LalaDgluMdapDala[p] 		
12612	AGM4PCP	Yes	"N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase"	[c] : anhgm4p + h2o --> ala-D + anhgm3p	Murein Recycling		b1192	AMF	"LdcA is a cytoplasmic LD-carboxypeptidase
four different similar susbstrates
PMID: 10428950"	-3.36489	3.34628	[c] : anhgm4p[c] + h2o[c] --> ala-D[c] + anhgm3p[c] 		
12613	AGM4PCPpp	Yes	"N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase (periplasmic)"	[p] : anhgm4p + h2o --> ala-D + anhgm3p	Murein Recycling			AMF	"the periplasmic enzyme is unknown
cytoplasmic is LdcA"	-3.36489	3.34628	[p] : anhgm4p[p] + h2o[p] --> ala-D[p] + anhgm3p[p] 		
12636	AGM4PH	Yes	"N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide beta -1,4-N-acetylglucosaminidase"	[c] : anhgm4p + h2o --> acgam + anhm4p	Murein Recycling		b1107	AMF	"will also cleave the muropeptides as efficiently as the anhydrousmuropeptides, and the free form with no peptides

PMID: 10940025"	-3.32755	3.07096	[c] : anhgm4p[c] + h2o[c] --> acgam[c] + anhm4p[c] 		
12633	AGM4Pt2pp	Yes	GlcNAc-anhMurNAc tetrapeptide transport in via proton symport (periplasm)	anhgm4p[p] + h[p] --> anhgm4p[c] + h[c]	Murein Recycling		b0433	AMF	"AmpG permease is a single-component permease dependent on the proton motive force - the exact stoich is still unknown, simpost was assumed

the only §-N-acetylglucosaminidase in Escherichia coli is cytoplasmic which then makes it necessary to transport these inside

the disaccharide itself was readily transported and that the N-acetylmuramic acid moiety must be present in the 1,6-anhydro form - - other cmpds can be added

PMID: 12426329
AMF"	0	0	[c] : anhgm4p[p] + h[p] --> anhgm4p[c] + h[c] 		
13207	AGM4Ptex	Yes	GlcNAc-anhMurNAc tetrapeptide transport via diffusion (extracellular to periplasm)	anhgm4p[e] <==> anhgm4p[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : anhgm4p[e] <==> anhgm4p[p] 		
12638	AGMH	Yes	"N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl beta -1,4-N-acetylglucosaminidase"	[c] : anhgm + h2o --> acgam + anhm	Murein Recycling		b1107	AMF	"will also cleave the muropeptides as efficiently as the anhydrousmuropeptides, and the free form with no peptides

PMID: 10940025"	-3.32755	3.07096	[c] : anhgm[c] + h2o[c] --> acgam[c] + anhm[c] 		
2549	AGMHE	No	ADP-D-glycero-D-manno-heptose epimerase	"[c] : adphep-D,D --> adphep-L,D"	Cell Envelope Biosynthesis	5.1.3.20	b3619	JLR		0	0.5	"[c] : adphep-D,D[c] --> adphep-L,D[c] "		
304	AGMT	No	agmatinase	[c] : agm + h2o --> ptrc + urea	Arginine and Proline Metabolism	3.5.3.11	b2937			-5.9727	4.66434	[c] : agm[c] + h2o[c] --> ptrc[c] + urea[c] 					
12634	AGMt2pp	Yes	GlcNAc-anhMurNAc transport in via proton symport (periplasm)	anhgm[p] + h[p] --> anhgm[c] + h[c]	Murein Recycling		b0433	AMF	"AmpG permease is a single-component permease dependent on the proton motive force - the exact stoich is still unknown, simpost was assumed

the only §-N-acetylglucosaminidase in Escherichia coli is cytoplasmic which then makes it necessary to transport these inside

the disaccharide itself was readily transported and that the N-acetylmuramic acid moiety must be present in the 1,6-anhydro form - - other cmpds can be added

PMID: 12426329
AMF"	0	0	[c] : anhgm[p] + h[p] --> anhgm[c] + h[c] 					
9036	AGMtex	Yes	agmatine transport via diffusion (extracellular to periplasm)	agm[e] <==> agm[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : agm[e] <==> agm[p] 					
19326	AGPAT120	Yes	1-tetradecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C12:0)	[c] : 1ddecg3p + ddcaACP --> ACP + pa120	Glycerophospholipid Metabolism	2.3.1.51	b3018	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.98374	4.73838	[c] : 1ddecg3p[c] + ddcaACP[c] --> ACP[c] + pa120[c] 					
19238	AGPAT140	Yes	1-tetradecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C14:0)	[c] : 1tdecg3p + myrsACP --> ACP + pa140	Glycerophospholipid Metabolism	2.3.1.51	b3018	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.98374	4.73838	[c] : 1tdecg3p[c] + myrsACP[c] --> ACP[c] + pa140[c] 					
19241	AGPAT141	Yes	1-tetradec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C14:1)	[c] : 1tdec7eg3p + tdeACP --> ACP + pa141	Glycerophospholipid Metabolism	2.3.1.51	b3018	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-0.390149	5.36289	[c] : 1tdec7eg3p[c] + tdeACP[c] --> ACP[c] + pa141[c] 					
19239	AGPAT160	Yes	1-hexadecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C16:0)	[c] : 1hdecg3p + palmACP --> ACP + pa160	Glycerophospholipid Metabolism	2.3.1.51	b3018	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.98374	4.73838	[c] : 1hdecg3p[c] + palmACP[c] --> ACP[c] + pa160[c] 					
19242	AGPAT161	Yes	1-hexadec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C16:1)	[c] : 1hdec9eg3p + hdeACP --> ACP + pa161	Glycerophospholipid Metabolism	2.3.1.51	b3018	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.98374	4.73838	[c] : 1hdec9eg3p[c] + hdeACP[c] --> ACP[c] + pa161[c] 					
19240	AGPAT180	Yes	1-octadecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C18:0)	[c] : 1odecg3p + ocdcaACP --> ACP + pa180	Glycerophospholipid Metabolism	2.3.1.51	b3018	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.98374	4.73838	[c] : 1odecg3p[c] + ocdcaACP[c] --> ACP[c] + pa180[c] 					
19243	AGPAT181	Yes	1-octadec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C18:1)	[c] : 1odec11eg3p + octeACP --> ACP + pa181	Glycerophospholipid Metabolism	2.3.1.51	b3018	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-0.390149	5.36289	[c] : 1odec11eg3p[c] + octeACP[c] --> ACP[c] + pa181[c] 					
309	AGPR	No	N-acetyl-g-glutamyl-phosphate reductase	[c] : acg5sa + nadp + pi <==> acg5p + h + nadph	Arginine and Proline Metabolism	1.2.1.38	b3958			0.164006	4.46406	[c] : acg5sa[c] + nadp[c] + pi[c] <==> acg5p[c] + nadph[c] 					
14030	AGt3	Yes	silver transport out via proton antiport	ag[c] + h[e] --> ag[e] + h[c]	"Transport, Outer Membrane"		( b0572  and  b0573  and  b0574  and  b0575 )	AMF	"Ag and Cu are transported across both membranes
see diagram in PMID: 12829274

PMID: 12813074
gives specificity of substrates and necessity for all three genes in the complex
AMF"	0	0	[c] : ag[c] + h[e] --> ag[e] + h[c] 					
366	AHC	No	adenosylhomocysteinase	[c] : ahcys + h2o <==> adn + hcys-L	Methionine Metabolism	3.3.1.1			JLR- no gene assignment.  Apparently this enzyme is NOT in E. coli.  Kept in because the other route produces hmfurn (possibly AI-2) which is a dead end.	2.29834	3.43387	[c] : ahcys[c] + h2o[c] <==> adn[c] + hcys-L[c] 					
2520	AHCYSNS	No	S-adenosylhomocysteine nucleosidase	[c] : ahcys + h2o --> ade + rhcys	Methionine Metabolism	3.2.2.9	b0159	"JLR
"		-0.27185	3.54371	[c] : ahcys[c] + h2o[c] --> ade[c] + rhcys[c] 					
396	AICART	No	phosphoribosylaminoimidazolecarboxamide formyltransferase	[c] : 10fthf + aicar <==> fprica + thf	Purine and Pyrimidine Biosynthesis	2.1.2.3	b4006			No energy	No energy	[c] : 10fthf[c] + aicar[c] <==> fprica[c] + thf[c] 					
1308	AIRC2	No	phosphoribosylaminoimidazole carboxylase	[c] : air + atp + hco3 --> 5caiz + adp + h + pi	Purine and Pyrimidine Biosynthesis		b0522	"JLR- reaction according to Neidhardt pg 563 and 569.  According to Meyer et al. Biochemistry 38: 3012-3018pp, this pathway is used in prokaryotes and uses hco3 instead of co2. "	JLR- (see ref)	6.01898	4.56516	[c] : air[c] + atp[c] + hco3[c] --> 5caiz[c] + adp[c] + pi[c] 					
1307	AIRC3	No	phosphoribosylaminoimidazole carboxylase (mutase rxn)	[c] : 5aizc <==> 5caiz	Purine and Pyrimidine Biosynthesis		b0523	JLR- E.coli uses a two enzymes in the phosphoribosylaminoimidazole carboxylase step to generate 5aizc	JLR- (see ref)	0	0.5	[c] : 5aizc[c] <==> 5caiz[c] 		
753	AKGDH	Yes	2-Oxogluterate dehydrogenase	[c] : akg + coa + nad --> co2 + nadh + succoa	Citric Acid Cycle		( b0116  and  b0726  and  b0727 )	"Changed from TEST_AKGDH
"		-6.55393	5.78379	[c] : akg[c] + coa[c] + nad[c] --> co2[c] + nadh[c] + succoa[c] 		
8954	AKGt2rpp	Yes	2-oxoglutarate reversible transport via symport (periplasm)	akg[p] + h[p] <==> akg[c] + h[c]	"Transport, Inner Membrane"		b2587	NCD		0	0	[c] : akg[p] + h[p] <==> akg[c] + h[c] 		
9037	AKGtex	Yes	alpha-ketoglutarate transport via diffusion (extracellular to periplasm)	akg[e] <==> akg[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : akg[e] <==> akg[p] 		
8785	ALAabcpp	Yes	L-alanine transport via ABC system (periplasm)	ala-L[p] + atp[c] + h2o[c] --> adp[c] + ala-L[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b3454  and  b3455  and  b3457  and  b3460  and  b3456 )			-7.01673	1.48181	[c] : ala-L[p] + atp[c] + h2o[c] --> adp[c] + ala-L[c] + h[c] + pi[c] 		
18458	ALAALAabcpp	Yes	D-alanyl-D-alanine (DalaDala) transport via ABC system (periplasm)	alaala[p] + atp[c] + h2o[c] --> adp[c] + alaala[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( ( b1487  and  b1486  and  b1485  and  b1484  and  b1483 )  or  ( b3544  and  b3543  and  b3542  and  b3541  and  b3540 ) )	"AMF
PMID: 99432174 and 9751644"	"characterized in PMID: 9751644 and
PMID: 10500118
for Ddp genes
AMF

characterized in PMID: 7536291
for Dpp genes
AMF"	-7.01673	1.48181	[c] : alaala[p] + atp[c] + h2o[c] --> adp[c] + alaala[c] + h[c] + pi[c] 		
18457	ALAALAD	Yes	D-alanine-D-alanine dipeptidase	[c] : alaala + h2o --> (2) ala-D	Murein Recycling	3.4.17.14	b1488	"AMF
"	"characterized in PMID: 9751644 and
PMID: 10500118
AMF"	-3.36489	3.34628	[c] : alaala[c] + h2o[c] --> (2) ala-D[c] 		
3520	ALAALAr	No	D-alanine-D-alanine ligase (reversible)	[c] : (2) ala-D + atp <==> adp + alaala + h + pi	Cell Envelope Biosynthesis	6.3.2.4	( b0381  or  b0092 )	JLR- added reversible form of ALAALA		-3.65185	3.59073	[c] : (2) ala-D[c] + atp[c] <==> adp[c] + alaala[c] + h[c] + pi[c] 		
18459	ALAALAtex	Yes	D-alanyl-D-alanine (DalaDala) transport via diffusion (extracellular to periplasm)	alaala[e] <==> alaala[p]	"Transport, Outer Membrane"			"AMF
PMID: 99432174 and 9751644"	"assumed diffusion through porin
AMF"	0	0	[c] : alaala[e] <==> alaala[p] 		
12683	ALAGLUE	Yes	L-alanyl-gamma-glutamate epimerase	[c] : LalaDglu <==> LalaLglu	Murein Recycling		b1325	"AMF
PMID: 11747447"	"PMID: 11747447
this enolase can act on a number of different dipeptide substrates, see citation for ref
AMF

nice figure in  PMID: 15901686"	0	0.5	[c] : LalaDglu[c] <==> LalaLglu[c] 		
298	ALAR	No	alanine racemase	[c] : ala-L <==> ala-D	Alanine and Aspartate Metabolism	5.1.1.1	( b4053  or  b1190 )			0	0.5	[c] : ala-L[c] <==> ala-D[c] 		
8786	ALAt2rpp	Yes	L-alanine reversible transport via proton symport (periplasm)	ala-L[p] + h[p] <==> ala-L[c] + h[c]	"Transport, Inner Membrane"		( b0007  or  b4208 )	NCD	"YaaJ is putative, and when cycA is deleted ala-L is transported less.

CycA mediates the uptake of L-alanine, D-alanine, glycine, D-serine, and Dcycloserine (Wargel et al. 1970; Cosloy 1973).....utilize H+ co-transport as the energy source (Swiss-Prot data base; http://www.expasy.org/sprot;
accession no. P39312). Together with fklB, cycA is thought to form the fklB-cycA operon, whose expression is regulated by the nitrogen assimilation control (Nac) protein
PMID: 15221223
AMF"	0	0	[c] : ala-L[p] + h[p] <==> ala-L[c] + h[c] 		
1640	ALATA_D2	No	D-alanine transaminase	[c] : ala-D + pydx5p --> pyam5p + pyr	Cofactor and Prosthetic Group Biosynthesis		b2551	JLR		-2.42139	2.1337	[c] : ala-D[c] + pydx5p[c] --> pyam5p[c] + pyr[c] 		
299	ALATA_L	No	L-alanine transaminase	[c] : akg + ala-L <==> glu-L + pyr	Alanine and Aspartate Metabolism	2.6.1.2			JLR- jeremy's list assigns it to alaB gene but can not find in genome or EcoCyc.	0	0.5	[c] : akg[c] + ala-L[c] <==> glu-L[c] + pyr[c] 		
1874	ALATA_L2	No	alanine transaminase	[c] : ala-L + pydx5p --> pyam5p + pyr	Cofactor and Prosthetic Group Biosynthesis		b2551	JLR		-2.42139	2.1337	[c] : ala-L[c] + pydx5p[c] --> pyam5p[c] + pyr[c] 		
9038	ALAtex	Yes	L-alanine transport via diffusion (extracellular to periplasm)	ala-L[e] <==> ala-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ala-L[e] <==> ala-L[p] 		
2919	ALATRS	Yes	Alanyl-tRNA synthetase	[c] : ala-L + atp + trnaala --> alatrna + amp + ppi	Update	6.1.1.7	b2697		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : ala-L[c] + atp[c] + h[c] + trnaala[c] --> alatrna[c] + amp[c] + ppi[c] 		
1204	ALCD19	No	alcohol dehydrogenase (glycerol)	[c] : glyald + h + nadh <==> glyc + nad	Alternate Carbon Metabolism	1.1.1.1	b0356	JLR- 		-5.16584	4.34649	[c] : glyald[c] + h[c] + nadh[c] <==> glyc[c] + nad[c] 		
247	ALCD2x	Yes	alcohol dehydrogenase (ethanol)	[c] : etoh + nad <==> acald + h + nadh	Update	1.1.1.1	( b1478  or  b1241  or  b0356 )	"A zinc protein. Acts on primary or secondary alcohols or hemi-acetals; the animal, but not the yeast, enzyme acts also on cyclic secondary alcohols.
"		5.16584	4.34649	[c] : etoh[c] + nad[c] <==> acald[c] + h[c] + nadh[c] 		
2522	ALDD19x	No	"aldehyde dehydrogenase (phenylacetaldehyde, NAD)"	[c] : h2o + nad + pacald --> (2) h + nadh + pac	Alternate Carbon Metabolism	1.2.1.39	b1385	JLR	padA and FeaB are the same gene	-9.85991	4.39284	[c] : h2o[c] + nad[c] + pacald[c] --> (2) h[c] + nadh[c] + pac[c] 		
248	ALDD2x	No	"aldehyde dehydrogenase (acetaldehyde, NAD)"	[c] : acald + h2o + nad --> ac + (2) h + nadh	Alternate Carbon Metabolism	1.2.1.3	b1300	"Only acetaldehyde considered for now. See also 1.2.1.4. Wide specificity, including oxidation of D-glucuronolactone to D-glucarate. Formerly EC 1.1.1.70"		-9.85991	4.39284	[c] : acald[c] + h2o[c] + nad[c] --> ac[c] + (2) h[c] + nadh[c] 		
249	ALDD2y	Yes	"aldehyde dehydrogenase (acetaldehyde, NADP)"	[c] : acald + h2o + nadp --> ac + (2) h + nadph	Update	1.2.1.4	b3588	See also ALDH1 (1.2.1.3)	"PMID: 15659684
NADP dependent
also acts on propionaldehyde and benzaldehyde
AMF"	-9.85991	4.39284	[c] : acald[c] + h2o[c] + nadp[c] --> ac[c] + (2) h[c] + nadph[c] 		
13216	ALDD3y	Yes	"aldehyde dehydrogenase (propanal, NADP)"	[c] : h2o + nadp + ppal --> (2) h + nadph + ppa	Update		b3588	AMF	"PMID: 15659684
NADP dependent
also acts on propionaldehyde and benzaldehyde
AMF

ppal - not in network yet, but could be, so added this reaction"	-9.85991	4.39284	[c] : h2o[c] + nadp[c] + ppal[c] --> (2) h[c] + nadph[c] + ppa[c] 		
206	ALDD4	Yes	"aldehyde dehydrogenase (butanal, NAD)"	[c] : btal + h2o + nad --> but + (2) h + nadh	Update				"not sure of a gene association, could be a number of different aldehyde dehydrogenases

reactions was added to act on btal, which is a product of a sulfite generating raection that E. coli is known to use as a sulfur source from the Biolog data
AMF"	-9.85991	4.39284	[c] : btal[c] + h2o[c] + nad[c] --> but[c] + (2) h[c] + nadh[c] 		
8787	ALLabcpp	Yes	D-allose transport via ABC system (periplasm)	all-D[p] + atp[c] + h2o[c] --> adp[c] + all-D[c] + h[c] + pi[c]	Update		( b4087  and  b4088  and  b4086 )			-7.01673	1.48181	[c] : all-D[p] + atp[c] + h2o[c] --> adp[c] + all-D[c] + h[c] + pi[c] 		
8041	ALLK	Yes	Allose kinase	[c] : all-D + atp --> adp + all6p + h	Update		b4084	JLR	"newer reference PMID: 16086580
isoated and characterized AlsK to be a all-D kinase, although others have thought otherwise

when overexpressed, AlsK can also fullfuill the glucokinase activity
AMF

PMID: 10559180 states that alsK might be involved, but deletion and expression studies indicate that it might not be responsible for this activity
AMF, JLR"	-4.65732	2.09859	[c] : all-D[c] + atp[c] --> adp[c] + all6p[c] 		
8040	ALLPI	Yes	Allose 6-phosphate isomerase	[c] : all6p <==> allul6p	Update		b4090	JLR	"Putative assignment, gene is required for allose utilization"	0.701765	9.00506	[c] : all6p[c] <==> allul6p[c] 		
7709	ALLTAMH	Yes	allantoate amidohydrolase	[c] : alltt + (2) h + (2) h2o --> co2 + (2) nh4 + urdglyc	Update	3.5.3.9	b0516	"JLR
two reactions: ureidoglycine is an intermediate"		1.1201	4.92394	[c] : alltt[c] + (2) h[c] + (2) h2o[c] --> co2[c] + (2) nh4[c] + urdglyc[c] 		
9041	ALLtex	Yes	Allose transport via diffusion (extracellular to periplasm)	all-D[e] <==> all-D[p]	"Transport, Outer Membrane"				"assumed diffusion
"	0	0	[c] : all-D[e] <==> all-D[p] 		
2809	ALLTN	No	allantoinase	[c] : alltn + h2o --> alltt + h	Nitrogen Metabolism	3.5.2.5	b0512			-6.82761	7.00364	[c] : alltn[c] + h2o[c] --> alltt[c] + h[c] 		
8788	ALLTNt2rpp	Yes	allantoin transport in via proton symport (periplasm)	alltn[p] + h[p] <==> alltn[c] + h[c]	Putative Transporters		b0511	JLR		0	0	[c] : alltn[p] + h[p] <==> alltn[c] + h[c] 		
9042	ALLTNtex	Yes	allantoin transport via diffusion (extracellular to periplasm)	alltn[e] <==> alltn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : alltn[e] <==> alltn[p] 		
8042	ALLULPE	Yes	Allulose 6-phosphate epimerase	[c] : allul6p <==> f6p	Update		b4085	JLR		-0.948467	7.22374	[c] : allul6p[c] <==> f6p[c] 
19946	ALPATE160pp	Yes	"apolipoprotein N-acyltransferase (phosphatidylethanolamine, periplasm)"	[p] : alpp + pe160 --> 2agpe160 + lpp	Lipoprotein		b0657	AMF	"PMID: 2033085 states that phosphatidylethanolamine and other major phospholipids such as phosphatidylglycerol and cardiolipin can serve as the donor of fatty acid in the N-acylation of apolipoprotein (Cardiolipin was not added as a substrate, but could be).
Only palmitate was mentioned as the acyl- chain length that was transfered, however other acyl- chain lenghts could be transfered as well.
AMF"	-0.504009	3.86938	[p] : alpp[p] + pe160[p] --> 2agpe160[p] + h[p] + lpp[p] 
19947	ALPATG160pp	Yes	"apolipoprotein N-acyltransferase (phosphatidylglycerol, periplasm)"	[p] : alpp + pg160 --> 2agpg160 + lpp	Lipoprotein		b0657	AMF	"PMID: 2033085 states that phosphatidylethanolamine and other major phospholipids such as phosphatidylglycerol and cardiolipin can serve as the donor of fatty acid in the N-acylation of apolipoprotein (Cardiolipin was not added as a substrate, but could be).
Only palmitate was mentioned as the acyl- chain length that was transfered, however other acyl- chain lenghts could be transfered as well.
AMF"	-0.504009	3.86938	[p] : alpp[p] + pg160[p] --> 2agpg160[p] + h[p] + lpp[p] 
14160	ALR2	Yes	aldose reductase (methylglyoxal)	[c] : h + mthgxl + nadph --> acetol + nadp	Update		( b3012  or  b0207  or  b1781  or  b3001 )	NCD	"PMID: 16077126
four E. coli AKRs, YafB, YqhE, YeaE, and YghZ, are involved in the production of acetol from MG. These enzymes were purified and shown to catalyze NADPH-dependent MG reduction to acetol.
AMF"	-5.16584	4.34649	[c] : h[c] + mthgxl[c] + nadph[c] --> acetol[c] + nadp[c] 
20015	ALR4x	Yes	aldose reductase (acetol)	[c] : acetol + h + nadh --> 12ppd-R + nad	Update		b3945	AMF	"PMID: 10049880
overexpressed gldA shown to generate the (R-) form of propanediol from acetol
AMF"	-4.73639	4.5435	[c] : acetol[c] + h[c] + nadh[c] --> 12ppd-R[c] + nad[c] 
490	ALTRH	No	altronate hydrolase	[c] : altrn --> 2ddglcn + h2o	Alternate Carbon Metabolism	4.2.1.7	b3091			-9.58412	3.68395	[c] : altrn[c] --> 2ddglcn[c] + h2o[c] 
12641	AM3PA	Yes	anhydrous-N-Acetylmuramyl-tripeptide amidase	[c] : anhm3p + h2o --> LalaDgluMdap + anhm	Murein Recycling		b0110	AMF	"AmpD is cylosolic
PMID: 15901686"	-3.36489	3.34628	[c] : anhm3p[c] + h2o[c] --> anhm[c] + LalaDgluMdap[c] 
12640	AM4PA	Yes	anhydrous-N-Acetylmuramyl-tetrapeptide amidase	[c] : anhm4p + h2o --> LalaDgluMdapDala + anhm	Murein Recycling		b0110	AMF	"AmpD is cylosolic
PMID: 15901686"	-3.36489	3.34628	[c] : anhm4p[c] + h2o[c] --> anhm[c] + LalaDgluMdapDala[c] 
12639	AM4PCP	Yes	"anhydrous-N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase"	[c] : anhm4p + h2o --> ala-D + anhm3p	Murein Recycling		b1192	AMF	"LdcA is a cytoplasmic LD-carboxypeptidase
four different similar susbstrates
PMID: 10428950"	-3.36489	3.34628	[c] : anhm4p[c] + h2o[c] --> ala-D[c] + anhm3p[c] 
3236	AMALT1	No	Amylomaltase (maltotriose)	[c] : malt + malttr --> glc-D + maltttr	Alternate Carbon Metabolism	2.4.1.25	b3416	JLR		0	0.5	[c] : malt[c] + malttr[c] --> glc-D[c] + maltttr[c] 
2514	AMALT2	No	Amylomaltase (maltotetraose)	[c] : malt + maltttr --> glc-D + maltpt	Alternate Carbon Metabolism	2.4.1.25	b3416	JLR		0	0.5	[c] : malt[c] + maltttr[c] --> glc-D[c] + maltpt[c] 
2515	AMALT3	No	Amylomaltase (maltopentaose)	[c] : malt + maltpt --> glc-D + malthx	Alternate Carbon Metabolism	2.4.1.25	b3416	JLR		0	0.5	[c] : malt[c] + maltpt[c] --> glc-D[c] + malthx[c] 
2516	AMALT4	No	Amylomaltase (maltohexaose)	[c] : malt + malthx --> glc-D + malthp	Alternate Carbon Metabolism	2.4.1.25	b3416	JLR		0	0.5	[c] : malt[c] + malthx[c] --> glc-D[c] + malthp[c] 
6184	AMANAPEr	Yes	N-acetylmannosamine 6-phosphate epimerase	[c] : acmanap <==> acgam6p	Update		b3223	JLR		0	0.5	[c] : acmanap[c] <==> acgam6p[c] 
2615	AMANK	No	N-acetyl-D-mannosamine kinase	[c] : acmana + atp --> acmanap + adp + h	Alternate Carbon Source	2.7.1.60	b3222	JLR - Kegg R02705	JLR-still putative	-4.65732	2.09859	[c] : acmana[c] + atp[c] --> acmanap[c] + adp[c] 
1652	AMAOTr	No	adenosylmethionine-8-amino-7-oxononanoate transaminase	[c] : 8aonn + amet <==> amob + dann	Cofactor and Prosthetic Group Biosynthesis	2.6.1.62	b0774	JLR- reversible version of AMAOT		0	0.5	[c] : 8aonn[c] + amet[c] <==> amob[c] + dann[c] 
1354	AMMQT8_2	No	S-adenosylmethione:2-demethylmenaquinone methyltransferase	[c] : 2dmmq8 + amet --> ahcys + h + mqn8	Cofactor and Prosthetic Group Biosynthesis		b3929	JLR- added similar reaction to AMMQT8 except that it produces menaquinone not menaquinol		No energy	No energy	[c] : 2dmmq8[c] + amet[c] --> ahcys[c] + h[c] + mqn8[c] 					
1969	AMPMS	No	4-amino-2-methyl-5-phosphomethylpyrimidine synthetase	[c] : air + h2o --> 4ampm + (2) for + (4) h	Cofactor and Prosthetic Group Biosynthesis		b3994	"JLR- not sure about byproduct
"	JLR- not sure about the byproducts. 	-51.0912	9.15509	[c] : air[c] + h2o[c] --> 4ampm[c] + (2) for[c] + (4) h[c] 					
2927	AMPN	No	AMP nucleosidase	[c] : amp + h2o --> ade + r5p	Nucleotide Salvage Pathway	3.2.2.4	b1982	JLR		-2.26379	3.60328	[c] : amp[c] + h2o[c] --> ade[c] + r5p[c] 					
10876	AMPTASECG	Yes	alanyl aminopeptidase (cys-gly)	[c] : cgly + h2o --> cys-L + gly	Update	3.4.11.2	( b0932  or  b4260  or  b2523  or  b0237 )	SAB	"PepN, B, D, A all perform this function
PMID: 11157967
AMF"	-3.36489	3.34628	[c] : cgly[c] + h2o[c] --> cys-L[c] + gly[c] 					
19731	AMPTASEPG	Yes	aminopeptidase (pro-gly)	[c] : h2o + progly --> gly + pro-L	Update	3.4.11.2	( b4260  or  b2523  or  b0932  or  b0237 )	AMF	"PMID: 1702779 demonstrates that pro-gly is a substrate for growth by classification of transporter - the actuall dipeptidase was not characterized
AMF"	-3.36489	3.34628	[c] : h2o[c] + progly[c] --> gly[c] + pro-L[c] 					
9043	AMPtex	Yes	AMP transport via diffusion (extracellular to periplasm)	amp[e] <==> amp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : amp[e] <==> amp[p] 					
13208	ANHGMtex	Yes	GlcNAc-anhMurNAc transport via diffusion (extracellular to periplasm)	anhgm[e] <==> anhgm[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : anhgm[e] <==> anhgm[p] 					
12680	ANHMK	Yes	"1,6-anhydrous-N-Acetylmuramate kinase"	[c] : anhm + atp + h2o --> acmum6p + adp + h	Murein Recycling		b1640	AMF	"PMID: 15901686
AMF"	3.82384	4.52604	[c] : anhm[c] + atp[c] + h2o[c] --> acmum6p[c] + adp[c] 					
330	ANPRT	No	anthranilate phosphoribosyltransferase	[c] : anth + prpp --> ppi + pran	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	2.4.2.18	b1263			-9.24673	3.24577	[c] : anth[c] + prpp[c] --> ppi[c] + pran[c] 					
329	ANS	No	anthranilate synthase	[c] : chor + gln-L --> anth + glu-L + h + pyr	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.1.3.27	( b1263  and  b1264 )			-43.2965	10.8165	[c] : chor[c] + gln-L[c] --> anth[c] + glu-L[c] + h[c] + pyr[c] 					
2802	AOBUTDs	Yes	L-2-amino-3-oxobutanoate decarboxylation	[c] : 2aobut + h --> aact + co2	Update			Spontaneous reaction	"spntaneous reaction
AMF"	-4.96805	1.79669	[c] : 2aobut[c] + h[c] --> aact[c] + co2[c] 					
1651	AOXSr	No	8-amino-7-oxononanoate synthase	[c] : ala-L + h + pmcoa <==> 8aonn + co2 + coa	Cofactor and Prosthetic Group Biosynthesis	2.3.1.47	b0776	JLR- reversible version of AOXS		1.3349	4.20263	[c] : ala-L[c] + h[c] + pmcoa[c] <==> 8aonn[c] + co2[c] + coa[c] 					
2537	AP4AH	No	Ap4A hydrolase	[c] : ap4a + h2o --> (2) adp + (2) h	Nucleotide Salvage Pathway	3.6.1.41	b0049	JLR		-6.6688	3.75933	[c] : ap4a[c] + h2o[c] --> (2) adp[c] 					
2538	AP5AH	No	Ap5A hydrolase	[c] : ap5a + h2o --> adp + atp + (2) h	Nucleotide Salvage Pathway		b0049	JLR		-6.6688	3.75933	[c] : ap5a[c] + h2o[c] --> adp[c] + atp[c] 					
117	APRAUR	No	5-amino-6-(5-phosphoribosylamino)uracil reductase	[c] : 5apru + h + nadph --> 5aprbu + nadp	Cofactor and Prosthetic Group Biosynthesis	1.1.1.193	b0414			-5.91475	8.65791	[c] : 5apru[c] + h[c] + nadph[c] --> 5aprbu[c] + nadp[c] 					
2836	ARAI	No	L-arabinose isomerase	[c] : arab-L <==> rbl-L	Alternate Carbon Metabolism	5.3.1.4	b0062			-0.246702	4.88847	[c] : arab-L[c] <==> rbl-L[c] 					
8789	ARBabcpp	Yes	L-arabinose transport via ABC system (periplasm)	arab-L[p] + atp[c] + h2o[c] --> adp[c] + arab-L[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b1901  and  b1900  and  b4460 )			-7.01673	1.48181	[c] : arab-L[p] + atp[c] + h2o[c] --> adp[c] + arab-L[c] + h[c] + pi[c] 					
8790	ARBt2rpp	Yes	L-arabinose transport via proton symport (periplasm)	arab-L[p] + h[p] <==> arab-L[c] + h[c]	"Transport, Inner Membrane"		b2841	JLR		0	0	[c] : arab-L[p] + h[p] <==> arab-L[c] + h[c] 					
13766	ARBt3ipp	Yes	L-arabinose transport via proton antiport (periplasm)	arab-L[c] + h[p] --> arab-L[p] + h[c]	"Transport, Inner Membrane"		b1528	AMF	"PMID: 10438792
charcetizes that SotB (ydeA) can export arabinose

PMID: 10671456 
states that SotB (ydea) xan export arabinose, but SotA exports arabinose

SetB, SetA functions are give in PMID: 10209755

AMF"	0	0	[c] : arab-L[c] + h[p] --> arab-L[p] + h[c] 					
9044	ARBtex	Yes	L-arabinose transport via diffusion (extracellular to periplasm)	arab-L[e] <==> arab-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : arab-L[e] <==> arab-L[p] 					
8770	ARBTNabcpp	Yes	aerobactin transport via ABC system (periplasm)	arbtn-fe3[p] + atp[c] + h2o[c] --> adp[c] + arbtn-fe3[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0153  and  b0151  and  b0152 )		"There are other molecules that are transported by this complex, listed on transportDB
http://tcdb.ucsd.edu/tcdb/tcfamilybrowse.php?tcname=3.A.1

PMID: 14668326
"	-7.01673	1.48181	[c] : arbtn-fe3[p] + atp[c] + h2o[c] --> adp[c] + arbtn-fe3[c] + h[c] + pi[c] 					
10849	ARBTNexs	Yes	aerobactin Fe-loading reaction (spontaneous)	[e] : arbtn + fe3 --> arbtn-fe3	Update			spontaneous reaction in extracellular space - function as siderophore MKA AMF	"spontaneous reaction in extracellular space - fulfills necessary function of aerobactin as a siderophore

aerobactin not produced by K-12 ecoli - but can utilize it

MKA

reaction is in network to reflact the recycling of siderophones and then becoming reactivated with Fe to be took up again into the system -  AMF
"	No energy	No energy	[e] : arbtn[e] + fe3[e] --> arbtn-fe3[e] 					
10846	ARBTNR1	Yes	aerobactin reductase	[c] : (2) arbtn-fe3 + fadh2 --> (2) arbtn + fad + (2) fe2 + (2) h	Update			MKA	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.

Aerobactin is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Not produced by K-12, just ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA"	No energy	No energy	[c] : (2) arbtn-fe3[c] + fadh2[c] --> (2) arbtn[c] + fad[c] + (2) fe2[c] + (2) h[c] 					
10847	ARBTNR2	Yes	aerobactin reductase	[c] : (2) arbtn-fe3 + fmnh2 --> (2) arbtn + (2) fe2 + fmn + (2) h	Update			MKA	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.

Ferrichrome is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Not produced by K-12, just ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA"	No energy	No energy	[c] : (2) arbtn-fe3[c] + fmnh2[c] --> (2) arbtn[c] + (2) fe2[c] + fmn[c] + (2) h[c] 					
10848	ARBTNR3	Yes	aerobactin reductase	[c] : (2) arbtn-fe3 + rbflvrd --> (2) arbtn + (2) fe2 + (2) h + ribflv	Update			MKA	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.  FAD may be used more often

Aerobactin is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Not produced by K-12, just ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA"	No energy	No energy	[c] : (2) arbtn-fe3[c] + rbflvrd[c] --> (2) arbtn[c] + (2) fe2[c] + (2) h[c] + ribflv[c] 					
11831	ARBTNtex	Yes	aerobactin secretion (to extracellular)	arbtn[p] + h[p] --> arbtn[e] + h[c]	"Transport, Outer Membrane"			actual motive force behind secretion unknown.  using proton pumping to approximate energy requirements - MKA AMF	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes
"	0	0	[c] : arbtn[p] + h[p] --> arbtn[e] + h[c] 					
9123	ARBTNtonex	Yes	aerobactin transport via ton system (extracellular)	arbtn-fe3[e] + h[p] --> arbtn-fe3[p] + h[c]	"Transport, Outer Membrane"				"mot sure on the outerm membrane transport protein, could be tola

PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR"	0	0	[c] : arbtn-fe3[e] + h[p] --> arbtn-fe3[p] + h[c] 					
11830	ARBTNtpp	Yes	aerobactin secretion (to periplasm)	arbtn[c] + h[p] --> arbtn[p] + h[c]	Update			actual motive force behind secretion unknown.  using proton pumping to approximate energy requirements - MKA AMF	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes"	0	0	[c] : arbtn[c] + h[p] --> arbtn[p] + h[c] 					
8791	ARGabcpp	Yes	L-arginine transport via ABC system (periplasm)	arg-L[p] + atp[c] + h2o[c] --> adp[c] + arg-L[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( ( b2310  and  b2307  and  b2306  and  b2308 )  or  ( b0863  and  b0860  and  b0861  and  b0864  and  b0862 ) )			-7.01673	1.48181	[c] : arg-L[p] + atp[c] + h2o[c] --> adp[c] + arg-L[c] + h[c] + pi[c] 					
8792	ARGAGMt7pp	Yes	Arginine/agmatine antiport (periplasm)	agm[c] + arg-L[p] <==> agm[p] + arg-L[c]	Update		b4115	"JLR
2.A.3.2.5"		0	0	[c] : agm[c] + arg-L[p] <==> agm[p] + arg-L[c] 					
305	ARGDC	No	arginine decarboxylase	[c] : arg-L + h --> agm + co2	Arginine and Proline Metabolism	4.1.1.19	b4117			-4.96805	1.79669	[c] : arg-L[c] + h[c] --> agm[c] + co2[c] 					
12260	ARGDCpp	Yes	arginine decarboxylase	[p] : arg-L + h --> agm + co2	Update	4.1.1.19	b2938		"Added from EcoCyc and PSORT enzyme location data, moved to periplasm
"	-4.96805	1.79669	[p] : arg-L[p] + h[p] --> agm[p] + co2[p] 					
8793	ARGORNt7pp	Yes	arginine/ornithine antiporter (periplasm)	arg-L[p] + orn[c] <==> arg-L[c] + orn[p]	"Transport, Inner Membrane"		b1605	JLR		0	0	[c] : arg-L[p] + orn[c] <==> arg-L[c] + orn[p] 		
2851	ARGSL	No	argininosuccinate lyase	[c] : argsuc <==> arg-L + fum	Arginine and Proline Metabolism	4.3.2.1	b3960			3.59749	3.50988	[c] : argsuc[c] <==> arg-L[c] + fum[c] 		
306	ARGSS	No	argininosuccinate synthase	[c] : asp-L + atp + citr-L --> amp + argsuc + h + ppi	Arginine and Proline Metabolism	6.3.4.5	b3172			1.04069	6.32464	[c] : asp-L[c] + atp[c] + citr-L[c] --> amp[c] + argsuc[c] + ppi[c] 		
9045	ARGtex	Yes	L-arginine transport via diffusion (extracellular to periplasm)	arg-L[e] <==> arg-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : arg-L[e] <==> arg-L[p] 		
1343	ARGTRS	Yes	Arginyl-tRNA synthetase	[c] : arg-L + atp + trnaarg --> amp + argtrna + ppi	Update	6.1.1.19	b1876	"NCD	"	Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : arg-L[c] + atp[c] + h[c] + trnaarg[c] --> amp[c] + argtrna[c] + ppi[c] 		
354	ASAD	No	aspartate-semialdehyde dehydrogenase	[c] : aspsa + nadp + pi <==> 4pasp + h + nadph	Threonine and Lysine Metabolism	1.2.1.11	b3433			0.164006	4.46406	[c] : aspsa[c] + nadp[c] + pi[c] <==> 4pasp[c] + nadph[c] 		
3841	ASCBPL	Yes	L-ascorbate 6-phosphate lactonase	[c] : ascb6p + h2o --> 3dhgulnp + h	Update		b4192	JLR	"YjfR is needed for ascorbate utilization, however the actual reaction is assumed to be this and is tentatively assigned to this protein.

PUTATIVE"	-19.7587	6.39266	[c] : ascb6p[c] + h2o[c] --> 3dhgulnp[c] 		
8794	ASCBptspp	Yes	L-ascorbate transport via PEP:Pyr PTS (periplasm)	ascb-L[p] + pep[c] --> ascb6p[c] + pyr[c]	Update		( b2415  and  b2416  and  b4195  and  b4194  and  b4193 )	JLR		-10.1729	3.20748	[c] : ascb-L[p] + pep[c] --> ascb6p[c] + pyr[c] 		
9046	ASCBtex	Yes	L-ascorbate transport via diffusion (extracellular to periplasm)	ascb-L[e] <==> ascb-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ascb-L[e] <==> ascb-L[p] 		
8975	ASNabcpp	Yes	L-asparagine transport via ABC system (periplasm)	asn-L[p] + atp[c] + h2o[c] --> adp[c] + asn-L[c] + h[c] + pi[c]	"Transport, Inner Membrane"					-7.01673	1.48181	[c] : asn-L[p] + atp[c] + h2o[c] --> adp[c] + asn-L[c] + h[c] + pi[c] 		
3521	ASNN	No	L-asparaginase	[c] : asn-L + h2o --> asp-L + nh4	Alanine and Aspartate Metabolism	3.5.1.1	( b1767  or  b0828 )			-4.69304	2.95123	[c] : asn-L[c] + h2o[c] --> asp-L[c] + nh4[c] 		
12261	ASNNpp	Yes	L-asparaginase	[p] : asn-L + h2o --> asp-L + nh4	Update	3.5.1.1	b2957		moved to periplasm from PSORT and EcoCyc data	-4.69304	2.95123	[p] : asn-L[p] + h2o[p] --> asp-L[p] + nh4[p] 		
259	ASNS1	No	asparagine synthase (glutamine-hydrolysing)	[c] : asp-L + atp + gln-L + h2o --> amp + asn-L + glu-L + h + ppi	Alanine and Aspartate Metabolism	6.3.5.4	b0674			-8.59346	2.5066	[c] : asp-L[c] + atp[c] + gln-L[c] + h2o[c] --> amp[c] + asn-L[c] + glu-L[c] + ppi[c] 		
3523	ASNS2	No	asparagine synthetase	[c] : asp-L + atp + nh4 --> amp + asn-L + h + ppi	Alanine and Aspartate Metabolism	6.3.1.1	b3744			-3.90043	3.80694	[c] : asp-L[c] + atp[c] + nh4[c] --> amp[c] + asn-L[c] + ppi[c] 		
8795	ASNt2rpp	Yes	L-asparagine reversible transport via proton symport (periplasm)	asn-L[p] + h[p] <==> asn-L[c] + h[c]	Putative Transporters		b1453	NCD	AnsP is putatively assigned to this reaction.  There are two transport systems see PMID 239925.  EcoCyc lists this as a putative transporter.	0	0	[c] : asn-L[p] + h[p] <==> asn-L[c] + h[c] 		
9047	ASNtex	Yes	L-asparagine transport via diffusion (extracellular to periplasm)	asn-L[e] <==> asn-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : asn-L[e] <==> asn-L[p] 		
1034	ASNTRS	Yes	Asparaginyl-tRNA synthetase	[c] : asn-L + atp + trnaasn --> amp + asntrna + ppi	Update	6.1.1.22	b0930		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : asn-L[c] + atp[c] + h[c] + trnaasn[c] --> amp[c] + asntrna[c] + ppi[c] 		
13780	ASO3t8pp	Yes	arsenite efflux via ATP hydrolysis (periplasm)	aso3[c] + atp[c] + h2o[c] --> adp[c] + aso3[p] + h[c] + pi[c]	"Transport, Inner Membrane"		b3502	AMF	"detoxification
not an abc transport system
PMID: 7860609
might cplex with ArsA (not in chromosome?) for arsenate transport"	-7.01673	1.48181	[c] : aso3[c] + atp[c] + h2o[c] --> adp[c] + aso3[p] + h[c] + pi[c] 		
13779	ASO3tex	Yes	arsenite transport via diffusion (extracellular to periplasm)	aso3[e] <==> aso3[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : aso3[e] <==> aso3[p] 		
3426	ASP1DC	No	aspartate 1-decarboxylase	[c] : asp-L + h --> ala-B + co2	Cofactor and Prosthetic Group Biosynthesis	4.1.1.11	b0131	"The E. coli enzyme contains a pyruvoyl group.
"		-4.96805	1.79669	[c] : asp-L[c] + h[c] --> ala-B[c] + co2[c] 		
8796	ASPabcpp	Yes	L-aspartate transport via ABC system (periplasm)	asp-L[p] + atp[c] + h2o[c] --> adp[c] + asp-L[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0655  and  b0654  and  b0653  and  b0652 )			-7.01673	1.48181	[c] : asp-L[p] + atp[c] + h2o[c] --> adp[c] + asp-L[c] + h[c] + pi[c] 		
3524	ASPCT	No	aspartate carbamoyltransferase	[c] : asp-L + cbp --> cbasp + h + pi	Purine and Pyrimidine Biosynthesis	2.1.3.2	( b4244  and  b4245 )			-10.9491	4.1903	[c] : asp-L[c] + cbp[c] --> cbasp[c] + h[c] + pi[c] 		
353	ASPK	No	aspartate kinase	[c] : asp-L + atp <==> 4pasp + adp	Threonine and Lysine Metabolism	2.7.2.4	( b0002  or  b3940  or  b4024 )			3.00718	2.24154	[c] : asp-L[c] + atp[c] + h[c] <==> 4pasp[c] + adp[c] 		
7863	ASPO3	No	L-aspartate oxidase	[c] : asp-L + q8 --> h + iasp + q8h2	Cofactor and Prosthetic Group Biosynthesis		b2574	JLR		-36.4019	21.657	[c] : asp-L[c] + q8[c] --> h[c] + iasp[c] + q8h2[c] 		
7866	ASPO4	No	L-aspartate oxidase	[c] : asp-L + mqn8 --> h + iasp + mql8	Cofactor and Prosthetic Group Biosynthesis		b2574	JLR		-34.95	17.5631	[c] : asp-L[c] + mqn8[c] --> h[c] + iasp[c] + mql8[c] 		
7864	ASPO5	No	L-aspartate oxidase	[c] : asp-L + fum --> h + iasp + succ	Cofactor and Prosthetic Group Biosynthesis		b2574	JLR		-27.5836	4.55758	[c] : asp-L[c] + fum[c] --> h[c] + iasp[c] + succ[c] 		
7867	ASPO6	No	L-aspartate oxidase	[c] : asp-L + o2 --> h + h2o2 + iasp	Cofactor and Prosthetic Group Biosynthesis		b2574	JLR		-40.6625	3.98474	[c] : asp-L[c] + o2[c] --> h[c] + h2o2[c] + iasp[c] 		
377	ASPT	No	L-aspartase	[c] : asp-L --> fum + nh4	Alanine and Aspartate Metabolism	4.3.1.1	b4139			2.26934	2.7678	[c] : asp-L[c] --> fum[c] + nh4[c] 		
8798	ASPt2_2pp	Yes	Aspartate transport via proton symport (2 H) (periplasm)	asp-L[p] + (2) h[p] --> asp-L[c] + (2) h[c]	"Transport, Inner Membrane"		b3528	JLR		0	0	[c] : asp-L[p] + (2) h[p] --> asp-L[c] + (2) h[c] 		
8799	ASPt2_3pp	Yes	L-asparate transport via proton symport (3 H) (periplasm)	asp-L[p] + (3) h[p] --> asp-L[c] + (3) h[c]	"Transport, Inner Membrane"		( b4138  or  b4123 )	JLR		0	0	[c] : asp-L[p] + (3) h[p] --> asp-L[c] + (3) h[c] 		
8797	ASPt2pp	Yes	L-aspartate transport in via proton symport (periplasm)	asp-L[p] + h[p] --> asp-L[c] + h[c]	"Transport, Inner Membrane"		b4077			0	0	[c] : asp-L[p] + h[p] --> asp-L[c] + h[c] 		
260	ASPTA	No	aspartate transaminase	[c] : akg + asp-L <==> glu-L + oaa	Alanine and Aspartate Metabolism	2.6.1.1	b0928			0	0.5	[c] : akg[c] + asp-L[c] <==> glu-L[c] + oaa[c] 		
9048	ASPtex	Yes	L-aspartate transport via diffusion (extracellular to periplasm)	asp-L[e] <==> asp-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : asp-L[e] <==> asp-L[p] 					
1033	ASPTRS	Yes	Aspartyl-tRNA synthetase	[c] : asp-L + atp + trnaasp --> amp + asptrna + ppi	Update	6.1.1.12	b1866		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : asp-L[c] + atp[c] + h[c] + trnaasp[c] --> amp[c] + asptrna[c] + ppi[c] 					
13778	ASR	Yes	arsenate reductase	[c] : aso4 + (2) gthrd --> aso3 + gthox + h2o	Update		b3503	AMF	"arsenate is toxic
PMID: 9261111
AMF"	No energy	No energy	[c] : aso4[c] + (2) gthrd[c] --> aso3[c] + gthox[c] + h2o[c] 					
3301	AST	No	Arginine succinyltransferase	[c] : arg-L + succoa --> coa + h + sucarg	Arginine and Proline Metabolism	2.3.1.109	b1747	JLR (R00832)		-2.48774	5.01459	[c] : arg-L[c] + succoa[c] --> coa[c] + h[c] + sucarg[c] 					
13921	ATHRDHr	Yes	L-allo-threonine dehydrogenase	[c] : athr-L + nadp <==> 2aobut + h + nadph	Update		b1539	"AMF
PMID: 12535615"	"reaction is characterized in PMID: 12535615

to act on L and D-serine, L-allo-threonine, D-threonine, and hydroxyisobutyrate

reaversibility is not for sure know, but hints that it may be"	4.73639	4.5435	[c] : athr-L[c] + nadp[c] <==> 2aobut[c] + h[c] + nadph[c] 					
12487	ATPHs	Yes	ATP spontanous amine hydrolysis	[c] : atp + h + h2o --> itp + nh4	Update			MKA - spontanous reaction in aerobic environment	"spontaneous reaction in aerobic environment
PMID: 12297000
The mutation protection mechanisms are caused by the incorporation into DNA of unwelcome nucleotides that are formed spontaneously.
AMF
atphs reaction not mentioned specifically, but seems logical"	-5.6874	4.84135	[c] : atp[c] + h[c] + h2o[c] --> itp[c] + nh4[c] 					
806	ATPM	No	ATP maintenance requirement	[c] : atp + h2o --> adp + h + pi	Unassigned					-7.01673	1.48181	[c] : atp[c] + h2o[c] --> adp[c] + h[c] + pi[c] 					
339	ATPPRT	No	ATP phosphoribosyltransferase	[c] : atp + prpp --> ppi + prbatp	Histidine Metabolism	2.4.2.17	b2019		"this reaction is needed to have the LPS lipid A derivative presented to the outer membrane surface - both moved across the periplasm and flipped across the outer membrane

not sure on the method of transport

this paper talks about the possibility of the transport PMID: 15576375

AMF"	-4.37496	3.86683	[c] : atp[c] + h[c] + prpp[c] --> ppi[c] + prbatp[c] 					
8800	ATPS4rpp	Yes	ATP synthase (four protons for one ATP) (periplasm)	adp[c] + (4) h[p] + pi[c] <==> atp[c] + (3) h[c] + h2o[c]	Oxidative Phosphorylation	3.6.3.14	( ( b3736  and  b3737  and  b3738 )  and  ( b3731  and  b3732  and  b3733  and  b3734  and  b3735 )  and  b3739 )	JLR- added reversible form of ATPS4 reactioin		7.01673	1.48181	[c] : adp[c] + (4) h[p] + pi[c] <==> atp[c] + (3) h[c] + h2o[c] 					
8801	BALAt2rpp	Yes	beta-alanine reversible transport via proton symport (periplasm)	ala-B[p] + h[p] <==> ala-B[c] + h[c]	Update		b4208	JLR	"CycA mediates the uptake of L-alanine, D-alanine, glycine, D-serine, and Dcycloserine (Wargel et al. 1970; Cosloy 1973).....utilize H+ co-transport as the energy source (Swiss-Prot data base; http://www.expasy.org/sprot;
accession no. P39312). Together with fklB, cycA is thought to form the fklB-cycA operon, whose expression is regulated by the nitrogen assimilation control (Nac) protein
PMID: 15221223
AMF"	0	0	[c] : ala-B[p] + h[p] <==> ala-B[c] + h[c] 					
9039	BALAtex	Yes	beta-alanine transport via diffusion (extracellular to periplasm)	ala-B[e] <==> ala-B[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ala-B[e] <==> ala-B[p] 					
2506	BETALDHx	No	betaine-aldehyde dehydrogenase	[c] : betald + h2o + nad --> glyb + (2) h + nadh	Unassigned	1.2.1.8	b0312	JLR		-9.85991	4.39284	[c] : betald[c] + h2o[c] + nad[c] --> glyb[c] + (2) h[c] + nadh[c] 					
2507	BETALDHy	No	betaine-aldehyde dehydrogenase	[c] : betald + h2o + nadp --> glyb + (2) h + nadph	Unassigned	1.2.1.8	b0312	JLR		-9.85991	4.39284	[c] : betald[c] + h2o[c] + nadp[c] --> glyb[c] + (2) h[c] + nadph[c] 					
351	BPNT	No	"3',5'-bisphosphate nucleotidase"	[c] : h2o + pap --> amp + pi	Cysteine Metabolism	3.1.3.7				-3.54819	2.12947	[c] : h2o[c] + pap[c] --> amp[c] + h[c] + pi[c] 					
3220	BSORx	No	Biotin sulfoxide reductase	[c] : btnso + h + nadh --> btn + h2o + nad	Cofactor and Prosthetic Group Biosynthesis		b3551	JLR	NAD(P)H as electron acceptor is not proven except for in Rhodobacter sphaeroides f. sp. denitrificans	No energy	No energy	[c] : btnso[c] + h[c] + nadh[c] --> btn[c] + h2o[c] + nad[c] 					
2406	BSORy	No	Biotin sulfoxide reductase	[c] : btnso + h + nadph --> btn + h2o + nadp	Cofactor and Prosthetic Group Biosynthesis		b3551	JLR	NAD(P)H as electron acceptor is not proven except for in Rhodobacter sphaeroides f. sp. denitrificans	No energy	No energy	[c] : btnso[c] + h[c] + nadph[c] --> btn[c] + h2o[c] + nadp[c] 					
1654	BTS2	No	biotin synthase (ala-L producing)	[c] : cys-L + dtbt <==> ala-L + btn + (2) h	Cofactor and Prosthetic Group Biosynthesis		b0775	"JLR- based on article (Biochemistry 2002, 41, 9145-9152)"	"JLR- new paper indicates that ala is the by-product (JSE's rxn was unknown).
Homodimer"	-14.7792	6.32314	[c] : cys-L[c] + dtbt[c] <==> ala-L[c] + btn[c] + (2) h[c] 					
2481	BUTCT	No	Acetyl-CoA:butyrate-CoA transferase	[c] : accoa + but --> ac + btcoa	Alternate Carbon Metabolism	2.8.3.8	( b2221  and  b2222 )	JLR (R01179)	"JLR- see NH21 for info on regulation

From ecocyc: The growth of E. coli on short-chain fatty acids (C3-C6) requires the activation of the acids to their respective thioesters. This activation is catalyzed by acetoacetyl-CoA transferase. [ Sramek75  ]
also, see PMID: 3025185
AMF"	0	0.5	[c] : accoa[c] + but[c] --> ac[c] + btcoa[c] 					
13610	BUTSO3abcpp	Yes	butanesulfonate transport via ABC system (periplasm)	atp[c] + butso3[p] + h2o[c] --> adp[c] + butso3[c] + h[c] + pi[c]	Update		( ( b0936  and  b0933  and  b0934 )  or  ( b0365  and  b0366  and  b0367 ) )	AMF	"Botht the ssu and the tau transporters will transport this, amound many others

see PMID:10781534

for a good diagram
AMF"	-7.01673	1.48181	[c] : atp[c] + butso3[p] + h2o[c] --> adp[c] + butso3[c] + h[c] + pi[c] 					
13613	BUTSO3tex	Yes	butanesulfonate transport via diffusion (extracellular to periplasm)	butso3[e] <==> butso3[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : butso3[e] <==> butso3[p] 					
8802	BUTt2rpp	Yes	"Butyrate transport via proton symport, reversible (periplasm)"	but[p] + h[p] <==> but[c] + h[c]	Putative Transporters		b2223	JLR	"JLR-based on Saier's database
see PMID: 3025185 for realated SCFA metabolism
AMF"	0	0	[c] : but[p] + h[p] <==> but[c] + h[c] 					
9049	BUTtex	Yes	Butyrate transport via diffusion (extracellular to periplasm)	but[e] <==> but[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : but[e] <==> but[p] 					
8803	CADVtpp	Yes	Lysine/Cadaverine antiporter (periplasm)	15dap[c] + h[p] + lys-L[p] --> 15dap[p] + h[c] + lys-L[c]	"Transport, Inner Membrane"		b4132	JLR- Depletion of proton gradient is not for sure	JLR- not confident about the h	0	0	[c] : 15dap[c] + h[p] + lys-L[p] --> 15dap[p] + h[c] + lys-L[c] 					
2544	CAT	No	catalase	[c] : (2) h2o2 --> (2) h2o + o2	Unassigned	1.11.1.6	( b1732  or  b3942 )	JLR		-48.952	1.5	[c] : (2) h2o2[c] --> (2) h2o[c] + o2[c] 					
8046	CBIAT	No	Cobinamide adenyltransferase	[c] : atp + cbi + h <==> adocbi + pppi	Cofactor and Prosthetic Group Biosynthesis	2.5.1.17	b1270	JLR (EC 2.5.1.17)	PMID: 7592411	No energy	No energy	[c] : atp[c] + cbi[c] <==> adocbi[c] + pppi[c] 					
9126	CBItonex	Yes	Cobinamide transport via ton system (extermal)	cbi[e] + h[p] --> cbi[p] + h[c]	"Transport, Outer Membrane"		( b3966  and  ( b1252  and  b3005  and  b3006 ) )	"AMF - PMID:8405078 and PMID: 10209752
assumption of 1 proton transported across the membrane
transport for B12 may be calcium dependant"	"PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR

B12 transport has been shown to be calcium dependent, but not represented in this reaction"	0	0	[c] : cbi[e] + h[p] --> cbi[p] + h[c] 					
9106	CBIuabcpp	Yes	"Cobinamide transport via ABC system (uptake, periplasm)"	atp[c] + cbi[p] + h2o[c] --> adp[c] + cbi[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b1711  and  b1709  and  b0158 )	AMF	"Transporter diagramed to also transport cbi in PMID: 7592411

The transport is physiologically verified in PMID: 342526 and is stated to be transported at 58% of cbl1"	-7.01673	1.48181	[c] : atp[c] + cbi[p] + h2o[c] --> adp[c] + cbi[c] + h[c] + pi[c] 					
8774	CBL1abcpp	Yes	Cob(1)alamin transport via ABC system (periplasm)	atp[c] + cbl1[p] + h2o[c] --> adp[c] + cbl1[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b1711  and  b1709  and  b0158 )	"JLR
AMF"	The transport is physiologically verified in PMID: 342526	-7.01673	1.48181	[c] : atp[c] + cbl1[p] + h2o[c] --> adp[c] + cbl1[c] + h[c] + pi[c] 					
9125	CBL1tonex	Yes	Cob(1)alamin transport via ton system (extermal)	cbl1[e] + h[p] --> cbl1[p] + h[c]	"Transport, Outer Membrane"		( b3966  and  ( b1252  and  b3005  and  b3006 ) )	"AMF - PMID:8405078 and PMID: 10209752
assumption of 1 proton transported across the membrane
transport for B12 may be calcium dependant"	"PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR

B12 transport has been shown to be calcium dependent, but not represented in this reaction"	0	0	[c] : cbl1[e] + h[p] --> cbl1[p] + h[c] 					
8047	CBLAT	No	cob(I)alamin adenosyltransferase	[c] : atp + cbl1 + h <==> adocbl + pppi	Cofactor and Prosthetic Group Biosynthesis	2.5.1.17	b1270	JLR (EC 2.5.1.17)	PMID: 7592411	No energy	No energy	[c] : atp[c] + cbl1[c] <==> adocbl[c] + pppi[c] 					
6183	CBMKr	Yes	Carbamate kinase	[c] : atp + co2 + nh4 <==> adp + cbp + (2) h	Update	2.7.2.2	( b0521  or  b0323  or  b2874 )	JLR	"ArcC is near allD which leads to the production of cbp via oxalureate.  Based on the need for this reaction in the reverse direction to use allantoin as a nitrogen source via oxalureate, added this reaction as reversible.

PUTATIVE"	4.80279	3.96873	[c] : atp[c] + co2[c] + nh4[c] <==> adp[c] + cbp[c] + (2) h[c] 					
2852	CBPS	No	carbamoyl-phosphate synthase (glutamine-hydrolysing)	[c] : (2) atp + gln-L + h2o + hco3 --> (2) adp + cbp + glu-L + (2) h + pi	Arginine and Proline Metabolism	6.3.5.5	( b0032  and  b0033 )		"JLR- jeremy's reaction uses CO2, used this reaction because it matches EcoCyc."	-6.10698	4.1058	[c] : (2) atp[c] + gln-L[c] + h2o[c] + hco3[c] --> (2) adp[c] + cbp[c] + glu-L[c] + (2) h[c] + pi[c] 					
13649	CD2abcpp	Yes	Cadmium (Cd+2) ABC transporter (periplasm)	atp[c] + cd2[c] + h2o[c] --> adp[c] + cd2[p] + h[c] + pi[c]	"Transport, Inner Membrane"		b3469	AMF	"characterized in PMID: 10660539
ATP-dependent efflux
The activity was specific for Pb(II), Cd(II), Zn(II), and Hg(II), with the highest activity obtained when the metals were present as thiolate complexes of cysteine or glutathione.

from transportDB:
 Zn2+-, Cd2+-, Co2+-, Hg2+-, Ni2+-, Cu2+, Pb2+-ATPase (efflux) (Hou and Mitra, 2003) for ecoli

http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=3.A.3
AMF"	-7.01673	1.48181	[c] : atp[c] + cd2[c] + h2o[c] --> adp[c] + cd2[p] + h[c] + pi[c] 					
13678	CD2tex	Yes	cadmium (Cd+2) transport via diffusion (extracellular to periplasm)	cd2[e] <==> cd2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cd2[e] <==> cd2[p] 					
19327	CDAPPA120	Yes	CDP-Diacylglycerol pyrophostatase (n-C12:0)	[c] : cdpdddecg + h2o --> cmp + (2) h + pa120	Glycerophospholipid Metabolism	3.6.1.26	b3918	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-6.6688	3.75933	[c] : cdpdddecg[c] + h2o[c] --> cmp[c] + pa120[c] 					
19254	CDAPPA140	Yes	CDP-Diacylglycerol pyrophostatase (n-C14:0)	[c] : cdpdtdecg + h2o --> cmp + (2) h + pa140	Glycerophospholipid Metabolism	3.6.1.26	b3918	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-6.6688	3.75933	[c] : cdpdtdecg[c] + h2o[c] --> cmp[c] + pa140[c] 					
19257	CDAPPA141	Yes	CDP-Diacylglycerol pyrophostatase (n-C14:1)	[c] : cdpdtdec7eg + h2o --> cmp + (2) h + pa141	Glycerophospholipid Metabolism	3.6.1.26	b3918	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-6.6688	3.75933	[c] : cdpdtdec7eg[c] + h2o[c] --> cmp[c] + pa141[c] 					
19255	CDAPPA160	Yes	CDP-Diacylglycerol pyrophostatase (n-C16:0)	[c] : cdpdhdecg + h2o --> cmp + (2) h + pa160	Glycerophospholipid Metabolism	3.6.1.26	b3918	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-6.6688	3.75933	[c] : cdpdhdecg[c] + h2o[c] --> cmp[c] + pa160[c] 					
19258	CDAPPA161	Yes	CDP-Diacylglycerol pyrophostatase (n-C16:1)	[c] : cdpdhdec9eg + h2o --> cmp + (2) h + pa161	Glycerophospholipid Metabolism	3.6.1.26	b3918	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-6.6688	3.75933	[c] : cdpdhdec9eg[c] + h2o[c] --> cmp[c] + pa161[c] 					
19256	CDAPPA180	Yes	CDP-Diacylglycerol pyrophostatase (n-C18:0)	[c] : cdpdodecg + h2o --> cmp + (2) h + pa180	Glycerophospholipid Metabolism	3.6.1.26	b3918	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-6.6688	3.75933	[c] : cdpdodecg[c] + h2o[c] --> cmp[c] + pa180[c] 					
19259	CDAPPA181	Yes	CDP-Diacylglycerol pyrophostatase (n-C18:1)	[c] : cdpdodec11eg + h2o --> cmp + (2) h + pa181	Glycerophospholipid Metabolism	3.6.1.26	b3918	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-6.6688	3.75933	[c] : cdpdodec11eg[c] + h2o[c] --> cmp[c] + pa181[c] 					
236	CDPMEK	No	4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase	[c] : 4c2me + atp --> 2p4c2me + adp + h	Cofactor and Prosthetic Group Biosynthesis		b1208	EC 2.7.1.148		-0.445006	3.52396	[c] : 4c2me[c] + atp[c] --> 2p4c2me[c] + adp[c] 					
14035	CDt3pp	Yes	cadmium (Cd+2) transport out via proton antiport (periplasm)	cd2[c] + h[p] --> cd2[p] + h[c]	"Tranpsort, Inner Membrane"		b0752		"these results indicate that ZitB is an antiporter catalyzing the obligatory exchange of Zn2+ or Cd2+ for H+. The exchange stoichiometry of metal ion for proton is likely to be 1:1
PMID: 14715669 
AMF"	0	0	[c] : cd2[c] + h[p] --> cd2[p] + h[c] 					
19429	CFAS160E	Yes	"cyclopropane fatty acid synthase (Phosphatidylethanolamine, n-C16:0)"	[c] : (2) amet + pe161 --> (2) ahcys + cpe160 + (2) h	Glycerophospholipid Metabolism	2.1.1.79	b1661	AMF	"characterized in PMID: 9409147
can act on other susbstrates
from Ecocyc:
CFA synthase exhibits activity toward phosphatidylglycerol, phosphatidylethanolamine, cardiolipin, and also toward phosphatidylcholine 
AMF"	No energy	No energy	[c] : (2) amet[c] + pe161[c] --> (2) ahcys[c] + cpe160[c] + (3) h[c] 					
19431	CFAS160G	Yes	"cyclopropane fatty acid synthase (Phosphatidylglycerol, n-C16:0)"	[c] : (2) amet + pg161 --> (2) ahcys + cpg160 + (2) h	Glycerophospholipid Metabolism	2.1.1.79	b1661	AMF	"characterized in PMID: 9409147
can act on other susbstrates
from Ecocyc:
CFA synthase exhibits activity toward phosphatidylglycerol, phosphatidylethanolamine, cardiolipin, and also toward phosphatidylcholine 
AMF"	No energy	No energy	[c] : (2) amet[c] + pg161[c] --> (2) ahcys[c] + cpg160[c] + (2) h[c] 					
19430	CFAS180E	Yes	"cyclopropane fatty acid synthase (Phosphatidylethanolamine, n-C18:0)"	[c] : (2) amet + pe181 --> (2) ahcys + cpe180 + (2) h	Glycerophospholipid Metabolism	2.1.1.79	b1661	AMF	"characterized in PMID: 9409147
can act on other susbstrates
from Ecocyc:
CFA synthase exhibits activity toward phosphatidylglycerol, phosphatidylethanolamine, cardiolipin, and also toward phosphatidylcholine 
AMF"	No energy	No energy	[c] : (2) amet[c] + pe181[c] --> (2) ahcys[c] + cpe180[c] + (3) h[c] 					
19432	CFAS180G	Yes	"cyclopropane fatty acid synthase (Phosphatidylglycerol, n-C18:0)"	[c] : (2) amet + pg181 --> (2) ahcys + cpg180 + (2) h	Glycerophospholipid Metabolism	2.1.1.79	b1661	AMF	"characterized in PMID: 9409147
can act on other susbstrates
from Ecocyc:
CFA synthase exhibits activity toward phosphatidylglycerol, phosphatidylethanolamine, cardiolipin, and also toward phosphatidylcholine 
AMF"	No energy	No energy	[c] : (2) amet[c] + pg181[c] --> (2) ahcys[c] + cpg180[c] + (2) h[c] 					
19640	CGLYabcpp	Yes	L-Cysteinylglycine (Cys-Gly) transport via ABC system (periplasm)	atp[c] + cgly[p] + h2o[c] --> adp[c] + cgly[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b3544  and  b3543  and  b3542  and  b3541  and  b3540 )	AMF	"This reaction assigned to the Dpp genes by assumption
Pro-Gly was confirmed to be transported by this Dpp cluster PMID: 1702779"	-7.01673	1.48181	[c] : atp[c] + cgly[p] + h2o[c] --> adp[c] + cgly[c] + h[c] + pi[c] 					
19734	CGLYtex	Yes	L-Cysteinylglycine transport via diffusion (extracellular to periplasm)	cgly[e] <==> cgly[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cgly[e] <==> cgly[p] 		
8804	CHLabcpp	Yes	choline transport via ABC system (periplasm)	atp[c] + chol[p] + h2o[c] --> adp[c] + chol[c] + h[c] + pi[c]	Putative Transporters		( b2128  and  b2129  and  b2130  and  b2131 )		JLR- EcoCyc lists that yehWXYZ form a putative ABC transporter 	-7.01673	1.48181	[c] : atp[c] + chol[p] + h2o[c] --> adp[c] + chol[c] + h[c] + pi[c] 		
8805	CHLt2rpp	Yes	"choline transport via proton symport, reversible (periplasm)"	chol[p] + h[p] <==> chol[c] + h[c]	"Transport, Inner Membrane"		( b0314  or  b1801 )	JLR	"YeaV is putative
"	0	0	[c] : chol[p] + h[p] <==> chol[c] + h[c] 		
9050	CHLtex	Yes	choline transport via diffusion (extracellular to periplasm)	chol[e] <==> chol[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : chol[e] <==> chol[p] 		
332	CHORM	No	chorismate mutase	[c] : chor --> pphn	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	5.4.99.5	( b2599  or  b2600 )			-25.2029	4.9786	[c] : chor[c] --> pphn[c] 		
333	CHORS	No	chorismate synthase	[c] : 3psme --> chor + pi	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.2.3.5	b2329	Previously EC 4.6.1.4. Now EC 4.2.3.5		-15.6509	3.84955	[c] : 3psme[c] --> chor[c] + h[c] + pi[c] 		
3000	CHRPL	No	Chorismate pyruvate lyase	[c] : chor --> 4hbz + pyr	Cofactor and Prosthetic Group Biosynthesis		b4039	JLR (EC 4.1.3.-)		-29.1788	11.3713	[c] : chor[c] --> 4hbz[c] + pyr[c] 		
2293	CINNDO	No	Cinnamate dioxygenase	[c] : cinnm + h + nadh + o2 --> cenchddd + nad	Alternate Carbon Metabolism		( b2538  and  b2539  and  b2540  and  b2542 )	JLR- see PMID 9603882		-73.6331	11.2416	[c] : cinnm[c] + h[c] + nadh[c] + o2[c] --> cenchddd[c] + nad[c] 		
2302	CITL	No	Citrate lyase	[c] : cit --> ac + oaa	Citric Acid Cycle	4.1.3.6	( ( b0615  and  b0616  and  b0617 )  and  b0614 )	JLR	"The citX gene product catalyzes the transfer of the citrate lyase prosthetic group to the apo-ACP, converting it to holo-ACP.PMID: 10924139
AMF

CitX attaches a moiety from 2tpr3dpcoa to CitD
"	2.0357	3.15103	[c] : cit[c] --> ac[c] + oaa[c] 		
8806	CITt7pp	Yes	Citrate transport via succinate antiport (periplasm)	cit[p] + succ[c] --> cit[c] + succ[p]	"Transport, Inner Membrane"		b0612	JLR		0	0	[c] : cit[p] + succ[c] --> cit[c] + succ[p] 		
9229	CITtex	Yes	citrate transport via diffusion (extracellular to periplasm)	cit[e] <==> cit[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cit[e] <==> cit[p] 		
13529	CLIPAtex	Yes	cold lipid A transport via vector (periplasm to extracellular)	lipa_cold[p] --> lipa_cold[e]	Lipopolysaccharide Biosynthesis / Recycling			"AMF
not sure how it travels across the periplam or flipped to outer serface of the membrane"	"this reaction is needed to have the LPS lipid A derivative presented to the outer membrane surface - both moved across the periplasm and flipped across the outer membrane

not sure on the method of transport

this paper talks about the possibility of the transport PMID: 15576375

AMF"	0	0	[c] : lipa_cold[p] --> lipa_cold[e] 		
19859	CLPNH120pp	Yes	"cardiolipin hydrolase (periplasm, n-C12:0)"	[p] : clpn120 + h2o --> h + pa120 + pg120	Glycerophospholipid Metabolism			"AMF
PMID: 360"	"PMID: 360
characterizes phospholipase D activity in E. coli.  The gene responsible is not characterized and it is not known if the reaction takes place on the inner membrane or on outer membrane or both.

PMID: 10634942 states that neither cls nor ybhO have cardiolipin hydrolase activity
AMF"	-2.01149	2.78659	[p] : clpn120[p] + h2o[p] --> pa120[p] + pg120[p] 		
19860	CLPNH140pp	Yes	"cardiolipin hydrolase (periplasm, n-C14:0)"	[p] : clpn140 + h2o --> h + pa140 + pg140	Glycerophospholipid Metabolism			"AMF
PMID: 360"	"PMID: 360
characterizes phospholipase D activity in E. coli.  The gene responsible is not characterized and it is not known if the reaction takes place on the inner membrane or on outer membrane or both.

PMID: 10634942 states that neither cls nor ybhO have cardiolipin hydrolase activity
AMF"	-2.01149	2.78659	[p] : clpn140[p] + h2o[p] --> pa140[p] + pg140[p] 		
19861	CLPNH141pp	Yes	"cardiolipin hydrolase (periplasm, n-C14:1)"	[p] : clpn141 + h2o --> h + pa141 + pg141	Glycerophospholipid Metabolism			"AMF
PMID: 360"	"PMID: 360
characterizes phospholipase D activity in E. coli.  The gene responsible is not characterized and it is not known if the reaction takes place on the inner membrane or on outer membrane or both.

PMID: 10634942 states that neither cls nor ybhO have cardiolipin hydrolase activity
AMF"	-2.01149	2.78659	[p] : clpn141[p] + h2o[p] --> pa141[p] + pg141[p] 		
19862	CLPNH160pp	Yes	"cardiolipin hydrolase (periplasm, n-C16:0)"	[p] : clpn160 + h2o --> h + pa160 + pg160	Glycerophospholipid Metabolism			"AMF
PMID: 360"	"PMID: 360
characterizes phospholipase D activity in E. coli.  The gene responsible is not characterized and it is not known if the reaction takes place on the inner membrane or on outer membrane or both.

PMID: 10634942 states that neither cls nor ybhO have cardiolipin hydrolase activity
AMF"	-2.01149	2.78659	[p] : clpn160[p] + h2o[p] --> pa160[p] + pg160[p] 		
19863	CLPNH161pp	Yes	"cardiolipin hydrolase (periplasm, n-C16:1)"	[p] : clpn161 + h2o --> h + pa161 + pg161	Glycerophospholipid Metabolism			"AMF
PMID: 360"	"PMID: 360
characterizes phospholipase D activity in E. coli.  The gene responsible is not characterized and it is not known if the reaction takes place on the inner membrane or on outer membrane or both.

PMID: 10634942 states that neither cls nor ybhO have cardiolipin hydrolase activity
AMF"	-2.01149	2.78659	[p] : clpn161[p] + h2o[p] --> pa161[p] + pg161[p] 
19864	CLPNH180pp	Yes	"cardiolipin hydrolase (periplasm, n-C18:0)"	[p] : clpn180 + h2o --> h + pa180 + pg180	Glycerophospholipid Metabolism			"AMF
PMID: 360"	"PMID: 360
characterizes phospholipase D activity in E. coli.  The gene responsible is not characterized and it is not known if the reaction takes place on the inner membrane or on outer membrane or both.

PMID: 10634942 states that neither cls nor ybhO have cardiolipin hydrolase activity
AMF"	-2.01149	2.78659	[p] : clpn180[p] + h2o[p] --> pa180[p] + pg180[p] 
19865	CLPNH181pp	Yes	"cardiolipin hydrolase (periplasm, n-C18:1)"	[p] : clpn181 + h2o --> h + pa181 + pg181	Glycerophospholipid Metabolism			"AMF
PMID: 360"	"PMID: 360
characterizes phospholipase D activity in E. coli.  The gene responsible is not characterized and it is not known if the reaction takes place on the inner membrane or on outer membrane or both.

PMID: 10634942 states that neither cls nor ybhO have cardiolipin hydrolase activity
AMF"	-2.01149	2.78659	[p] : clpn181[p] + h2o[p] --> pa181[p] + pg181[p] 
19771	CLPNS120pp	Yes	"cardiolipin synthase (periplasmic, n-C12:0)"	[p] : (2) pg120 <==> clpn120 + glyc	Glycerophospholipid Metabolism		( b1249  or  b0789 )	"JLR - (EC 2.7.8.-)
AMF"	"From PMID: 3918012
_The location of analog lipid synthesis and the intracellular distribution of the lipids formed have not been examined directly, but several lines of circumstantial evidence suggest answers to these questions. E. coli cells formed mannitol lipids irrespective of the presence of the mtl-2 allele, which should have caused a defect in specific enzyme II of the phosphotransferase system (2, 16), the sole transport system for mannitol (9). Therefore, the most probable site of the cardiolipin synthase reaction for analog lipid formation is the periplasmic side of the cytoplasmic membrane. This also supports the notion that mannitol was incorporated into the lipids without prior phosphorylation or other structural modifications._

Suggests reversibility:
_If this reaction is reversible and if the substrate specificity is not strict, then the alcoholysis of cardiolipin in the presence of high concentration of, for instance, D-mannitol may yield phosphatidylmannitol and phosphatidylglycerol, and further condensation may give rise to diphosphatidylmannitol (Fig. 3)_

yhbO can catalyze CL formation, but reported to not be functional inside of the cell.  PMID: 10634942.  however, it is curious that ybhO was reported unable to complement a cls mutation. However, it is not clear that the genome segment tested contained a functional promoter. - Cronan PMID: 14527277
Not sure of the location of the active site of ybhO
AMF"	0	0.5	[p] : (2) pg120[p] <==> clpn120[p] + glyc[p] 
19813	CLPNS140pp	Yes	"cardiolipin synthase (periplasmic, n-C14:0)"	[p] : (2) pg140 <==> clpn140 + glyc	Glycerophospholipid Metabolism		( b1249  or  b0789 )	"JLR - (EC 2.7.8.-)
AMF - not sure of reversibility"	"From PMID: 3918012
_The location of analog lipid synthesis and the intracellular distribution of the lipids formed have not been examined directly, but several lines of circumstantial evidence suggest answers to these questions. E. coli cells formed mannitol lipids irrespective of the presence of the mtl-2 allele, which should have caused a defect in specific enzyme II of the phosphotransferase system (2, 16), the sole transport system for mannitol (9). Therefore, the most probable site of the cardiolipin synthase reaction for analog lipid formation is the periplasmic side of the cytoplasmic membrane. This also supports the notion that mannitol was incorporated into the lipids without prior phosphorylation or other structural modifications._

Suggests reversibility:
_If this reaction is reversible and if the substrate specificity is not strict, then the alcoholysis of cardiolipin in the presence of high concentration of, for instance, D-mannitol may yield phosphatidylmannitol and phosphatidylglycerol, and further condensation may give rise to diphosphatidylmannitol (Fig. 3)_

yhbO- reported to not be functional inside of the cell.  PMID: 10634942
it is curious that ybhO was reported unable to complement a cls mutation. However, it is not clear that the genome segment tested contained a functional promoter. - Cronan PMID: 14527277
AMF"	0	0.5	[p] : (2) pg140[p] <==> clpn140[p] + glyc[p] 
19814	CLPNS141pp	Yes	"cardiolipin synthase (periplasmic, n-C14:1)"	[p] : (2) pg141 <==> clpn141 + glyc	Glycerophospholipid Metabolism		( b1249  or  b0789 )	"JLR - (EC 2.7.8.-)
AMF - not sure of reversibility"	"From PMID: 3918012
_The location of analog lipid synthesis and the intracellular distribution of the lipids formed have not been examined directly, but several lines of circumstantial evidence suggest answers to these questions. E. coli cells formed mannitol lipids irrespective of the presence of the mtl-2 allele, which should have caused a defect in specific enzyme II of the phosphotransferase system (2, 16), the sole transport system for mannitol (9). Therefore, the most probable site of the cardiolipin synthase reaction for analog lipid formation is the periplasmic side of the cytoplasmic membrane. This also supports the notion that mannitol was incorporated into the lipids without prior phosphorylation or other structural modifications._

Suggests reversibility:
_If this reaction is reversible and if the substrate specificity is not strict, then the alcoholysis of cardiolipin in the presence of high concentration of, for instance, D-mannitol may yield phosphatidylmannitol and phosphatidylglycerol, and further condensation may give rise to diphosphatidylmannitol (Fig. 3)_

yhbO- reported to not be functional inside of the cell.  PMID: 10634942
it is curious that ybhO was reported unable to complement a cls mutation. However, it is not clear that the genome segment tested contained a functional promoter. - Cronan PMID: 14527277
AMF"	0	0.5	[p] : (2) pg141[p] <==> clpn141[p] + glyc[p] 
19815	CLPNS160pp	Yes	"cardiolipin synthase (periplasmic, n-C16:0)"	[p] : (2) pg160 <==> clpn160 + glyc	Glycerophospholipid Metabolism		( b1249  or  b0789 )	JLR - (EC 2.7.8.-)	"From PMID: 3918012
_The location of analog lipid synthesis and the intracellular distribution of the lipids formed have not been examined directly, but several lines of circumstantial evidence suggest answers to these questions. E. coli cells formed mannitol lipids irrespective of the presence of the mtl-2 allele, which should have caused a defect in specific enzyme II of the phosphotransferase system (2, 16), the sole transport system for mannitol (9). Therefore, the most probable site of the cardiolipin synthase reaction for analog lipid formation is the periplasmic side of the cytoplasmic membrane. This also supports the notion that mannitol was incorporated into the lipids without prior phosphorylation or other structural modifications._

Suggests reversibility:
_If this reaction is reversible and if the substrate specificity is not strict, then the alcoholysis of cardiolipin in the presence of high concentration of, for instance, D-mannitol may yield phosphatidylmannitol and phosphatidylglycerol, and further condensation may give rise to diphosphatidylmannitol (Fig. 3)_

yhbO- reported to not be functional inside of the cell.  PMID: 10634942
it is curious that ybhO was reported unable to complement a cls mutation. However, it is not clear that the genome segment tested contained a functional promoter. - Cronan PMID: 14527277
AMF"	0	0.5	[p] : (2) pg160[p] <==> clpn160[p] + glyc[p] 
19816	CLPNS161pp	Yes	"cardiolipin synthase (periplasmic, n-C16:1)"	[p] : (2) pg161 <==> clpn161 + glyc	Glycerophospholipid Metabolism		( b1249  or  b0789 )	"JLR - (EC 2.7.8.-)
AMF"	"From PMID: 3918012
_The location of analog lipid synthesis and the intracellular distribution of the lipids formed have not been examined directly, but several lines of circumstantial evidence suggest answers to these questions. E. coli cells formed mannitol lipids irrespective of the presence of the mtl-2 allele, which should have caused a defect in specific enzyme II of the phosphotransferase system (2, 16), the sole transport system for mannitol (9). Therefore, the most probable site of the cardiolipin synthase reaction for analog lipid formation is the periplasmic side of the cytoplasmic membrane. This also supports the notion that mannitol was incorporated into the lipids without prior phosphorylation or other structural modifications._

Suggests reversibility:
_If this reaction is reversible and if the substrate specificity is not strict, then the alcoholysis of cardiolipin in the presence of high concentration of, for instance, D-mannitol may yield phosphatidylmannitol and phosphatidylglycerol, and further condensation may give rise to diphosphatidylmannitol (Fig. 3)_

yhbO- reported to not be functional inside of the cell.  PMID: 10634942
it is curious that ybhO was reported unable to complement a cls mutation. However, it is not clear that the genome segment tested contained a functional promoter. - Cronan PMID: 14527277
AMF"	0	0.5	[p] : (2) pg161[p] <==> clpn161[p] + glyc[p] 
19817	CLPNS180pp	Yes	"cardiolipin synthase (periplasmic, n-C18:0)"	[p] : (2) pg180 <==> clpn180 + glyc	Glycerophospholipid Metabolism		( b1249  or  b0789 )	"JLR - (EC 2.7.8.-)
AMF"	"From PMID: 3918012
_The location of analog lipid synthesis and the intracellular distribution of the lipids formed have not been examined directly, but several lines of circumstantial evidence suggest answers to these questions. E. coli cells formed mannitol lipids irrespective of the presence of the mtl-2 allele, which should have caused a defect in specific enzyme II of the phosphotransferase system (2, 16), the sole transport system for mannitol (9). Therefore, the most probable site of the cardiolipin synthase reaction for analog lipid formation is the periplasmic side of the cytoplasmic membrane. This also supports the notion that mannitol was incorporated into the lipids without prior phosphorylation or other structural modifications._

Suggests reversibility:
_If this reaction is reversible and if the substrate specificity is not strict, then the alcoholysis of cardiolipin in the presence of high concentration of, for instance, D-mannitol may yield phosphatidylmannitol and phosphatidylglycerol, and further condensation may give rise to diphosphatidylmannitol (Fig. 3)_

yhbO- reported to not be functional inside of the cell.  PMID: 10634942
it is curious that ybhO was reported unable to complement a cls mutation. However, it is not clear that the genome segment tested contained a functional promoter. - Cronan PMID: 14527277
AMF"	0	0.5	[p] : (2) pg180[p] <==> clpn180[p] + glyc[p] 
19818	CLPNS181pp	Yes	"cardiolipin synthase (periplasmic, n-C18:1)"	[p] : (2) pg181 <==> clpn181 + glyc	Glycerophospholipid Metabolism		( b1249  or  b0789 )	"JLR - (EC 2.7.8.-)
AMF"	"From PMID: 3918012
_The location of analog lipid synthesis and the intracellular distribution of the lipids formed have not been examined directly, but several lines of circumstantial evidence suggest answers to these questions. E. coli cells formed mannitol lipids irrespective of the presence of the mtl-2 allele, which should have caused a defect in specific enzyme II of the phosphotransferase system (2, 16), the sole transport system for mannitol (9). Therefore, the most probable site of the cardiolipin synthase reaction for analog lipid formation is the periplasmic side of the cytoplasmic membrane. This also supports the notion that mannitol was incorporated into the lipids without prior phosphorylation or other structural modifications._

Suggests reversibility:
_If this reaction is reversible and if the substrate specificity is not strict, then the alcoholysis of cardiolipin in the presence of high concentration of, for instance, D-mannitol may yield phosphatidylmannitol and phosphatidylglycerol, and further condensation may give rise to diphosphatidylmannitol (Fig. 3)_

yhbO- reported to not be functional inside of the cell.  PMID: 10634942
it is curious that ybhO was reported unable to complement a cls mutation. However, it is not clear that the genome segment tested contained a functional promoter. - Cronan PMID: 14527277
AMF"	0	0.5	[p] : (2) pg181[p] <==> clpn181[p] + glyc[p] 
14019	CLt3rpp	Yes	chloride transport out via proton antiport (periplasm)	cl[p] + h[c] <==> cl[c] + h[p]	"Transport, Inner Membrane"		b0155	AMF	"from citation and transport database
1.A.11.5.1
AMF"	0	0	[c] : cl[p] + h[c] <==> cl[c] + h[p] 
14020	CLtex	Yes	chloride (Cl-1) transport via diffusion (extracellular to periplasm)	cl[e] <==> cl[p]	"Transport, Outer Membrane"				"assumed diffusion
AMF"	0	0	[c] : cl[e] <==> cl[p] 
1570	CMPN	No	CMP nucleosidase	[c] : cmp + h2o --> csn + r5p	Nucleotide Salvage Pathway	3.2.2.10		"JLR - also acts on dUMP, dCMP,dTMP, and presumably TMP and UMP"		-2.26379	3.60328	[c] : cmp[c] + h2o[c] --> csn[c] + r5p[c] 
12303	CMPtex	Yes	CMP transport via diffusion (extracellular to periplasm)	cmp[e] <==> cmp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cmp[e] <==> cmp[p] 
9052	CO2tex	Yes	CO2 transport via diffusion (extracellular to periplasm)	co2[e] <==> co2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : co2[e] <==> co2[p] 
8977	CO2tpp	Yes	CO2 transporter via diffusion (periplasm)	co2[p] <==> co2[c]	"Transport, Inner Membrane"			"tv
renamed from CO2TPr to CO2t
NCD"		0	0	[c] : co2[p] <==> co2[c] 
13670	COBALT2abcpp	Yes	Cobalt (Co+2) ABC transporter (periplasm)	atp[c] + cobalt2[c] + h2o[c] --> adp[c] + cobalt2[p] + h[c] + pi[c]	"Transport, Inner Membrane"		b3469	AMF	"characterized in PMID: 10660539
ATP-dependent efflux
The activity was specific for Pb(II), Cd(II), Zn(II), and Hg(II), with the highest activity obtained when the metals were present as thiolate complexes of cysteine or glutathione.

from transportDB:
 Zn2+-, Cd2+-, Co2+-, Hg2+-, Ni2+-, Cu2+, Pb2+-ATPase (efflux) (Hou and Mitra, 2003) for ecoli

http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=3.A.3
AMF"	-7.01673	1.48181	[c] : atp[c] + cobalt2[c] + h2o[c] --> adp[c] + cobalt2[p] + h[c] + pi[c] 					
13685	COBALT2tex	Yes	cobalt (Co+2) transport via diffusion (extracellular to periplasm)	cobalt2[e] <==> cobalt2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cobalt2[e] <==> cobalt2[p] 					
13666	COBALTtpp	Yes	cobalt transport in/out via permease (no H+)	cobalt2[p] <==> cobalt2[c]	"Transport, Inner Membrane"		b3816		"The CorA permeases of S. typhimurium and E. coli mediate both influx and efflux of Mg2+. They transport Mg2+, Co2+ and Ni2+ but not Fe2+ (Papp and Maguire, 2004).

transport DB

http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=1.A.35

AMF"	0	0	[c] : cobalt2[p] <==> cobalt2[c] 					
13508	COLIPAabcpp	Yes	core oligosaccharide lipid A transport via ABC system (periplasm)	atp[c] + colipa[c] + h2o[c] --> adp[c] + colipa[p] + h[c] + pi[c]	Lipopolysaccharide Biosynthesis / Recycling		b0914		"PMID: 12045108 gives a reaview on LPS biosynthesis and states that it can transport PE

also, atpase acitvity was activated by kdo2-lipidA and other hexa-acylated compounds, also kd02-lipid4A could be transported by MsbA.
states that it can transport pretty much all lipids
PMID: 15052329

AMF"	-7.01673	1.48181	[c] : atp[c] + colipa[c] + h2o[c] --> adp[c] + colipa[p] + h[c] + pi[c] 					
13523	COLIPAtex	Yes	core oligosaccharide lipid A transport via vector (periplasm to extracellular)	colipa[p] --> colipa[e]	Lipopolysaccharide Biosynthesis / Recycling			"AMF
not sure how it travels across the periplam or flipped to outer serface of the membrane"	"this reaction is needed to have the LPS lipid A derivative presented to the outer membrane surface - both moved across the periplasm and flipped across the outer membrane

not sure on the method of transport

this paper talks about the possibility of the transport PMID: 15576375

AMF"	0	0	[c] : colipa[p] --> colipa[e] 					
14052	CPGNabcpp	Yes	coprogen transport via ABC system (periplasm)	atp[c] + cpgn[p] + h2o[c] --> adp[c] + cpgn[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0153  and  b0151  and  b0152 )		"There are other molecules that are transported by this complex, listed on transportDB
http://tcdb.ucsd.edu/tcdb/tcfamilybrowse.php?tcname=3.A.1

PMID: 14668326"	-7.01673	1.48181	[c] : atp[c] + cpgn[p] + h2o[c] --> adp[c] + cpgn[c] + h[c] + pi[c] 					
14053	CPGNexs	Yes	coprogen Fe-loading reaction (spontaneaous)	[e] : cpgn-un + fe3 --> cpgn	Update				"reaction reflects function of siderophore 

Fe(III) hydroxamate is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  not produced by K-12 ecoli, but they can ingest it and utilize the Fe it traps.  then releases siderophore to collect more Fe

MKA

reaction is in network to reflact the recycling of siderophones and then becoming reactivated with Fe to be took up again into the system -  AMF"	No energy	No energy	[e] : cpgn-un[e] + fe3[e] --> cpgn[e] 					
14054	CPGNR1	Yes	coprogen(Fe(III)) reductase	[c] : (2) cpgn + fadh2 --> (2) cpgn-un + fad + (2) fe2 + (2) h	Update				"indirectly (?) reduced by activity of Fre   

cpgn is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  not produced by K-12 ecoli, but they can ingest it and utilize the Fe it traps.  then releases siderophore to collect more Fe

MKA
AMF"	No energy	No energy	[c] : (2) cpgn[c] + fadh2[c] --> (2) cpgn-un[c] + fad[c] + (2) fe2[c] + (2) h[c] 					
14055	CPGNR2	Yes	coprogen(Fe(III)) reductase	[c] : (2) cpgn + fmnh2 --> (2) cpgn-un + (2) fe2 + fmn + (2) h	Update				"indirectly (?) reduced by activity of Fre   

cpgn is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  not produced by K-12 ecoli, but they can ingest it and utilize the Fe it traps.  then releases siderophore to collect more Fe

MKA
AMF"	No energy	No energy	[c] : (2) cpgn[c] + fmnh2[c] --> (2) cpgn-un[c] + (2) fe2[c] + fmn[c] + (2) h[c] 					
14056	CPGNR3	Yes	coprogen(Fe(III)) reductase	[c] : (2) cpgn + rbflvrd --> (2) cpgn-un + (2) fe2 + (2) h + ribflv	Update				"indirectly (?) reduced by activity of Fre   

cpgn is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  not produced by K-12 ecoli, but they can ingest it and utilize the Fe it traps.  then releases siderophore to collect more Fe

MKA
AMF"	No energy	No energy	[c] : (2) cpgn[c] + rbflvrd[c] --> (2) cpgn-un[c] + (2) fe2[c] + (2) h[c] + ribflv[c] 					
9131	CPGNtonex	Yes	Coprogen transport via ton system (extracellular)	cpgn[e] + h[p] --> cpgn[p] + h[c]	"Transport, Outer Membrane"		( b1102  and  ( b1252  and  b3005  and  b3006 ) )	"AMF - PMID:8405078 and PMID: 10209752
assumption of 1 proton transported across the membrane"	"chategorized as the Iut transporter - I think the OhmP gene is the replacement

PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR"	0	0	[c] : cpgn[e] + h[p] --> cpgn[p] + h[c] 					
14058	CPGNUtex	Yes	coprogen unloaded secretion (extracellular)	cpgn-un[p] + h[p] --> cpgn-un[e] + h[c]	Update			"presumed reaction - no transporters known.   symport/antiport unknown MKA AMF
"	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes
AMF"	0	0	[c] : cpgn-un[p] + h[p] --> cpgn-un[e] + h[c] 					
14057	CPGNUtpp	Yes	coprogen unloaded secretion	cpgn-un[c] + h[p] --> cpgn-un[p] + h[c]	Update			"presumed reaction - no transporters known.   symport/antiport unknown MKA AMF
"	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes
AMF"	0	0	[c] : cpgn-un[c] + h[p] --> cpgn-un[p] + h[c] 					
1650	CPPPGO	No	coproporphyrinogen oxidase (O2 required)	[c] : cpppg3 + (2) h + o2 --> (2) co2 + (2) h2o + pppg9	Cofactor and Prosthetic Group Biosynthesis	1.3.3.3	b2436	JLR		No energy	No energy	[c] : cpppg3[c] + (2) h[c] + o2[c] --> (2) co2[c] + (2) h2o[c] + pppg9[c] 					
12337	CPPPGO2	Yes	Oxygen Independent coproporphyrinogen-III oxidase	[c] : (2) amet + cpppg3 --> (2) co2 + (2) dad-5 + (2) met-L + pppg9	Update		b3867	"Mechanism Based on Layer et al (2002), JBC
AMF - not totally sure on reaction stoich, took mostly from KEGG"	"AMF -
Mechanism Based on Layer et al (2002), JBC
AMF - not totally sure on reaction stoich, took mostly from KEGG"	No energy	No energy	[c] : (2) amet[c] + cpppg3[c] --> (2) co2[c] + (2) dad-5[c] + (2) met-L[c] + pppg9[c] 					
13630	CRNabcpp	Yes	L-carnitine transport via ABC system (periplasm)	atp[c] + crn[p] + h2o[c] --> adp[c] + crn[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b2677  and  b2678  and  b2679 )	AMF	"PMID: 12163501
states that other transport systems capable
of taking up L-carnitine (for example, ProP and ProU) D-carnitine...
AMF"	-7.01673	1.48181	[c] : atp[c] + crn[p] + h2o[c] --> adp[c] + crn[c] + h[c] + pi[c] 					
2556	CRNBTCT	No	gamma-butyrobetainyl-CoA: carnitine CoA transferase	[c] : bbtcoa + crn <==> crncoa + gbbtn	Oxidative Phosphorylation		b0038	JLR		0	0.5	[c] : bbtcoa[c] + crn[c] <==> crncoa[c] + gbbtn[c] 
12178	CRNCAL	Yes	Carnitine-CoA Ligase	[c] : coa + crn + h --> crncoa + h2o	Update		b0037	AMF	"proposed function, not entirely sure of reaction
ecocyc cites: PMID: 7815937
makes physiological sence
AMF"	5.85263	4.37924	[c] : coa[c] + crn[c] + h[c] --> crncoa[c] + h2o[c] 
13638	CRNCAR	Yes	carnitine-CoA racemase	[c] : crncoa <==> crnDcoa	Update		b0036	AMF	"proposed function, not entirely sure of reaction
ecocyc cites: PMID: 7815937
makes physiological sence
AMF"	0	0.5	[c] : crncoa[c] <==> crnDcoa[c] 
2557	CRNCBCT	No	crotonobetainyl-CoA: carnitine CoA transferase	[c] : crn + ctbtcoa <==> crncoa + ctbt	Oxidative Phosphorylation		b0038	JLR		0	0.5	[c] : crn[c] + ctbtcoa[c] <==> crncoa[c] + ctbt[c] 
2558	CRNCDH	No	Carnityl-CoA dehydratse	[c] : crncoa <==> ctbtcoa + h2o	Oxidative Phosphorylation		b0036	JLR		0.278853	2.66722	[c] : crncoa[c] <==> ctbtcoa[c] + h2o[c] 
13631	CRNDabcpp	Yes	D-carnitine transport via ABC system (periplasm)	atp[c] + crn-D[p] + h2o[c] --> adp[c] + crn-D[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b2677  and  b2678  and  b2679 )	AMF	"PMID: 12163501
states that other transport systems capable
of taking up L-carnitine (for example, ProP and ProU) D-carnitine...
AMF"	-7.01673	1.48181	[c] : atp[c] + crn-D[p] + h2o[c] --> adp[c] + crn-D[c] + h[c] + pi[c] 
13637	CRNDCAL	Yes	D-Carnitine-CoA Ligase	[c] : coa + crn-D + h --> crnDcoa + h2o	Update		b0037		"proposed function, not entirely sure of reaction
ecocyc cites: PMID: 7815937
makes physiological sence
AMF"	5.85263	4.37924	[c] : coa[c] + crn-D[c] + h[c] --> crnDcoa[c] + h2o[c] 
13628	CRNDt2rpp	Yes	D-carnitine outward transport (H+ antiport)	crn-D[p] + h[p] <==> crn-D[c] + h[c]	"Transport, Inner Membrane"		b4111	AMF	"PMID: 12163501
states that other transport systems capable
of taking up L-carnitine (for example, ProP and ProU) D-carnitine...
AMF"	0	0	[c] : crn-D[p] + h[p] <==> crn-D[c] + h[c] 
13627	CRNt2rpp	Yes	L-carnitine outward transport (H+ antiport)	crn[p] + h[p] <==> crn[c] + h[c]	"Transport, Inner Membrane"		b4111	AMF	"PMID: 12163501
states that other transport systems capable
of taking up L-carnitine (for example, ProP and ProU) D-carnitine...
AMF"	0	0	[c] : crn[p] + h[p] <==> crn[c] + h[c] 
8807	CRNt7pp	Yes	Carnitine/butyrobetaine antiporter (periplasm)	crn[p] + gbbtn[c] --> crn[c] + gbbtn[p]	"Transport, Inner Membrane"		b0040	JLR	"antiporter with general specificity for carnitine and butyrobetaine
PMID: 12163501
AMF"	0	0	[c] : crn[p] + gbbtn[c] --> crn[c] + gbbtn[p] 
13626	CRNt8pp	Yes	L-carnitine/D-carnitine antiporter (periplasm)	crn[p] + crn-D[c] --> crn[c] + crn-D[p]	"Transport, Inner Membrane"		b0040	AMF	"antiporter with general specificity for carnitine and butyrobetaine
PMID: 12163501
AMF"	0	0	[c] : crn[p] + crn-D[c] --> crn[c] + crn-D[p] 
9053	CRNtex	Yes	L-carnitine transport via diffusion (extracellular to periplasm)	crn[e] <==> crn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : crn[e] <==> crn[p] 
286	CS	No	citrate synthase	[c] : accoa + h2o + oaa --> cit + coa + h	Citric Acid Cycle		b0720	"old EC number (4.1.3.7) is obsolete -- transferred to 2.3.3.1
NCD"		-7.88833	5.66905	[c] : accoa[c] + h2o[c] + oaa[c] --> cit[c] + coa[c] + h[c] 
3526	CSND	No	Cytosine deaminase	[c] : csn + h + h2o --> nh4 + ura	Nucleotide Salvage Pathway	3.5.4.1	b0337	JLR		-5.6874	4.84135	[c] : csn[c] + h[c] + h2o[c] --> nh4[c] + ura[c] 
8808	CSNt2pp	Yes	cytosine transport in via proton symport (periplasm)	csn[p] + h[p] --> csn[c] + h[c]	"Transport, Inner Membrane"		b0336			0	0	[c] : csn[p] + h[p] --> csn[c] + h[c] 
9054	CSNtex	Yes	cytosine transport via diffusion (extracellular to periplasm)	csn[e] <==> csn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : csn[e] <==> csn[p] 
13632	CTBTabcpp	Yes	crotonobetaine transport via ABC system (periplasm)	atp[c] + ctbt[p] + h2o[c] --> adp[c] + ctbt[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b2677  and  b2678  and  b2679 )	AMF	"PMID: 12163501
states that other transport systems capable
of taking up L-carnitine (for example, ProP and ProU) D-carnitine...
AMF"	-7.01673	1.48181	[c] : atp[c] + ctbt[p] + h2o[c] --> adp[c] + ctbt[c] + h[c] + pi[c] 					
12179	CTBTCAL	Yes	Crotonobetaine-CoA Ligase	[c] : coa + ctbt + h --> ctbtcoa + h2o	Update		b0037	AMF	"proposed function, not entirely sure of reaction
ecocyc cites: PMID: 7815937
makes physiological sence
AMF"	5.85263	4.37924	[c] : coa[c] + ctbt[c] + h[c] --> ctbtcoa[c] + h2o[c] 					
13629	CTBTt2rpp	Yes	cronobetaine outward transport (H+ antiport)	ctbt[p] + h[p] <==> ctbt[c] + h[c]	"Transport, Inner Membrane"		b4111	AMF	"PMID: 12163501
states that other transport systems capable
of taking up L-carnitine (for example, ProP and ProU) D-carnitine...
AMF"	0	0	[c] : ctbt[p] + h[p] <==> ctbt[c] + h[c] 					
2696	CTPS2	No	CTP synthase (glutamine)	[c] : atp + gln-L + h2o + utp --> adp + ctp + glu-L + (2) h + pi	Purine and Pyrimidine Biosynthesis	6.3.4.2	b2780			-6.02236	5.77496	[c] : atp[c] + gln-L[c] + h2o[c] + utp[c] --> adp[c] + ctp[c] + glu-L[c] + (2) h[c] + pi[c] 					
13650	CU1abcpp	Yes	Copper (Cu +1) ABC transporter (periplasm)	atp[c] + cu[c] + h2o[c] --> adp[c] + cu[p] + h[c] + pi[c]	"Transport, Inner Membrane"		b0484	AMF	"characetized in PMID: 12351646 
AMF"	-7.01673	1.48181	[c] : atp[c] + cu[c] + h2o[c] --> adp[c] + cu[p] + h[c] + pi[c] 					
13657	CU1Opp	Yes	Cuprous Oxidase (Cu+1)	[p] : (4) cu + (4) h + o2 <==> (4) cu2 + (2) h2o	Update		b0123	"EC # 1.16.3.-
AMF"	"characterized in PMID: 15516598 
activated by CuII
AMF"	No energy	No energy	[p] : (4) cu[p] + (4) h[p] + o2[p] <==> (4) cu2[p] + (2) h2o[p] 					
13668	CU2abcpp	Yes	Copper (Cu+2) ABC transporter (periplasm)	atp[c] + cu2[c] + h2o[c] --> adp[c] + cu2[p] + h[c] + pi[c]	"Transport, Inner Membrane"		b3469	AMF	"characterized in PMID: 10660539
ATP-dependent efflux
The activity was specific for Pb(II), Cd(II), Zn(II), and Hg(II), with the highest activity obtained when the metals were present as thiolate complexes of cysteine or glutathione.

from transportDB:
 Zn2+-, Cd2+-, Co2+-, Hg2+-, Ni2+-, Cu2+, Pb2+-ATPase (efflux) (Hou and Mitra, 2003) for ecoli

http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=3.A.3
AMF"	-7.01673	1.48181	[c] : atp[c] + cu2[c] + h2o[c] --> adp[c] + cu2[p] + h[c] + pi[c] 					
13684	CU2tex	Yes	copper (Cu+2) transport via diffusion (extracellular to periplasm)	cu2[e] <==> cu2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cu2[e] <==> cu2[p] 					
14029	CUt3	Yes	copper transport out via proton antiport	cu[c] + h[e] --> cu[e] + h[c]	"Transport, Outer Membrane"		( b0572  and  b0573  and  b0574  and  b0575 )		"Ag and Cu are transported across both membranes
see diagram in PMID: 12829274

PMID: 12813074
gives specificity of substrates and necessity for all three genes in the complex
AMF"	0	0	[c] : cu[c] + h[e] --> cu[e] + h[c] 					
3632	CYANST	No	Cyanide sulfurtransferase	[c] : cyan + tsul --> h + so3 + tcynt	Unassigned	2.8.1.1	b3425	JLR		No energy	No energy	[c] : cyan[c] + tsul[c] --> so3[c] + tcynt[c] 					
13719	CYANSTpp	Yes	Cyanide sulfurtransferase (periplasmic)	[p] : cyan + tsul --> h + so3 + tcynt	Update	2.8.1.1	b1308	"JLR
AMF"	"pspE, encodes a thiosulfate:cyanide sulfurtransferase (EC 2.8.1.1; rhodanese).
PMID: 11997041
AMF

PspE is periplasmic
PMID: 1324873
"	No energy	No energy	[p] : cyan[p] + tsul[p] --> so3[p] + tcynt[p] 					
13730	CYANtex	Yes	Cyanide transport via diffusion (extracellular to periplasm)	cyan[e] <==> cyan[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cyan[e] <==> cyan[p] 					
3306	CYNTAH	No	Cyanate aminohydrolase	[c] : cynt + (3) h + hco3 --> (2) co2 + nh4	Nitrogen Metabolism		b0340	JLR		-28.9501	5.79907	[c] : cynt[c] + (3) h[c] + hco3[c] --> (2) co2[c] + nh4[c] 					
8809	CYNTt2pp	Yes	Cyanate transport via proton symport (periplasm)	cynt[p] + h[p] --> cynt[c] + h[c]	Putative Transporters		b0341	JLR	JLR- ref says tranport is energy coupled	0	0	[c] : cynt[p] + h[p] --> cynt[c] + h[c] 					
9055	CYNTtex	Yes	Cyanate transport via diffusion (extracellular to periplasm)	cynt[e] <==> cynt[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cynt[e] <==> cynt[p] 					
8754	CYSabc2pp	Yes	L-cysteine export via ABC system (cytoplasm to periplasm)	atp[c] + cys-L[c] + h2o[c] --> adp[c] + cys-L[p] + h[c] + pi[c]	Update		( b0886  and  b0887 )		"PMID: 12393891
has been experimentally verified to export L-cysteine from the cytoplasm to the periplasm

also functions in the assembley of cytochrome bd

aslo verified in PMID: 16040611
AMF"	-7.01673	1.48181	[c] : atp[c] + cys-L[c] + h2o[c] --> adp[c] + cys-L[p] + h[c] + pi[c] 					
8965	CYSabcpp	Yes	L-cysteine uptake via ABC system (periplasm)	atp[c] + cys-L[p] + h2o[c] --> adp[c] + cys-L[c] + h[c] + pi[c]	"Transport, Inner Membrane"				"AMF - no gene association, rxn CYSabc2pp is known to act in reverse direction CydCD"	-7.01673	1.48181	[c] : atp[c] + cys-L[p] + h2o[c] --> adp[c] + cys-L[c] + h[c] + pi[c] 					
13978	CYSDabcpp	Yes	D-cysteine uptake via ABC system (periplasm)	atp[c] + cys-D[p] + h2o[c] --> adp[c] + cys-D[c] + h[c] + pi[c]	"Transport, Inner Membrane"				"AMF - no gene association

cys-D can be used as a sulfur souce and enzyme is characterized which utilizes it PMID: 11527960
AMF
"	-7.01673	1.48181	[c] : atp[c] + cys-D[p] + h2o[c] --> adp[c] + cys-D[c] + h[c] + pi[c] 					
13987	CYSDDS	Yes	D-cysteine desulfhydrase	[c] : cys-D + h2o --> h2s + nh4 + pyr	Update	4.4.1.15	b1919	"AMF
PMID: 11527960"	"characterized in citation
AMF
could be other substrates
"	1.54928	3.31585	[c] : cys-D[c] + h2o[c] --> h2s[c] + nh4[c] + pyr[c] 					
1268	CYSDS	Yes	Cysteine Desulfhydrase	[c] : cys-L + h2o --> h2s + nh4 + pyr	Cysteine Metabolism	4.1.99.1	( b3008  or  b3708 )	"JLR- also acts on L-tryptophan and L-serine
EC 4.4.1.1"	"MetC and TnaA both have activity, deletions of the two show that there is still another enzyme with this enzyme activity."	1.54928	3.31585	[c] : cys-L[c] + h2o[c] --> h2s[c] + nh4[c] + pyr[c] 					
13975	CYSDtex	Yes	D-cysteine transport via diffusion (extracellular to periplasm)	cys-D[e] <==> cys-D[p]	"Transport, Outer Membrane"				"assumed diffusion
"	0	0	[c] : cys-D[e] <==> cys-D[p] 					
350	CYSS	No	cysteine synthase	[c] : acser + h2s --> ac + cys-L + h	Cysteine Metabolism		( b2414  or  b2421 )	EC changed to 2.5.1.47 from 4.2.99.8		-12.5351	2.9139	[c] : acser[c] + h2s[c] --> ac[c] + cys-L[c] + h[c] 					
13896	CYSSADS	Yes	L-cysteine sulfinic acid desulfurase	[c] : 3sala + (2) h --> ala-L + so2	Update	4.1.1.12	b2810		"enzyme is well characterized in PMID: 9278392
3sala is currently a dead end
AMF"	No energy	No energy	[c] : 3sala[c] + h[c] --> ala-L[c] + so2[c] 					
9056	CYStex	Yes	L-cysteine transport via diffusion (extracellular to periplasm)	cys-L[e] <==> cys-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cys-L[e] <==> cys-L[p] 					
2870	CYSTL	No	cystathionine b-lyase	[c] : cyst-L + h2o --> hcys-L + nh4 + pyr	Methionine Metabolism	4.4.1.8	( b3008  or  b1622 )			-6.81055	4.16719	[c] : cyst-L[c] + h2o[c] --> hcys-L[c] + nh4[c] + pyr[c] 					
13991	CYStpp	Yes	L-cysteine export via facilitated transport	cys-L[c] --> cys-L[p]	"Transport, Inner Membrane"		( b2578  or  b1533 )	"AMF
PMID: 12562784"	"YfiK characterized in PMID: 12562784 

EamA characterized in PMID: 10844694
EamA substrate specificity and the energization of the efflux pump is unknown.
AMF"	0	0	[c] : cys-L[c] --> cys-L[p] 					
1028	CYSTRS	Yes	Cysteinyl-tRNA synthetase	[c] : atp + cys-L + trnacys --> amp + cystrna + ppi	Update	6.1.1.16	b0526		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + cys-L[c] + h[c] + trnacys[c] --> amp[c] + cystrna[c] + ppi[c] 					
8970	CYTBD2pp	Yes	cytochrome oxidase bd (menaquinol-8: 2 protons) (periplasm)	(2) h[c] + mql8[c] + (0.5) o2[c] --> (2) h[p] + h2o[c] + mqn8[c]	Update		( b0978  and  b0979 )	"JLR
EC 1.10.2.2 and 1.9.3.1"	CbdAB was tested with a ubiquinol analog (duroquinol) and a menaquinol analog (menadiol).  CbdAB had higher activity with menadiol.  Assumed had same proton generating capabilities as Cyd.	-30.1884	17.1289	[c] : (2) h[c] + mql8[c] + (0.5) o2[c] --> (2) h[p] + h2o[c] + mqn8[c] 					
8969	CYTBDpp	Yes	cytochrome oxidase bd (ubiquinol-8: 2 protons) (periplasm)	(2) h[c] + (0.5) o2[c] + q8h2[c] --> (2) h[p] + h2o[c] + q8[c]	Oxidative Phosphorylation		( ( b0733  and  b0734 )  or  ( b0978  and  b0979 ) )	"JLR
EC 1.10.2.2 and 1.9.3.1"	CbdAB was tested with a ubiquinol analog (duroquinol) and a menaquinol analog (menadiol).  CbdAB had higher activity with menadiol. Assumed had same proton generating capabilities as Cyd.	-28.7365	21.3063	[c] : (2) h[c] + (0.5) o2[c] + q8h2[c] --> (2) h[p] + h2o[c] + q8[c] 					
8971	CYTBO3pp	Yes	cytochrome oxidase bo3 (ubiquinol-8: 2.5 protons) (periplasm)	(2.5) h[c] + (0.5) o2[c] + q8h2[c] --> (2.5) h[p] + h2o[c] + q8[c]	Oxidative Phosphorylation		( b0429  and  b0430  and  b0431  and  b0432 )	"JLR
EC 1.10.2.2 and 1.9.3.1"		-28.7365	21.3063	[c] : (2.5) h[c] + (0.5) o2[c] + q8h2[c] --> (2.5) h[p] + h2o[c] + q8[c] 					
3527	CYTD	No	cytidine deaminase	[c] : cytd + h + h2o --> nh4 + uri	Nucleotide Salvage Pathway	3.5.4.5	b2143			-5.6874	4.84135	[c] : cytd[c] + h[c] + h2o[c] --> nh4[c] + uri[c] 					
6174	CYTDH	Yes	Cytidine hydrolase	[c] : cytd + h2o --> csn + rib-D	Update	3.2.2.8	( b2162  or  b0651  or  b0030 )	JLR		-2.26379	3.60328	[c] : cytd[c] + h2o[c] --> csn[c] + rib-D[c] 					
439	CYTDK2	No	cytidine kinase (GTP)	[c] : cytd + gtp --> cmp + gdp + h	Nucleotide Salvage Pathway		b2066			-4.65732	2.09859	[c] : cytd[c] + gtp[c] --> cmp[c] + gdp[c] 
8810	CYTDt2pp	Yes	cytidine transport in via proton symport (periplasm)	cytd[p] + h[p] --> cytd[c] + h[c]	"Transport, Inner Membrane"		( b2393  or  b2964 )			0	0	[c] : cytd[p] + h[p] --> cytd[c] + h[c] 
8811	CYTDt2rpp	Yes	"cytidine transport in via proton symport, reversible (periplasm)"	cytd[p] + h[p] <==> cytd[c] + h[c]	"Transport, Inner Membrane"		b2406	JLR		0	0	[c] : cytd[p] + h[p] <==> cytd[c] + h[c] 
9057	CYTDtex	Yes	cytidine transport via diffusion (extracellular to periplasm)	cytd[e] <==> cytd[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : cytd[e] <==> cytd[p] 
184	CYTK1	No	cytidylate kinase (CMP)	[c] : atp + cmp <==> adp + cdp	Nucleotide Salvage Pathway	2.7.4.14	b0910			0	0.5	[c] : atp[c] + cmp[c] <==> adp[c] + cdp[c] 
185	CYTK2	No	cytidylate kinase (dCMP)	[c] : atp + dcmp <==> adp + dcdp	Nucleotide Salvage Pathway	2.7.4.14	b0910			0	0.5	[c] : atp[c] + dcmp[c] <==> adp[c] + dcdp[c] 
1139	DAAD	No	D-Amino acid dehydrogenase	[c] : ala-D + fad + h2o --> fadh2 + nh4 + pyr	Alanine and Aspartate Metabolism	1.4.99.1	b1189	"tv
"		-4.90351	7.05148	[c] : ala-D[c] + fad[c] + h2o[c] --> fadh2[c] + nh4[c] + pyr[c] 
3514	DADA	No	Deoxyadenosine deaminase	[c] : dad-2 + h + h2o --> din + nh4	Nucleotide Salvage Pathway		b1623	JLR		-5.6874	4.84135	[c] : dad-2[c] + h[c] + h2o[c] --> din[c] + nh4[c] 
183	DADK	No	deoxyadenylate kinase	[c] : atp + damp <==> adp + dadp	Nucleotide Salvage Pathway	2.7.4.11	b0474	AMP can also act as acceptor		0	0.5	[c] : atp[c] + damp[c] <==> adp[c] + dadp[c] 
8812	DADNt2pp	Yes	deoxyadenosine transport in via proton symport (periplasm)	dad-2[p] + h[p] --> dad-2[c] + h[c]	"Transport, Inner Membrane"		( b2393  or  b2964 )			0	0	[c] : dad-2[p] + h[p] --> dad-2[c] + h[c] 
9058	DADNtex	Yes	deoxyadenosine transport via diffusion (extracellular to periplasm)	dad-2[e] <==> dad-2[p]	"Transport, Outer Membrane"		b0411		"assumed passive diffusion through the outer peptidoglycan layer

Tsx is responsible for the permeation of ribo- and deoxy-nucleosides, across the outer membrane of E. coli"	0	0	[c] : dad-2[e] <==> dad-2[p] 
19334	DAGK120	Yes	diacylglycerol kinase (n-C12:0)	[c] : 12dgr120 + atp --> adp + h + pa120	Glycerophospholipid Metabolism	2.7.1.107	b4042	AMF	"PMID: 8071224 shows active site on the cytoplasmic side
reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : 12dgr120[c] + atp[c] --> adp[c] + pa120[c] 
19293	DAGK140	Yes	diacylglycerol kinase (n-C14:0)	[c] : 12dgr140 + atp --> adp + h + pa140	Glycerophospholipid Metabolism	2.7.1.107	b4042	AMF	"PMID: 8071224 shows active site on the cytoplasmic side
reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : 12dgr140[c] + atp[c] --> adp[c] + pa140[c] 
19296	DAGK141	Yes	diacylglycerol kinase (n-C14:1)	[c] : 12dgr141 + atp --> adp + h + pa141	Glycerophospholipid Metabolism	2.7.1.107	b4042	AMF	"PMID: 8071224 shows active site on the cytoplasmic side
reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : 12dgr141[c] + atp[c] --> adp[c] + pa141[c] 
19294	DAGK160	Yes	diacylglycerol kinase (n-C16:0)	[c] : 12dgr160 + atp --> adp + h + pa160	Glycerophospholipid Metabolism	2.7.1.107	b4042	AMF	"PMID: 8071224 shows active site on the cytoplasmic side
reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : 12dgr160[c] + atp[c] --> adp[c] + pa160[c] 
19297	DAGK161	Yes	diacylglycerol kinase (n-C16:1)	[c] : 12dgr161 + atp --> adp + h + pa161	Glycerophospholipid Metabolism	2.7.1.107	b4042	AMF	"PMID: 8071224 shows active site on the cytoplasmic side
reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : 12dgr161[c] + atp[c] --> adp[c] + pa161[c] 
19295	DAGK180	Yes	diacylglycerol kinase (n-C18:0)	[c] : 12dgr180 + atp --> adp + h + pa180	Glycerophospholipid Metabolism	2.7.1.107	b4042	AMF	"PMID: 8071224 shows active site on the cytoplasmic side
reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : 12dgr180[c] + atp[c] --> adp[c] + pa180[c] 
19298	DAGK181	Yes	diacylglycerol kinase (n-C18:1)	[c] : 12dgr181 + atp --> adp + h + pa181	Glycerophospholipid Metabolism	2.7.1.107	b4042	AMF	"PMID: 8071224 shows active site on the cytoplasmic side
reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : 12dgr181[c] + atp[c] --> adp[c] + pa181[c] 
8813	DALAt2rpp	Yes	D-alanine transport via proton symport (periplasm)	ala-D[p] + h[p] <==> ala-D[c] + h[c]	"Transport, Inner Membrane"		b4208	JLR	"CycA mediates the uptake of L-alanine, D-alanine, glycine, D-serine, and Dcycloserine (Wargel et al. 1970; Cosloy 1973).....utilize H+ co-transport as the energy source (Swiss-Prot data base; http://www.expasy.org/sprot;
accession no. P39312). Together with fklB, cycA is thought to form the fklB-cycA operon, whose expression is regulated by the nitrogen assimilation control (Nac) protein
PMID: 15221223
AMF"	0	0	[c] : ala-D[p] + h[p] <==> ala-D[c] + h[c] 
9040	DALAtex	Yes	D-Alanine transport via diffusion (extracellular to periplasm)	ala-D[e] <==> ala-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ala-D[e] <==> ala-D[p] 
12304	DAMPtex	Yes	dAMP transport via diffusion (extracellular to periplasm)	damp[e] <==> damp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : damp[e] <==> damp[p] 
8978	DAPabcpp	Yes	M-diaminopimelic acid ABC transport (periplasm)	26dap-M[p] + atp[c] + h2o[c] --> 26dap-M[c] + adp[c] + h[c] + pi[c]	"Transport, Inner Membrane"			JLR		-7.01673	1.48181	[c] : 26dap-M[p] + atp[c] + h2o[c] --> 26dap-M[c] + adp[c] + h[c] + pi[c] 
11882	DAPAL	Yes	"2,3-diaminopropionate amonnia lyase"	[c] : 23dappa + h2o --> (2) nh4 + pyr	Update	4.3.1.15	b2871	"MKA
AMF"	"PMID: 12596860

Paper states clearly that this enzyme perfroms this transformation fo botht eh L and the D- form, but that is not distuinguished in this reaction

0.5% cat. activity on D-Serine  -> so serine not added as a substrate

AMF

"	-5.12646	3.66667	[c] : 23dappa[c] + h2o[c] --> (2) nh4[c] + pyr[c] 
355	DAPDC	No	diaminopimelate decarboxylase	[c] : 26dap-M + h --> co2 + lys-L	Threonine and Lysine Metabolism	4.1.1.20	b2838			-4.96805	1.79669	[c] : 26dap-M[c] + h[c] --> co2[c] + lys-L[c] 
356	DAPE	No	diaminopimelate epimerase	[c] : 26dap-LL <==> 26dap-M	Threonine and Lysine Metabolism	5.1.1.7	b3809			0	0.5	[c] : 26dap-LL[c] <==> 26dap-M[c] 
9018	DAPtex	Yes	"1,5-Diaminopentane transport via diffusion (extracellular to periplasm)"	15dap[e] <==> 15dap[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : 15dap[e] <==> 15dap[p] 
19335	DASYN120	Yes	CDP-diacylglycerol synthetase (n-C12:0)	[c] : ctp + h + pa120 --> cdpdddecg + ppi	Glycerophospholipid Metabolism	2.7.7.41	b0175	"AMF
not sure of reversibility"	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.92466	3.75933	[c] : ctp[c] + pa120[c] --> cdpdddecg[c] + ppi[c] 
19248	DASYN140	Yes	CDP-diacylglycerol synthetase (n-C14:0)	[c] : ctp + h + pa140 --> cdpdtdecg + ppi	Glycerophospholipid Metabolism	2.7.7.41	b0175	"AMF
not sure of reversibility"	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.92466	3.75933	[c] : ctp[c] + pa140[c] --> cdpdtdecg[c] + ppi[c] 
19251	DASYN141	Yes	CDP-diacylglycerol synthetase (n-C14:1)	[c] : ctp + h + pa141 --> cdpdtdec7eg + ppi	Glycerophospholipid Metabolism	2.7.7.41	b0175	"AMF
not sure of reversibility"	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.92466	3.75933	[c] : ctp[c] + pa141[c] --> cdpdtdec7eg[c] + ppi[c] 
19249	DASYN160	Yes	CDP-diacylglycerol synthetase (n-C16:0)	[c] : ctp + h + pa160 --> cdpdhdecg + ppi	Glycerophospholipid Metabolism	2.7.7.41	b0175	"AMF
not sure of reversibility"	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.92466	3.75933	[c] : ctp[c] + pa160[c] --> cdpdhdecg[c] + ppi[c] 
19252	DASYN161	Yes	CDP-diacylglycerol synthetase (n-C16:1)	[c] : ctp + h + pa161 --> cdpdhdec9eg + ppi	Glycerophospholipid Metabolism	2.7.7.41	b0175	"AMF
not sure of reversibility"	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.92466	3.75933	[c] : ctp[c] + pa161[c] --> cdpdhdec9eg[c] + ppi[c] 
19250	DASYN180	Yes	CDP-diacylglycerol synthetase (n-C18:0)	[c] : ctp + h + pa180 --> cdpdodecg + ppi	Glycerophospholipid Metabolism	2.7.7.41	b0175	"AMF
not sure of reversibility"	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.92466	3.75933	[c] : ctp[c] + pa180[c] --> cdpdodecg[c] + ppi[c] 
19253	DASYN181	Yes	CDP-diacylglycerol synthetase (n-C18:1)	[c] : ctp + h + pa181 --> cdpdodec11eg + ppi	Glycerophospholipid Metabolism	2.7.7.41	b0175	"AMF
not sure of reversibility"	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-1.92466	3.75933	[c] : ctp[c] + pa181[c] --> cdpdodec11eg[c] + ppi[c] 		
10776	DATPHs	Yes	dATP spontanous amine hydrolysis	[c] : datp + h + h2o --> ditp + nh4	Update			MKA - spontanous reaction in aerobic environment	"PMID: 12297000
The mutation protection mechanisms are caused by the incorporation into DNA of unwelcome nucleotides that are formed spontaneously.
AMF
atphs reaction not mentioned specifically, but seems logical"	-5.6874	4.84135	[c] : datp[c] + h[c] + h2o[c] --> ditp[c] + nh4[c] 		
118	DB4PS	No	"3,4-Dihydroxy-2-butanone-4-phosphate synthase"	[c] : ru5p-D --> db4p + for + h	Cofactor and Prosthetic Group Biosynthesis		b3041	"No EC number: ribA in B. subtilis catalyzes two reactions (GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthase)"		-21.1602	2.39549	[c] : ru5p-D[c] --> db4p[c] + for[c] + h[c] 		
3529	DBTS	Yes	dethiobiotin synthase	[c] : atp + co2 + dann --> adp + dtbt + (3) h + pi	Cofactor and Prosthetic Group Biosynthesis	6.3.3.3	b0778		"NH irreversible pg 705
JLR
AMF"	-16.1275	8.06832	[c] : atp[c] + co2[c] + dann[c] --> adp[c] + dtbt[c] + (3) h[c] + pi[c] 		
9059	DCAtex	Yes	Decanoate transport via diffusion (extracellular to periplasm)	dca[e] <==> dca[p]	"Transport, Outer Membrane"				"assumed passive diffusion through the outer peptidoglycan layer

can also pass through FadL"	0	0	[c] : dca[e] <==> dca[p] 		
12305	DCMPtex	Yes	dCMP transport via diffusion (extracellular to periplasm)	dcmp[e] <==> dcmp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : dcmp[e] <==> dcmp[p] 		
3531	DCTPD	No	dCTP deaminase	[c] : dctp + h + h2o --> dutp + nh4	Nucleotide Salvage Pathway	3.5.4.13	b2065	tv		-5.6874	4.84135	[c] : dctp[c] + h[c] + h2o[c] --> dutp[c] + nh4[c] 		
3528	DCYTD	No	deoxycytidine deaminase	[c] : dcyt + h + h2o --> duri + nh4	Nucleotide Salvage Pathway	3.5.4.14	b2143			-5.6874	4.84135	[c] : dcyt[c] + h[c] + h2o[c] --> duri[c] + nh4[c] 		
8814	DCYTt2pp	Yes	deoxycytidine transport in via proton symport (periplasm)	dcyt[p] + h[p] --> dcyt[c] + h[c]	"Transport, Inner Membrane"		( b2393  or  b2964 )			0	0	[c] : dcyt[p] + h[p] --> dcyt[c] + h[c] 		
9060	DCYTtex	Yes	deoxycytidine transport via diffusion (extracellular to periplasm)	dcyt[e] <==> dcyt[p]	"Transport, Outer Membrane"		b0411		"assumed passive diffusion through the outer peptidoglycan layer

Tsx is responsible for the permeation of ribo- and deoxy-nucleosides, across the outer membrane of E. coli"	0	0	[c] : dcyt[e] <==> dcyt[p] 		
9239	DDCAtexi	Yes	Fatty acid (dodecanoate) transport via facilitated irreversible diffusion (extracellular to periplasm)	ddca[e] --> ddca[p]	"Transport, Outer Membrane"		b2344		"Transport of C12 - C18 fatty acids are facilitated by the outer membrane FadL protein (PMID: 103228825), inner membrane transport and subsequently outer membrane can require FACOAL enzyme (PMID: 15067008)

smaller FA can also pass through, C6 - C11, but can also diffuse, so they weren't associated"	0	0	[c] : ddca[e] --> ddca[p] 		
3232	DDGALK	No	2-dehydro-3-deoxygalactonokinase	[c] : 2dh3dgal + atp --> 2dh3dgal6p + adp + h	Alternate Carbon Metabolism	2.7.1.58	b3693	JLR		-4.65732	2.09859	[c] : 2dh3dgal[c] + atp[c] --> 2dh3dgal6p[c] + adp[c] 		
8815	DDGLCNt2rpp	Yes	"2-dehydro-3-deoxy-D-gluconate transport via proton symport, reversible (periplasm)"	2ddglcn[p] + h[p] <==> 2ddglcn[c] + h[c]	"Transport, Inner Membrane"		b3909	JLR		0	0	[c] : 2ddglcn[p] + h[p] <==> 2ddglcn[c] + h[c] 		
9023	DDGLCNtex	Yes	2-dehydro-3-deoxy-D-gluconate transport via diffusion (extracellular to periplasm)	2ddglcn[e] <==> 2ddglcn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : 2ddglcn[e] <==> 2ddglcn[p] 		
238	DDGLK	No	2-dehydro-3-deoxygluconokinase	[c] : 2ddglcn + atp --> 2ddg6p + adp + h	Alternate Carbon Metabolism	2.7.1.45	b3526			-4.65732	2.09859	[c] : 2ddglcn[c] + atp[c] --> 2ddg6p[c] + adp[c] 		
3851	DDPA	No	3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase	[c] : e4p + h2o + pep --> 2dda7p + pi	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.1.2.15	( b2601  or  b0754  or  b1704 )			-15.4498	3.93876	[c] : e4p[c] + h2o[c] + pep[c] --> 2dda7p[c] + h[c] + pi[c] 		
2502	DDPGALA	No	2-dehydro-3-deoxy-6-phosphogalactonate aldolase	[c] : 2dh3dgal6p <==> g3p + pyr	Alternate Carbon Metabolism	4.1.2.21	b4477	JLR		2.91741	2.32549	[c] : 2dh3dgal6p[c] <==> g3p[c] + pyr[c] 		
2814	DGK1	No	deoxyguanylate kinase (dGMP:ATP)	[c] : atp + dgmp <==> adp + dgdp	Nucleotide Salvage Pathway	2.7.4.8	b3648	Added EC- JLR		0	0.5	[c] : atp[c] + dgmp[c] <==> adp[c] + dgdp[c] 		
12306	DGMPtex	Yes	dGMP transport via diffusion (extracellular to periplasm)	dgmp[e] <==> dgmp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : dgmp[e] <==> dgmp[p] 		
8816	DGSNt2pp	Yes	deoxyguanosine transport in via proton symport (periplasm)	dgsn[p] + h[p] --> dgsn[c] + h[c]	"Transport, Inner Membrane"		b2964			0	0	[c] : dgsn[p] + h[p] --> dgsn[c] + h[c] 		
9062	DGSNtex	Yes	deoxyguanosine transport via diffusion (extracellular to periplasm)	dgsn[e] <==> dgsn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : dgsn[e] <==> dgsn[p] 		
321	DHAD1	No	"dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate)"	[c] : 23dhmb --> 3mob + h2o	"Valine, Leucine, and Isoleucine Metabolism"	4.2.1.9	b3771			-8.04444	3.19069	[c] : 23dhmb[c] --> 3mob[c] + h2o[c] 		
1019	DHAD2	No	"Dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate)"	[c] : 23dhmp --> 3mop + h2o	"Valine, Leucine, and Isoleucine Metabolism"		b3771			-8.04444	3.19069	[c] : 23dhmp[c] --> 3mop[c] + h2o[c] 		
3274	DHAPT	No	Dihydroxyacetone phosphotransferase	[c] : dha + pep --> dhap + pyr	Alternate Carbon Metabolism		( b1200  and  b1199  and  b1198  and  b2415  and  b2416 )	JLR	"JLR- dhaK1 = dhaK, dhaK2= dhaL, dhaH = dhaM.  All three and EI and Hpr are also required."	-10.1729	3.20748	[c] : dha[c] + pep[c] --> dhap[c] + pyr[c] 		
9063	DHAtex	Yes	Dihydroxyacetone transport via diffusion (extracellular to periplasm)	dha[e] <==> dha[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : dha[e] <==> dha[p] 		
8980	DHAtpp	Yes	Dihydroxyacetone transport via facilitated diffusion (periplasm)	dha[p] <==> dha[c]	"Transport, Inner Membrane"			JLR	JLR- thought to be transported via glycerol transporter (glpF)	0	0	[c] : dha[p] <==> dha[c] 		
43	DHBD	No	"2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase"	[c] : 23ddhb + nad <==> 23dhb + h + nadh	Cofactor and Prosthetic Group Biosynthesis	1.3.1.28	b0596			-4.66513	14.9119	[c] : 23ddhb[c] + nad[c] <==> 23dhb[c] + h[c] + nadh[c] 		
13598	DHBS	Yes	"2,3-dihydroxybenzoate adenylate synthase"	[c] : 23dhb + atp + h --> 23dhba + ppi	Update	2.7.7.58	b0594	"AMF
"	"EntE may be part of larger protein complex w/ EntB, D, F to generate enterobactin (enterochelin)    MKA

http://biocyc.org/ECOLI/new-image?type=PATHWAY&object=ENTBACSYN-PWY
AMF"	-2.0592	2.82385	[c] : 23dhb[c] + atp[c] + h[c] --> 23dhba[c] + ppi[c] 		
13696	DHBSH	Yes	"2,3-dihydroxybenzoylserine hydrolase"	[c] : 23dhbzs + h2o --> 23dhb + ser-L	Update			"AMF
not sure of the reaction name, taken from opposite reaction of 2,3-dihydroxybenzoate-serine ligase"	"reaction needed to degrade 23dhbzs from fes gene product, took as the reverse of the 2,3-dihydroxybenzoate-serine ligase reaction.

REaction is speculative based on the function of fes

AMF
"	-3.36489	3.34628	[c] : 23dhbzs[c] + h2o[c] --> 23dhb[c] + ser-L[c] 		
2295	DHCIND	No	"2,3-dihydroxycinnamate dehydrogenase"	[c] : cenchddd + nad --> dhcinnm + h + nadh	Alternate Carbon Metabolism		b2541	JLR - see PMID:9603882		-4.66513	14.9119	[c] : cenchddd[c] + nad[c] --> dhcinnm[c] + h[c] + nadh[c] 		
7713	DHCINDO	No	"2,3-dihydroxycinnamate 1,2-dioxygenase"	[c] : dhcinnm + o2 --> h + hkntd	Alternate Carbon Metabolism		b0348	JLR- see PMID: 9603882		-69.9514	13.2166	[c] : dhcinnm[c] + o2[c] --> h[c] + hkntd[c] 		
358	DHDPRy	No	dihydrodipicolinate reductase (NADPH)	[c] : 23dhdp + h + nadph --> nadp + thdp	Threonine and Lysine Metabolism	1.3.1.26	b0031			0.110207	4.03611	[c] : 23dhdp[c] + h[c] + nadph[c] --> nadp[c] + thdp[c] 		
3532	DHDPS	No	dihydrodipicolinate synthase	[c] : aspsa + pyr --> 23dhdp + h + (2) h2o	Threonine and Lysine Metabolism	4.2.1.52	b2478			-23.3594	5.43711	[c] : aspsa[c] + pyr[c] --> 23dhdp[c] + h[c] + (2) h2o[c] 		
77	DHFR	No	dihydrofolate reductase	[c] : dhf + h + nadph <==> nadp + thf	Cofactor and Prosthetic Group Biosynthesis	1.5.1.3	( b0048  or  b1606 )	"The enzyme from animals and some micro-organisms also slowly reduces folate to 5,6,7,8-tetrahydrofolate"	"see PMID: 14617668 for FolM
AMF"	-4.33225	5.70603	[c] : dhf[c] + h[c] + nadph[c] <==> nadp[c] + thf[c] 		
7825	DHFS	No	dihydrofolate synthase	[c] : atp + dhpt + glu-L --> adp + dhf + h + pi	Cofactor and Prosthetic Group Biosynthesis	6.3.2.12	b2315			-3.65185	3.59073	[c] : atp[c] + dhpt[c] + glu-L[c] --> adp[c] + dhf[c] + h[c] + pi[c] 		
3449	DHNAOT	No	"1,4-dihydroxy-2-naphthoate octaprenyltransferase"	[c] : dhna + octdp --> 2dmmq8 + co2 + h + ppi	Cofactor and Prosthetic Group Biosynthesis		b3930	"EC 2.5.1-; menA
Reaction is uncharged the loss of 2H (conversion from quinol to quinone form is thought to be spontaneous)."		-18.1545	15.0982	[c] : dhna[c] + octdp[c] --> 2dmmq8[c] + co2[c] + h[c] + ppi[c] 		
1833	DHNPA2	No	dihydroneopterin aldolase	[c] : dhnpt --> 6hmhpt + gcald	Cofactor and Prosthetic Group Biosynthesis		b3058	JLR- similar to DHNPA except the 'pterin product is different	"JLR- had to add 6hmhpt to database, different then 2ahhmp (ketone vs. OH).  "	4.43267	3.73524	[c] : dhnpt[c] --> 6hmhpt[c] + gcald[c] 		
1079	DHORD2	No	dihydoorotic acid dehydrogenase (quinone8)	[c] : dhor-S + q8 --> orot + q8h2	Purine and Pyrimidine Biosynthesis	1.3.3.1	b0945	JLR		-16.2252	20.9305	[c] : dhor-S[c] + q8[c] --> orot[c] + q8h2[c] 		
1977	DHORD5	No	dihydroorotic acid (menaquinone-8)	[c] : dhor-S + mqn8 --> mql8 + orot	Purine and Pyrimidine Biosynthesis	1.3.3.1	b0945	JLR		-14.7733	17.0945	[c] : dhor-S[c] + mqn8[c] --> mql8[c] + orot[c] 		
444	DHORTS	No	dihydroorotase	[c] : dhor-S + h2o <==> cbasp + h	Purine and Pyrimidine Biosynthesis	3.5.2.3	b1062			-5.58628	6.91384	[c] : dhor-S[c] + h2o[c] <==> cbasp[c] + h[c] 		
2294	DHPPD	No	"2,3-dihydroxyphenylpropionate dehydrogenase"	[c] : cechddd + nad --> dhpppn + h + nadh	Alternate Carbon Metabolism		b2541	JLR -see PMID 9603882		-4.66513	14.9119	[c] : cechddd[c] + nad[c] --> dhpppn[c] + h[c] + nadh[c] 		
3634	DHPPDA2	No	diaminohydroxyphosphoribosylaminopryrimidine deaminase (25drapp)	[c] : 25drapp + h + h2o --> 5apru + nh4	Cofactor and Prosthetic Group Biosynthesis	3.5.4.26	b0414	"Riboflavin-specific deaminase
AR"	JLR- added reaction and 25drapp to the database 25drapp is not the same as 25dhpp (check LIGAND and NH page 658)	-18.3419	9.15317	[c] : 25drapp[c] + h[c] + h2o[c] --> 5apru[c] + nh4[c] 		
7823	DHPS2	No	dihydropteroate synthase	[c] : 4abz + 6hmhptpp --> dhpt + ppi	Cofactor and Prosthetic Group Biosynthesis	2.5.1.15	b3177	JLR- similar to DHPS except uses 6hmhptpp (has ketone rather than OH)		-9.24673	3.24577	[c] : 4abz[c] + 6hmhptpp[c] --> dhpt[c] + ppi[c] 		
2826	DHPTDCs	Yes	"4,5-dihydroxy-2,3-pentanedione cyclization (spontaneous)"	[c] : dhptd --> h2o + hmfurn	Methionine Metabolism			JLR	JLR- it is believed that hmfurn is linked to AI-2 an extracellular signaling molecule	2.08811	6.80038	[c] : dhptd[c] --> h[c] + h2o[c] + hmfurn[c] 		
13773	DHPTPE	Yes	dihydroneopterin triphosphate 2'-epimerase	[c] : ahdt <==> dhmptp	Update		b2303	AMF	"chacetrized in PMID: 9006053
AMF"	0	0.5	[c] : ahdt[c] <==> dhmptp[c] 		
327	DHQD	No	3-dehydroquinate dehydratase	[c] : 3dhq <==> 3dhsk + h2o	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.2.1.10	b1693			-8.68232	3.99177	[c] : 3dhq[c] <==> 3dhsk[c] + h2o[c] 		
2859	DHQS	No	3-dehydroquinate synthase	[c] : 2dda7p --> 3dhq + pi	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"		b3389	"Previously EC 4.6.1.3. now EC 4.2.3.4, 3-dehydroquinate synthase
"		-13.7145	6.95117	[c] : 2dda7p[c] --> 3dhq[c] + h[c] + pi[c] 		
12356	DIMPtex	Yes	dIMP transport via diffusion (extracellular to periplasm)	dimp[e] <==> dimp[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : dimp[e] <==> dimp[p] 		
8817	DINSt2pp	Yes	deoxyinosine transport in via proton symport (periplasm)	din[p] + h[p] --> din[c] + h[c]	"Transport, Inner Membrane"		b2964			0	0	[c] : din[p] + h[p] --> din[c] + h[c] 					
9064	DINStex	Yes	deoxyinosine transport via diffusion (extracellular to periplasm)	din[e] <==> din[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : din[e] <==> din[p] 					
2905	DKGLCNR1	No	"2,5-diketo-D-gluconate reductase"	[c] : 25dkglcn + h + nadph --> 2dhguln + nadp	Alternate Carbon Metabolism		( b0207  or  b3012 )	JLR	"PMID: 10427017 proves YqhE function
PMID: 11934293 shows that it has additional function on ethyl 2-methylacetoacetate compounds, but cant find a physilogical location for the metabolites
"	-4.73639	4.5435	[c] : 25dkglcn[c] + h[c] + nadph[c] --> 2dhguln[c] + nadp[c] 					
2149	DKGLCNR2x	No	"2,5-diketo-D-gluconate reductase (NADH)"	[c] : 25dkglcn + h + nadh --> 5dglcn + nad	Alternate Carbon Metabolism		b3553	JLR	JLR- Ref says that nadph is preferred	-4.73639	4.5435	[c] : 25dkglcn[c] + h[c] + nadh[c] --> 5dglcn[c] + nad[c] 					
2147	DKGLCNR2y	No	"2,5-diketo-D-gluconate reductase (NADPH)"	[c] : 25dkglcn + h + nadph --> 5dglcn + nadp	Alternate Carbon Metabolism		b3553	JLR		-4.73639	4.5435	[c] : 25dkglcn[c] + h[c] + nadph[c] --> 5dglcn[c] + nadp[c] 					
1631	DKMPPD	No	"2,3-diketo-5-methylthio-1-phosphopentane degradation reaction"	[c] : dkmpp + h2o + o2 --> 2kmb + for + (2) h + pi	Arginine and Proline Metabolism			JLR- based on B. subtilis and K. pneumoniae reactions (not sure about the h2o and h)	JLR-based on B.subtilis paper  needed h2o and h to balance	-121.423	2.83554	[c] : dkmpp[c] + h2o[c] + o2[c] --> 2kmb[c] + for[c] + (3) h[c] + pi[c] 					
1984	DKMPPD2	No	"2,3-diketo-5-methylthio-1-phosphopentane degradation reaction"	[c] : dkmpp + (3) h2o --> 2kmb + for + (6) h + pi	Arginine and Proline Metabolism			JLR- Added H2O to left side so that oxygen requirement (as in reaction DKMPPD) isn't there	"JLR- this not a real reaction had to add h2o so that the reaction didn't require oxygen, see DKMPPD reaction."	-46.2228	4.44863	[c] : dkmpp[c] + (3) h2o[c] --> 2kmb[c] + for[c] + (7) h[c] + pi[c] 					
8818	D-LACt2pp	Yes	D-lactate transport via proton symport (periplasm)	h[p] + lac-D[p] <==> h[c] + lac-D[c]	"Transport, Inner Membrane"		( b3603  or  b2975 )	JLR		0	0	[c] : h[p] + lac-D[p] <==> h[c] + lac-D[c] 					
9161	D-LACtex	Yes	D-lactate transport via diffusion (extracellular to periplasm)	lac-D[e] <==> lac-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : lac-D[e] <==> lac-D[p] 					
108	DMATT	No	dimethylallyltranstransferase	[c] : dmpp + ipdp --> grdp + ppi	Cofactor and Prosthetic Group Biosynthesis	2.5.1.1	b0421			-14.4146	2.92602	[c] : dmpp[c] + ipdp[c] --> grdp[c] + ppi[c] 					
3440	DMPPS	No	1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (dmpp)	[c] : h + h2mb4p + nadh --> dmpp + h2o + nad	Cofactor and Prosthetic Group Biosynthesis		b0029	JLR- unsure about cofactor stoichiometry	"JLR- these reactions are not biochemically verified, the cofactors required are unknown"	-15.8358	4.35212	[c] : h[c] + h2mb4p[c] + nadh[c] --> dmpp[c] + h2o[c] + nad[c] 					
1350	DMQMT	No	3-Dimethylubiquinonol 3-methyltransferase	[c] : 2omhmbl + amet --> ahcys + h + q8h2	Cofactor and Prosthetic Group Biosynthesis		b2232	JLR		No energy	No energy	[c] : 2omhmbl[c] + amet[c] --> ahcys[c] + h[c] + q8h2[c] 					
2144	DMSOR1	No	Dimethyl sulfoxide reductase (Menaquinol 8)	[c] : dmso + mql8 --> dms + h2o + mqn8	Oxidative Phosphorylation		( ( b0894  and  b0895  and  b0896 )  or  ( b1587  and  b1588  and  b1589  and  b1590 ) )	JLR	"Note that chimeric enzymes such as dmsA-ynfGH can also work (see ref for complete listing-- AGH,ABH,FGC)."	No energy	No energy	[c] : dmso[c] + mql8[c] --> dms[c] + h2o[c] + mqn8[c] 					
8981	DMSOR1pp	Yes	Dimethyl sulfoxide reductase (Menaquinol 8) (periplasm)	dmso[p] + mql8[c] --> dms[p] + h2o[p] + mqn8[c]	Oxidative Phosphorylation		( b1873  and  b1872 )	JLR	assumed torZ uses same quinones as torA	No energy	No energy	[c] : dmso[p] + mql8[c] --> dms[p] + h2o[p] + mqn8[c] 					
2904	DMSOR2	No	Dimethyl sulfoxide reductase (Demethylmenaquinol 8)	[c] : 2dmmql8 + dmso --> 2dmmq8 + dms + h2o	Oxidative Phosphorylation		( b0894  and  b0895  and  b0896 )	JLR		No energy	No energy	[c] : 2dmmql8[c] + dmso[c] --> 2dmmq8[c] + dms[c] + h2o[c] 					
8982	DMSOR2pp	Yes	Dimethyl sulfoxide reductase (Demethylmenaquinol 8) (periplasm)	2dmmql8[c] + dmso[p] --> 2dmmq8[c] + dms[p] + h2o[p]	Oxidative Phosphorylation		( b1873  and  b1872 )	JLR	assumed torZ uses same quinones as torA	No energy	No energy	[c] : 2dmmql8[c] + dmso[p] --> 2dmmq8[c] + dms[p] + h2o[p] 					
9066	DMSOtex	Yes	Dimethyl sulfoxide transport via diffusion (extracellular to periplasm)	dmso[e] <==> dmso[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : dmso[e] <==> dmso[p] 					
9065	DMStex	Yes	Dimethyl sulfide transport via diffusion (extracellular to periplasm)	dms[e] <==> dms[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : dms[e] <==> dms[p] 					
1832	DNMPPA	No	Dihydroneopterin monophosphate dephosphorylase	[c] : dhpmp + h2o --> dhnpt + pi	Cofactor and Prosthetic Group Biosynthesis			JLR- Neidhardt page 667		-2.35942	1.9257	[c] : dhpmp[c] + h2o[c] --> dhnpt[c] + h[c] + pi[c] 					
1831	DNTPPA	No	Dihydroneopterin triphosphate pyrophosphatase	[c] : ahdt + h2o --> dhpmp + h + ppi	Cofactor and Prosthetic Group Biosynthesis		( b1865  or  b0099 )	JLR- Neidhardt pg 667		-8.59346	2.5066	[c] : ahdt[c] + h2o[c] --> dhpmp[c] + ppi[c] 					
2505	DOGULNR	No	"2,3 dioxo-L-gulonate reductase"	[c] : 23doguln + h + nadh --> 3dhguln + nad	Alternate Carbon Metabolism		b3575	JLR	"AMF
"	-4.73639	4.5435	[c] : 23doguln[c] + h[c] + nadh[c] --> 3dhguln[c] + nad[c] 					
12242	DOPAtex	Yes	dopamine transport via diffusion (extracellular to periplasm)	dopa[e] <==> dopa[p]	"Transport, Outer Membrane"				"PMID: 3309152 original paper source
PMID: 11729263 - review where it states that that tyroxdapp and 42a12booxpp are confirmed susbstrates and can be used in K-12 for nitrogen source only, not sure if they are transported inside the cell or not or if they can't be processed after transport"	0	0	[c] : dopa[e] <==> dopa[p] 					
2790	DPCOAK	No	dephospho-CoA kinase	[c] : atp + dpcoa --> adp + coa + h	Cofactor and Prosthetic Group Biosynthesis	2.7.1.24	b0103		"PMID: 11292795 characterizes the gene
AMF
"	-3.46855	2.28701	[c] : atp[c] + dpcoa[c] --> adp[c] + coa[c] 					
81	DPR	No	2-dehydropantoate 2-reductase	[c] : 2dhp + h + nadph --> nadp + pant-R	Cofactor and Prosthetic Group Biosynthesis	1.1.1.169	( b0425  or  b3774 )			-4.73639	4.5435	[c] : 2dhp[c] + h[c] + nadph[c] --> nadp[c] + pant-R[c] 					
4640	DRPA	No	deoxyribose-phosphate aldolase	[c] : 2dr5p --> acald + g3p	Alternate Carbon Metabolism	4.1.2.4	b4381			1.83247	6.2528	[c] : 2dr5p[c] --> acald[c] + g3p[c] 					
19633	DSBAO1	Yes	DsbA protein reoxidation reaction (aerobic)	dsbard[p] + q8[c] --> dsbaox[p] + q8h2[c]	Update		b1185	"see PMID: 16040611
AMF"	"DsbA acts on proteins, DsbB acts on DsbA
a figure is in PMID: 16040611
AMF"	No energy	No energy	[c] : dsbard[p] + q8[c] --> dsbaox[p] + q8h2[c] 					
19634	DSBAO2	Yes	DsbA protein reoxidation reaction (anaerobic)	dsbard[p] + mqn8[c] --> dsbaox[p] + mql8[c]	Update		b1185	"see PMID: 16040611
AMF"	"DsbA acts on proteins, DsbB acts on DsbA
a figure is in PMID: 16040611
AMF"	No energy	No energy	[c] : dsbard[p] + mqn8[c] --> dsbaox[p] + mql8[c] 					
19638	DSBCGT	Yes	DsbC:glutathione thiotransferase	[p] : dsbcox + (2) gthrd --> dsbcrd + gthox	Update		b2893	"see PMID: 16040611
AMF"	"PMID: 16040611
AMF"	No energy	No energy	[p] : dsbcox[p] + (2) gthrd[p] --> dsbcrd[p] + gthox[p] 					
19635	DSBDR	Yes	DsbD reductase	[c] : dsbdox + trdrd --> dsbdrd + trdox	Update		b4136	"see PMID: 16040611
AMF"	"Transfer of protons from thirodoxin protein to DsbD
see PMID: 16040611
AMF"	No energy	No energy	[c] : dsbdox[c] + trdrd[c] --> dsbdrd[c] + trdox[c] 					
19639	DSBGGT	Yes	DsbG:glutathione thiotransferase	[p] : dsbgox + (2) gthrd --> dsbgrd + gthox	Update		b0604	"see PMID: 16040611
AMF"	"PMID: 16040611
AMF"	No energy	No energy	[p] : dsbgox[p] + (2) gthrd[p] --> dsbgrd[p] + gthox[p] 					
13925	DSERDHr	Yes	D-serine dehydrogenase	[c] : nadp + ser-D <==> 2amsa + h + nadph	Update		b1539	"AMF
PMID: 12535615
EC 1.1.1.276"	"reaction is characterized in PMID: 12535615

to act on L and D-serine, L-allo-threonine, D-threonine, and hydroxyisobutyrate

reaversibility is not for sure know, but hints that it may be"	5.16584	4.34649	[c] : nadp[c] + ser-D[c] <==> 2amsa[c] + h[c] + nadph[c] 					
8819	DSERt2rpp	Yes	D-serine transport via proton symport (periplasm)	h[p] + ser-D[p] <==> h[c] + ser-D[c]	"Transport, Inner Membrane"		b4208	JLR	"CycA mediates the uptake of L-alanine, D-alanine, glycine, D-serine, and Dcycloserine (Wargel et al. 1970; Cosloy 1973).....utilize H+ co-transport as the energy source (Swiss-Prot data base; http://www.expasy.org/sprot;
accession no. P39312). Together with fklB, cycA is thought to form the fklB-cycA operon, whose expression is regulated by the nitrogen assimilation control (Nac) protein
PMID: 15221223
AMF"	0	0	[c] : h[p] + ser-D[p] <==> h[c] + ser-D[c] 					
9200	DSERtex	Yes	D-serine transport via diffusion (extracellular to periplasm)	ser-D[e] <==> ser-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ser-D[e] <==> ser-D[p] 		
13938	DTHRDHr	Yes	D-threonine dehydrogenase	[c] : nadp + thr-D <==> 2aobut + h + nadph	Update		b1539	"AMF
PMID: 12535615"	"reaction is characterized in PMID: 12535615

to act on L and D-serine, L-allo-threonine, D-threonine, and hydroxyisobutyrate

reaversibility is not for sure know, but hints that it may be"	4.73639	4.5435	[c] : nadp[c] + thr-D[c] <==> 2aobut[c] + h[c] + nadph[c] 		
2815	DTMPK	No	dTMP kinase	[c] : atp + dtmp <==> adp + dtdp	Nucleotide Salvage Pathway	2.7.4.9	b1098			0	0.5	[c] : atp[c] + dtmp[c] <==> adp[c] + dtdp[c] 		
12307	DTMPtex	Yes	dTMP transport via diffusion (extracellular to periplasm)	dtmp[e] <==> dtmp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : dtmp[e] <==> dtmp[p] 		
12308	DUMPtex	Yes	dUMP transport via diffusion (extracellular to periplasm)	dump[e] <==> dump[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : dump[e] <==> dump[p] 		
2691	DURIK1	No	deoxyuridine kinase (ATP:Deoxyuridine)	[c] : atp + duri --> adp + dump + h	Nucleotide Salvage Pathway		b1238			-4.65732	2.09859	[c] : atp[c] + duri[c] --> adp[c] + dump[c] 		
1084	DURIPP	No	deoxyuridine phosphorylase	[c] : duri + pi <==> 2dr1p + ura	Nucleotide Salvage Pathway		( b4382  or  b4384 )	JLR 		1.28439	3.76698	[c] : duri[c] + h[c] + pi[c] <==> 2dr1p[c] + ura[c] 		
8820	DURIt2pp	Yes	deoxyuridine transport in via proton symport (periplasm)	duri[p] + h[p] --> duri[c] + h[c]	"Transport, Inner Membrane"		( b2393  or  b2964 )			0	0	[c] : duri[p] + h[p] --> duri[c] + h[c] 		
9067	DURItex	Yes	deoxyuridine transport via diffusion (extracellular to periplasm)	duri[e] <==> duri[p]	"Transport, Outer Membrane"		b0411		"assumed passive diffusion through the outer peptidoglycan layer

Tsx is responsible for the permeation of ribo- and deoxy-nucleosides, across the outer membrane of E. coli"	0	0	[c] : duri[e] <==> duri[p] 		
189	DUTPDP	No	dUTP diphosphatase	[c] : dutp + h2o --> dump + h + ppi	Nucleotide Salvage Pathway	3.6.1.23	b3640			-8.59346	2.5066	[c] : dutp[c] + h2o[c] --> dump[c] + ppi[c] 		
1577	DXPRIi	No	1-deoxy-D-xylulose reductoisomerase	[c] : dxyl5p + h + nadph --> 2me4p + nadp	Cofactor and Prosthetic Group Biosynthesis		b0173	JLR- added irreversible form of DXPRI.  EC 1.1.1.267	"The reaction is reversible in vitro, but in vivo the reaction is driven unidirectionally by equilibrium

PMID: 12230556
AMF

so, by reading the statement above, one could make the arguement for reversible, but by the next consecutive reation is irreversbile anyway is the only reaction that uses the product

"	-4.28413	5.39334	[c] : dxyl5p[c] + h[c] + nadph[c] --> 2me4p[c] + nadp[c] 		
234	DXPS	No	1-deoxy-D-xylulose 5-phosphate synthase	[c] : g3p + h + pyr --> co2 + dxyl5p	Cofactor and Prosthetic Group Biosynthesis		b0420	"EC 4.1.3.37 transferred to:
EC 2.2.1.7
NJ"		-7.40877	2.3118	[c] : g3p[c] + h[c] + pyr[c] --> co2[c] + dxyl5p[c] 		
3200	DXYLK	No	1-Deoxy-D-xylulose kinase	[c] : atp + dxyl --> adp + dxyl5p + h	Cofactor and Prosthetic Group Biosynthesis		b3564	JLR		-4.04488	6.21545	[c] : atp[c] + dxyl[c] --> adp[c] + dxyl5p[c] 		
1722	E4PD	No	Erythrose 4-phosphate dehydrogenase	[c] : e4p + h2o + nad <==> 4per + (2) h + nadh	Cofactor and Prosthetic Group Biosynthesis		b2927	JLR- Reaction from KEGG R01825		-9.85991	4.39284	[c] : e4p[c] + h2o[c] + nad[c] <==> 4per[c] + (2) h[c] + nadh[c] 		
19188	EAR100x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C10:0)	[c] : h + nadh + tdec2eACP --> dcaACP + nad	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-14.5994	4.65656	[c] : h[c] + nadh[c] + tdec2eACP[c] --> dcaACP[c] + nad[c] 		
19202	EAR100y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C10:0)	[c] : h + nadph + tdec2eACP --> dcaACP + nadp	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadph[c] + tdec2eACP[c] --> dcaACP[c] + nadp[c] 		
19189	EAR120x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:0)	[c] : h + nadh + tddec2eACP --> ddcaACP + nad	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadh[c] + tddec2eACP[c] --> ddcaACP[c] + nad[c] 		
19201	EAR120y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:0)	[c] : h + nadph + tddec2eACP --> ddcaACP + nadp	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadph[c] + tddec2eACP[c] --> ddcaACP[c] + nadp[c] 		
19216	EAR121x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:1)	[c] : h + nadh + t3c5ddeceACP --> cddec5eACP + nad	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-14.5994	4.65656	[c] : h[c] + nadh[c] + t3c5ddeceACP[c] --> cddec5eACP[c] + nad[c] 		
19217	EAR121y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:1)	[c] : h + nadph + t3c5ddeceACP --> cddec5eACP + nadp	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-14.5994	4.65656	[c] : h[c] + nadph[c] + t3c5ddeceACP[c] --> cddec5eACP[c] + nadp[c] 		
19190	EAR140x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C14:0)	[c] : h + nadh + tmrs2eACP --> myrsACP + nad	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadh[c] + tmrs2eACP[c] --> myrsACP[c] + nad[c] 		
19200	EAR140y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:0)	[c] : h + nadph + tmrs2eACP --> myrsACP + nadp	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadph[c] + tmrs2eACP[c] --> myrsACP[c] + nadp[c] 		
19225	EAR141x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C14:1)	[c] : h + nadh + t3c7mrseACP --> nad + tdeACP	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-16.193	5.778	[c] : h[c] + nadh[c] + t3c7mrseACP[c] --> nad[c] + tdeACP[c] 		
19226	EAR141y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:1)	[c] : h + nadph + t3c7mrseACP --> nadp + tdeACP	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-16.193	5.778	[c] : h[c] + nadph[c] + t3c7mrseACP[c] --> nadp[c] + tdeACP[c] 		
19191	EAR160x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:0)	[c] : h + nadh + tpalm2eACP --> nad + palmACP	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadh[c] + tpalm2eACP[c] --> nad[c] + palmACP[c] 		
19199	EAR160y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:0)	[c] : h + nadph + tpalm2eACP --> nadp + palmACP	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadph[c] + tpalm2eACP[c] --> nadp[c] + palmACP[c] 		
19228	EAR161x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:1)	[c] : h + nadh + t3c9palmeACP --> hdeACP + nad	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-14.5994	4.65656	[c] : h[c] + nadh[c] + t3c9palmeACP[c] --> hdeACP[c] + nad[c] 		
19229	EAR161y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:1)	[c] : h + nadph + t3c9palmeACP --> hdeACP + nadp	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-14.5994	4.65656	[c] : h[c] + nadph[c] + t3c9palmeACP[c] --> hdeACP[c] + nadp[c] 		
19323	EAR180x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:0)	[c] : h + nadh + toctd2eACP --> nad + ocdcaACP	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-14.5994	4.65656	[c] : h[c] + nadh[c] + toctd2eACP[c] --> nad[c] + ocdcaACP[c] 		
19324	EAR180y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:0)	[c] : h + nadph + toctd2eACP --> nadp + ocdcaACP	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-14.5994	4.65656	[c] : h[c] + nadph[c] + toctd2eACP[c] --> nadp[c] + ocdcaACP[c] 		
19230	EAR181x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:1)	[c] : h + nadh + t3c11vaceACP --> nad + octeACP	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-16.193	5.778	[c] : h[c] + nadh[c] + t3c11vaceACP[c] --> nad[c] + octeACP[c] 		
19231	EAR181y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:1)	[c] : h + nadph + t3c11vaceACP --> nadp + octeACP	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698
not sure of reversibility
AMF"	-16.193	5.778	[c] : h[c] + nadph[c] + t3c11vaceACP[c] --> nadp[c] + octeACP[c] 		
19185	EAR40x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C4:0)	[c] : but2eACP + h + nadh --> butACP + nad	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : but2eACP[c] + h[c] + nadh[c] --> butACP[c] + nad[c] 					
19192	EAR40y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C4:0)	[c] : but2eACP + h + nadph --> butACP + nadp	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : but2eACP[c] + h[c] + nadph[c] --> butACP[c] + nadp[c] 					
19186	EAR60x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C6:0)	[c] : h + nadh + thex2eACP --> hexACP + nad	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadh[c] + thex2eACP[c] --> hexACP[c] + nad[c] 					
19193	EAR60y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C6:0)	[c] : h + nadph + thex2eACP --> hexACP + nadp	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadph[c] + thex2eACP[c] --> hexACP[c] + nadp[c] 					
19187	EAR80x	Yes	enoyl-[acyl-carrier-protein] reductase (NADH) (n-C8:0)	[c] : h + nadh + toct2eACP --> nad + ocACP	Cell Envelope Biosynthesis	1.3.1.9	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadh[c] + toct2eACP[c] --> nad[c] + ocACP[c] 					
19198	EAR80y	Yes	enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C8:0)	[c] : h + nadph + toct2eACP --> nadp + ocACP	Cell Envelope Biosynthesis	1.3.1.10	b1288	"AMF
not sure of reversibility"	"citation states that it is NADH dependant, mentions another NADPH enzyme but doesnt give a gene, PMID: 8119879
More recent citation shows that FabI can use NADH or NADPH, PMID: 9022698"	-14.5994	4.65656	[c] : h[c] + nadph[c] + toct2eACP[c] --> nadp[c] + ocACP[c] 					
13562	ECA4COLIPAtex	Yes	enterobacterial common antigen (x4) core oligosaccharide lipid A transport (periplasm to extracellular)	eca4colipa[p] --> eca4colipa[e]	Lipopolysaccharide Biosynthesis / Recycling			AMF	"this reaction is needed to have the LPS lipid A derivative presented to the outer membrane surface - both moved across the periplasm and flipped across the outer membrane

not sure on the method of transport

this paper talks about the possibility of the transport PMID: 15576375

AMF"	0	0	[c] : eca4colipa[p] --> eca4colipa[e] 					
13561	ECA4OALpp	Yes	enterobacterial common antigen (x4) O-antigen ligase (periplasm)	[p] : colipa + eca4und --> eca4colipa + h + udcpdp	Lipopolysaccharide Biosynthesis / Recycling		b3622	AMF	"

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108"	No energy	No energy	[p] : colipa[p] + eca4und[p] --> eca4colipa[p] + udcpdp[p] 					
13558	ECAP1pp	Yes	enterobacterial common antigen polymerase (periplasm)	[p] : (2) unagamuf --> eca2und + h + udcpdp	Lipopolysaccharide Biosynthesis / Recycling		( b3793  and  b3785 )	AMF	"characterization of WzxE gene, also talks about WzzE and WzyE function

paper states that only WzyE can transport UNAGA, others state differently
PMID: 12621029

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108"	No energy	No energy	[p] : (2) unagamuf[p] --> eca2und[p] + udcpdp[p] 					
13559	ECAP2pp	Yes	enterobacterial common antigen polymerase (periplasm)	[p] : eca2und + unagamuf --> eca3und + h + udcpdp	Lipopolysaccharide Biosynthesis / Recycling		( b3793  and  b3785 )	AMF	"characterization of WzxE gene, also talks about WzzE and WzyE function

paper states that only WzyE can transport UNAGA, others state differently
PMID: 12621029

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108"	No energy	No energy	[p] : eca2und[p] + unagamuf[p] --> eca3und[p] + udcpdp[p] 					
13560	ECAP3pp	Yes	enterobacterial common antigen polymerase (periplasm)	[p] : eca3und + unagamuf --> eca4und + h + udcpdp	Lipopolysaccharide Biosynthesis / Recycling		( b3793  and  b3785 )	AMF	"characterization of WzxE gene, also talks about WzzE and WzyE function

paper states that only WzyE can transport UNAGA, others state differently
PMID: 12621029

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108"	No energy	No energy	[p] : eca3und[p] + unagamuf[p] --> eca4und[p] + udcpdp[p] 					
13551	ECAtpp	Yes	"enterobacterial common antigen transferase (flippase, cytoplasm to periplasm)"	unagamuf[c] --> unagamuf[p]	Lipopolysaccharide Biosynthesis / Recycling		b3792	AMF	"characterization of WzxE gene, also talks about WzzE and WzyE function

paper states that only WzyE can transport UNAGA, others state differently
PMID: 12621029

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108"	0	0	[c] : unagamuf[c] --> unagamuf[p] 					
29	ECOAH1	Yes	3-hydroxyacyl-CoA dehydratase (3-hydroxybutanoyl-CoA)	[c] : 3hbcoa <==> b2coa + h2o	Membrane Lipid Metabolism	4.2.1.17	( b3846  or  b2341 )			0.278853	2.66722	[c] : 3hbcoa[c] <==> b2coa[c] + h2o[c] 					
30	ECOAH2	Yes	3-hydroxyacyl-CoA dehydratase (3-hydroxyhexanoyl-CoA)	[c] : 3hhcoa <==> h2o + hx2coa	Membrane Lipid Metabolism	4.2.1.17	( b3846  or  b2341 )			0.278853	2.66722	[c] : 3hhcoa[c] <==> h2o[c] + hx2coa[c] 					
31	ECOAH3	Yes	3-hydroxyacyl-CoA dehydratase (3-hydroxyoctanoyl-CoA)	[c] : 3hocoa <==> h2o + oc2coa	Membrane Lipid Metabolism	4.2.1.17	( b3846  or  b2341 )			0.278853	2.66722	[c] : 3hocoa[c] <==> h2o[c] + oc2coa[c] 					
404	ECOAH4	Yes	3-hydroxyacyl-CoA dehydratase (3-hydroxydecanoyl-CoA)	[c] : 3hdcoa <==> dc2coa + h2o	Membrane Lipid Metabolism	4.2.1.17	( b3846  or  b2341 )			0.278853	2.66722	[c] : 3hdcoa[c] <==> dc2coa[c] + h2o[c] 					
5403	ECOAH5	Yes	3-hydroxyacyl-CoA dehydratase (3-hydroxydodecanoyl-CoA)	[c] : 3hddcoa <==> dd2coa + h2o	Membrane Lipid Metabolism	4.2.1.17	( b3846  or  b2341 )	JC		0.278853	2.66722	[c] : 3hddcoa[c] <==> dd2coa[c] + h2o[c] 					
406	ECOAH6	Yes	3-hydroxyacyl-CoA dehydratase (3-hydroxytetradecanoyl-CoA)	[c] : 3htdcoa <==> h2o + td2coa	Membrane Lipid Metabolism	4.2.1.17	( b3846  or  b2341 )			0.278853	2.66722	[c] : 3htdcoa[c] <==> h2o[c] + td2coa[c] 					
5404	ECOAH7	Yes	3-hydroxyacyl-CoA dehydratase (3-hydroxyhexadecanoyl-CoA)	[c] : 3hhdcoa <==> h2o + hdd2coa	Membrane Lipid Metabolism	4.2.1.17	( b3846  or  b2341 )	JC		0.278853	2.66722	[c] : 3hhdcoa[c] <==> h2o[c] + hdd2coa[c] 					
8135	ECOAH8	Yes	3-hydroxyacyl-CoA dehydratase (3-hydroxyoctadecanoyl-CoA)	[c] : 3hodcoa <==> h2o + od2coa	Membrane Lipid Metabolism	4.2.1.17	( b3846  or  b2341 )	JLR		0.278853	2.66722	[c] : 3hodcoa[c] <==> h2o[c] + od2coa[c] 					
277	EDA	No	2-dehydro-3-deoxy-phosphogluconate aldolase	[c] : 2ddg6p --> g3p + pyr	Pentose Phosphate Pathway	4.1.2.14	b1850	SMP		2.91741	2.32549	[c] : 2ddg6p[c] --> g3p[c] + pyr[c] 					
1127	EDD	No	6-phosphogluconate dehydratase	[c] : 6pgc --> 2ddg6p + h2o	Pentose Phosphate Pathway	4.2.1.12	b1851	"tv, jp
it (EC number)"		-9.58412	3.68395	[c] : 6pgc[c] --> 2ddg6p[c] + h2o[c] 					
3377	EDTXS1	No	Endotoxin Synthesis (lauroyl transferase)	[c] : ddcaACP + kdo2lipid4 --> ACP + kdo2lipid4L	Cell Envelope Biosynthesis		b1054	JLR		-1.98374	4.73838	[c] : ddcaACP[c] + kdo2lipid4[c] --> ACP[c] + kdo2lipid4L[c] 					
3378	EDTXS2	No	Endotoxin Synthesis (myristoyl transferase)	[c] : kdo2lipid4L + myrsACP --> ACP + lipa	Cell Envelope Biosynthesis		b1855	JLR- NH page 1043		-1.98374	4.73838	[c] : kdo2lipid4L[c] + myrsACP[c] --> ACP[c] + lipa[c] 					
3379	EDTXS3	No	Endotoxin Synthesis (palmitoleoyl ACP)	[c] : hdeACP + kdo2lipid4 --> ACP + kdo2lipid4p	Cell Envelope Biosynthesis		b2378	JLR-see PMID 10092655		-1.98374	4.73838	[c] : hdeACP[c] + kdo2lipid4[c] --> ACP[c] + kdo2lipid4p[c] 					
3380	EDTXS4	No	Endotoxin Synthesis (myristoyl transferase)	[c] : kdo2lipid4p + myrsACP --> ACP + lipa_cold	Cell Envelope Biosynthesis		b1855	JLR see PMID 10092655		-1.98374	4.73838	[c] : kdo2lipid4p[c] + myrsACP[c] --> ACP[c] + lipa_cold[c] 					
13530	ENLIPAtex	Yes	phosphoethanolamine lipid A transport via vector (periplasm to extracellular)	enlipa[p] --> enlipa[e]	Lipopolysaccharide Biosynthesis / Recycling			"AMF
not sure how it travels across the periplam or flipped to outer serface of the membrane"	"this reaction is needed to have the LPS lipid A derivative presented to the outer membrane surface - both moved across the periplasm and flipped across the outer membrane

not sure on the method of transport

this paper talks about the possibility of the transport PMID: 15576375

AMF"	0	0	[c] : enlipa[p] --> enlipa[e] 					
266	ENO	No	enolase	[c] : 2pg <==> h2o + pep	Glycolysis/Gluconeogenesis	4.2.1.11	b2779	SMP		-2.11522	3.77957	[c] : 2pg[c] <==> h2o[c] + pep[c] 					
7521	ENTCS	No	enterochelin synthase	[c] : (3) 23dhba + (3) seramp --> (6) amp + enter + (9) h	Update		b0583	JLR	"rxn may occur in a large protien complex composed of Ent D, B, F& E  MKA

http://biocyc.org/ECOLI/new-image?type=PATHWAY&object=ENTBACSYN-PWY

AMF"	4.02233	25.7598	[c] : (3) 23dhba[c] + (3) seramp[c] --> (6) amp[c] + enter[c] + (6) h[c] 					
13695	ENTERES	Yes	Enterochelin Esterase	[c] : enter + (3) h2o --> (3) 23dhbzs + (3) h	Update		b0585	AMF	"function taken from PMID: 150859 and from Ecocyc PMID: 1534808

AMF"	-20.5957	11.8778	[c] : enter[c] + (3) h2o[c] --> (3) 23dhbzs[c] + (3) h[c] 					
13698	ENTERES2	Yes	Enterochelin Esterase (Fe containing)	[c] : feenter + (3) h2o --> (3) 23dhbzs + fe3 + (3) h	Update		b0585	AMF	"function taken from PMID: 150859 and from Ecocyc PMID: 1534808

AMF"	No energy	No energy	[c] : feenter[c] + (3) h2o[c] --> (3) 23dhbzs[c] + fe3[c] + (3) h[c] 					
2535	ETHAAL	No	Ethanolamine ammonia-lyase	[c] : etha --> acald + nh4	Cell Envelope Biosynthesis	4.3.1.7	( b2440  and  b2441 )	JLR		-6.6875	2.67138	[c] : etha[c] --> acald[c] + nh4[c] 					
12328	ETHAt2pp	Yes	ethanolamine transport in/out via proton symport	etha[p] + h[p] <==> etha[c] + h[c]	Update			AMF	"AMF
assumption of transport
no gene association known"	0	0	[c] : etha[p] + h[p] <==> etha[c] + h[c] 		
12254	ETHAtex	Yes	ethanolamine transport via diffusion (extracellular)	etha[e] <==> etha[p]	"Transport, Outer Membrane"			AMF	assumed diffusion	0	0	[c] : etha[e] <==> etha[p] 		
13608	ETHSO3abcpp	Yes	ethanesulfonate transport via ABC system (periplasm)	atp[c] + ethso3[p] + h2o[c] --> adp[c] + ethso3[c] + h[c] + pi[c]	Update		( b0936  and  b0933  and  b0934 )		"only the ssu transport system will transport this and L-cysteate, amoung others

L-cysteate not included since the degradation products are dead ends

see PMID: 11750815
AMF"	-7.01673	1.48181	[c] : atp[c] + ethso3[p] + h2o[c] --> adp[c] + ethso3[c] + h[c] + pi[c] 		
13612	ETHSO3tex	Yes	ethanesulfonate transport via diffusion (extracellular to periplasm)	ethso3[e] <==> ethso3[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ethso3[e] <==> ethso3[p] 		
8983	ETOHt2rpp	Yes	ethanol reversible transport via proton symport (periplasm)	etoh[p] + h[p] <==> etoh[c] + h[c]	"Transport, Inner Membrane"			JLR		0	0	[c] : etoh[p] + h[p] <==> etoh[c] + h[c] 		
9068	ETOHtex	Yes	ethanol transport via diffusion (extracellular to periplasm)	etoh[e] <==> etoh[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : etoh[e] <==> etoh[p] 		
20118	EX_12ppd-R(e)	Yes	"(R)-Propane-1,2-diol exchange"	[e] : 12ppd-R <==>										
2618	EX_12ppd-S(e)	Yes	"(S)-Propane-1,2-diol exchange"	[e] : 12ppd-S <==>										
13951	EX_14glucan(e)	Yes	"1,4-alpha-D-glucan exchange"	[e] : 14glucan <==>										
4142	EX_15dap(e)	Yes	"1,5-Diaminopentane exchange"	[e] : 15dap <==>										
10590	EX_23appa	Yes	"2,3-diaminopropionate exchange"	[e] : 23dappa <==>				MKA - pressumed reaction						
12423	EX_23camp(e)	Yes	"2',3'-Cyclic AMP exchange"	[e] : 23camp <==>										
12424	EX_23ccmp(e)	Yes	"2',3'-Cyclic CMP exchange"	[e] : 23ccmp <==>										
12425	EX_23cgmp(e)	Yes	"2',3'-Cyclic GMP exchange"	[e] : 23cgmp <==>										
12426	EX_23cump(e)	Yes	"2',3'-Cyclic UMP exchange"	[e] : 23cump <==>										
2024	EX_26dap-M(e)	Yes	"meso-2,6-Diaminoheptanedioate exchange"	[e] : 26dap-M <==>										
2620	EX_2ddglcn(e)	Yes	2-Dehydro-3-deoxy-D-gluconate exchange	[e] : 2ddglcn <==>										
12302	EX_34dhpac(e)	Yes	"3,4-Dihydroxyphenylacetaldehyde exchange"	[e] : 34dhpac <==>										
12427	EX_3amp(e)	Yes	3'-AMP exchange	[e] : 3amp <==>										
12428	EX_3cmp(e)	Yes	3'-cmp exchange	[e] : 3cmp <==>										
12429	EX_3gmp(e)	Yes	3'-GMP exchange	[e] : 3gmp <==>										
2625	EX_3hcinnm(e)	Yes	3-hydroxycinnamic acid exchange	[e] : 3hcinnm <==>										
2626	EX_3hpppn(e)	Yes	3-(3-hydroxy-phenyl)propionate exchange	[e] : 3hpppn <==>										
12430	EX_3ump(e)	Yes	3'-UMP exchange	[e] : 3ump <==>										
827	EX_4abut(e)	Yes	4-Aminobutanoate exchange	[e] : 4abut <==>										
12293	EX_4hoxpacd(e)	Yes	4-Hydroxyphenylacetaldehyde exchange	[e] : 4hoxpacd <==>										
828	EX_ac(e)	Yes	Acetate exchange	[e] : ac <==>										
3659	EX_acac(e)	Yes	Acetoacetate exchange	[e] : acac <==>										
1456	EX_acald(e)	Yes	Acetaldehyde exchange	[e] : acald <==>										
13940	EX_acgal(e)	Yes	N-Acetyl-D-galactosamine exchange	[e] : acgal <==>										
13943	EX_acgal1p(e)	Yes	N-Acetyl-D-galactosamine 1-phosphate exchange	[e] : acgal1p <==>										
1045	EX_acgam(e)	Yes	N-Acetyl-D-glucosamine exchange	[e] : acgam <==>										
13959	EX_acgam1p(e)	Yes	N-Acetyl-D-glucosamine 1-phosphate exchange	[e] : acgam1p <==>													
2627	EX_acmana(e)	Yes	N-Acetyl-D-mannosamine exchange	[e] : acmana <==>													
8160	EX_acmum(e)	Yes	N-Acetylmuramate exchange	[e] : acmum <==>													
2025	EX_acnam(e)	Yes	N-Acetylneuraminate exchange	[e] : acnam <==>													
13586	EX_acolipa(e)	Yes	4-Amino-4-deoxy-L-arabinose modified core oligosaccharide lipid A exchange	[e] : acolipa <==>													
14047	EX_acser(e)	Yes	O-Acetyl-L-serine exchange	[e] : acser <==>													
826	EX_ade(e)	Yes	Adenine exchange	[e] : ade <==>													
758	EX_adn(e)	Yes	Adenosine exchange	[e] : adn <==>													
9238	EX_adocbl(e)	Yes	Adenosylcobalamin exchange	[e] : adocbl <==>													
14045	EX_ag(e)	Yes	silver exchange	[e] : ag <==>													
8155	EX_agm(e)	Yes	Agmatine exchange	[e] : agm <==>													
829	EX_akg(e)	Yes	2-Oxoglutarate exchange	[e] : akg <==>													
18860	EX_alaala(e)	Yes	D-Alanyl-D-alanine exchange	[e] : alaala <==>													
8154	EX_ala-B(e)	Yes	beta-Alanine exchange	[e] : ala-B <==>													
1064	EX_ala-D(e)	Yes	D-Alanine exchange	[e] : ala-D <==>													
830	EX_ala-L(e)	Yes	L-Alanine exchange	[e] : ala-L <==>													
8162	EX_all-D(e)	Yes	D-Allose exchange	[e] : all-D <==>													
1126	EX_alltn(e)	Yes	Allantoin exchange	[e] : alltn <==>													
2026	EX_amp(e)	Yes	AMP exchange	[e] : amp <==>													
13213	EX_anhgm(e)	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid exchange	[e] : anhgm <==>													
13209	EX_anhgm3p(e)	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide exchange	[e] : anhgm3p <==>													
13210	EX_anhgm4p(e)	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide exchange	[e] : anhgm4p <==>													
680	EX_arab-L(e)	Yes	L-Arabinose exchange	[e] : arab-L <==>													
14051	EX_arbtn(e)	Yes	aerobactin minus Fe3 exchange	[e] : arbtn <==>													
9236	EX_arbtn-fe3(e)	Yes	Aerobactin exchange	[e] : arbtn-fe3 <==>													
831	EX_arg-L(e)	Yes	L-Arginine exchange	[e] : arg-L <==>													
8153	EX_ascb-L(e)	Yes	L-Ascorbate exchange	[e] : ascb-L <==>													
832	EX_asn-L(e)	Yes	L-Asparagine exchange	[e] : asn-L <==>													
13953	EX_aso3(e)	Yes	arsenite exchange	[e] : aso3 <==>													
833	EX_asp-L(e)	Yes	L-Aspartate exchange	[e] : asp-L <==>													
2629	EX_but(e)	Yes	Butyrate (n-C4:0) exchange	[e] : but <==>													
13616	EX_butso3(e)	Yes	butanesulfonate exchange	[e] : butso3 <==>													
9235	EX_cbi(e)	Yes	Cobinamide exchange	[e] : cbi <==>													
2630	EX_cbl1(e)	Yes	Cob(I)alamin exchange	[e] : cbl1 <==>													
9536	EX_cd2(e)	Yes	Cadmium exchange	[e] : cd2 <==>													
10940	EX_cgly(e)	Yes	Cys-Gly exchange	[e] : cgly <==>													
1047	EX_chol(e)	Yes	Choline exchange	[e] : chol <==>													
1048	EX_cit(e)	Yes	Citrate exchange	[e] : cit <==>													
9537	EX_cl(e)	Yes	Chloride exchange	[e] : cl <==>													
10943	EX_cmp(e)	Yes	CMP exchange	[e] : cmp <==>													
805	EX_co2(e)	Yes	CO2 exchange	[e] : co2 <==>													
6675	EX_cobalt2(e)	Yes	Co2+ exchange	[e] : cobalt2 <==>													
13585	EX_colipa(e)	Yes	core oligosaccharide lipid A exchange	[e] : colipa <==>													
9237	EX_cpgn(e)	Yes	coprogen exchange	[e] : cpgn <==>													
18861	EX_cpgn-un(e)	Yes	coprogen unloaded (no Fe(III)) exchange	[e] : cpgn-un <==>													
706	EX_crn(e)	Yes	L-Carnitine exchange	[e] : crn <==>													
835	EX_csn(e)	Yes	Cytosine exchange	[e] : csn <==>													
14048	EX_cu(e)	Yes	Cu+ exchange	[e] : cu <==>													
6685	EX_cu2(e)	Yes	Cu2+ exchange	[e] : cu2 <==>													
13944	EX_cyan(e)	Yes	Hydrogen cyanide exchange	[e] : cyan <==>													
4148	EX_cynt(e)	Yes	Cyanate exchange	[e] : cynt <==>													
14046	EX_cys-D(e)	Yes	D-Cysteine exchange	[e] : cys-D <==>													
1065	EX_cys-L(e)	Yes	L-Cysteine exchange	[e] : cys-L <==>													
836	EX_cytd(e)	Yes	Cytidine exchange	[e] : cytd <==>													
4137	EX_dad-2(e)	Yes	Deoxyadenosine exchange	[e] : dad-2 <==>													
12323	EX_damp(e)	Yes	dAMP exchange	[e] : damp <==>													
8161	EX_dca(e)	Yes	Decanoate (n-C10:0) exchange	[e] : dca <==>													
12321	EX_dcmp(e)	Yes	dCMP exchange	[e] : dcmp <==>													
837	EX_dcyt(e)	Yes	Deoxycytidine exchange	[e] : dcyt <==>													
2588	EX_ddca(e)	Yes	Dodecanoate (n-C12:0) exchange	[e] : ddca <==>													
12324	EX_dgmp(e)	Yes	dGMP exchange	[e] : dgmp <==>													
1610	EX_dgsn(e)	Yes	Deoxyguanosine exchange	[e] : dgsn <==>													
2027	EX_dha(e)	Yes	Dihydroxyacetone exchange	[e] : dha <==>													
12357	EX_dimp(e)	Yes	dIMP exchange	[e] : dimp <==>													
1611	EX_din(e)	Yes	Deoxyinosine exchange	[e] : din <==>													
2762	EX_dms(e)	Yes	Dimethyl sulfide exchange	[e] : dms <==>													
2763	EX_dmso(e)	Yes	Dimethyl sulfoxide exchange	[e] : dmso <==>													
12041	EX_dopa(e)	Yes	Dopamine exchange	[e] : dopa <==>													
18862	EX_dtmp(e)	Yes	dTMP exchange	[e] : dtmp <==>													
12317	EX_dump(e)	Yes	dUMP exchange	[e] : dump <==>													
1066	EX_duri(e)	Yes	Deoxyuridine exchange	[e] : duri <==>													
13593	EX_eca4colipa(e)	Yes	(enterobacterial common antigen)x4 core oligosaccharide lipid A exchange	[e] : eca4colipa <==>													
13584	EX_enlipa(e)	Yes	phosphoethanolamine KDO(2)-lipid (A) exchange	[e] : enlipa <==>													
10836	EX_enter(e)	Yes	Enterochelin exchange	[e] : enter <==>													
8149	EX_etha(e)	Yes	Ethanolamine exchange	[e] : etha <==>													
13617	EX_ethso3(e)	Yes	ethanesulfonate exchange	[e] : ethso3 <==>													
839	EX_etoh(e)	Yes	Ethanol exchange	[e] : etoh <==>													
13214	EX_fald(e)	Yes	Formaldehyde exchange	[e] : fald <==>													
1310	EX_fe2(e)	Yes	Fe2+ exchange	[e] : fe2 <==>													
707	EX_fe3(e)	Yes	Fe3+ exchange	[e] : fe3 <==>													
9230	EX_fe3dcit(e)	Yes	Fe(III)dicitrate exchange	[e] : fe3dcit <==>													
13956	EX_fe3dhbzs(e)	Yes	"ferric 2,3-dihydroxybenzoylserine exchange"	[e] : fe3dhbzs <==>													
9231	EX_fe3hox(e)	Yes	Fe(III)hydroxamate exchange	[e] : fe3hox <==>													
10835	EX_fe3hox-un(e)	Yes	"Fe(III)hydoxamate, unloaded exchange"	[e] : fe3hox-un <==>													
9232	EX_fecrm(e)	Yes	Ferrichrome exchange	[e] : fecrm <==>													
10845	EX_fecrm-un(e)	Yes	Ferrichrome minus Fe(III) exchange	[e] : fecrm-un <==>													
9233	EX_feenter(e)	Yes	Fe-enterobactin exchange	[e] : feenter <==>													
9234	EX_feoxam(e)	Yes	ferroxamine exchange	[e] : feoxam <==>													
12287	EX_feoxam-un(e)	Yes	ferroxamine minus Fe(3) exchange	[e] : feoxam-un <==>													
1067	EX_for(e)	Yes	Formate exchange	[e] : for <==>													
681	EX_fru(e)	Yes	D-Fructose exchange	[e] : fru <==>													
11506	EX_frulys(e)	Yes	fructoselysine exchange	[e] : frulys <==>													
10016	EX_fruur(e)	Yes	D-Fructuronate exchange	[e] : fruur <==>													
2617	EX_fuc1p-L(e)	Yes	L-Fucose 1-phosphate exchange	[e] : fuc1p-L <==>													
2028	EX_fuc-L(e)	Yes	L-Fucose exchange	[e] : fuc-L <==>													
840	EX_fum(e)	Yes	Fumarate exchange	[e] : fum <==>													
12320	EX_g1p(e)	Yes	D-Glucose 1-phosphate exchange	[e] : g1p <==>													
12288	EX_g3pc(e)	Yes	sn-Glycero-3-phosphocholine exchange	[e] : g3pc <==>													
12289	EX_g3pe(e)	Yes	sn-Glycero-3-phosphoethanolamine exchange	[e] : g3pe <==>													
12290	EX_g3pg(e)	Yes	Glycerophosphoglycerol exchange	[e] : g3pg <==>													
12291	EX_g3pi(e)	Yes	sn-Glycero-3-phospho-1-inositol exchange	[e] : g3pi <==>													
12292	EX_g3ps(e)	Yes	Glycerophosphoserine exchange	[e] : g3ps <==>													
2619	EX_g6p(e)	Yes	D-Glucose 6-phosphate exchange	[e] : g6p <==>													
682	EX_gal(e)	Yes	D-Galactose exchange	[e] : gal <==>													
12319	EX_gal1p(e)	Yes	alpha-D-Galactose 1-phosphate exchange	[e] : gal1p <==>													
13601	EX_gal-bD(e)	Yes	beta D-Galactose exchange	[e] : gal-bD <==>													
2621	EX_galct-D(e)	Yes	D-Galactarate exchange	[e] : galct-D <==>													
4149	EX_galctn-D(e)	Yes	D-Galactonate exchange	[e] : galctn-D <==>													
2029	EX_galt(e)	Yes	Galactitol exchange	[e] : galt <==>													
2628	EX_galur(e)	Yes	D-Galacturonate exchange	[e] : galur <==>													
708	EX_gam(e)	Yes	D-Glucosamine exchange	[e] : gam <==>													
2764	EX_gbbtn(e)	Yes	gamma-butyrobetaine exchange	[e] : gbbtn <==>													
8166	EX_gdp(e)	Yes	GDP exchange	[e] : gdp <==>													
99	EX_glc(e)	Yes	D-Glucose exchange	[e] : glc-D <==>													
709	EX_glcn(e)	Yes	D-Gluconate exchange	[e] : glcn <==>													
4151	EX_glcr(e)	Yes	D-Glucarate exchange	[e] : glcr <==>													
2640	EX_glcur(e)	Yes	D-Glucuronate exchange	[e] : glcur <==>													
13942	EX_glcur1p(e)	Yes	D-Glucuronate 1-phosphate exchange	[e] : glcur1p <==>													
710	EX_gln-L(e)	Yes	L-Glutamine exchange	[e] : gln-L <==>													
841	EX_glu-L(e)	Yes	L-Glutamate exchange	[e] : glu-L <==>													
1068	EX_gly(e)	Yes	Glycine exchange	[e] : gly <==>													
2030	EX_glyald(e)	Yes	D-Glyceraldehyde exchange	[e] : glyald <==>													
4150	EX_glyb(e)	Yes	Glycine betaine exchange	[e] : glyb <==>													
711	EX_glyc(e)	Yes	Glycerol exchange	[e] : glyc <==>													
13960	EX_glyc2p(e)	Yes	Glycerol 2-phosphate exchange	[e] : glyc2p <==>													
2031	EX_glyc3p(e)	Yes	Glycerol 3-phosphate exchange	[e] : glyc3p <==>													
2616	EX_glyclt(e)	Yes	Glycolate exchange	[e] : glyclt <==>													
13592	EX_glyc-R(e)	Yes	(R)-Glycerate exchange	[e] : glyc-R <==>													
10945	EX_gmp(e)	Yes	GMP exchange	[e] : gmp <==>													
1069	EX_gsn(e)	Yes	Guanosine exchange	[e] : gsn <==>													
1614	EX_gthox(e)	Yes	Oxidized glutathione exchange	[e] : gthox <==>													
2571	EX_gthrd(e)	Yes	Reduced glutathione exchange	[e] : gthrd <==>													
8167	EX_gtp(e)	Yes	GTP exchange	[e] : gtp <==>													
842	EX_gua(e)	Yes	Guanine exchange	[e] : gua <==>													
104	EX_h(e)	Yes	H+ exchange	[e] : h <==>													
1070	EX_h2(e)	Yes	H2 exchange	[e] : h2 <==>													
100	EX_h2o(e)	Yes	H2O exchange	[e] : h2o <==>													
10946	EX_h2o2(e)	Yes	Hydrogen peroxide exchange	[e] : h2o2 <==>													
2570	EX_h2s(e)	Yes	Hydrogen sulfide exchange	[e] : h2s <==>													
13587	EX_hacolipa(e)	Yes	hepta-acylated core oligosaccharide lipid A (E. coli) exchange	[e] : hacolipa <==>													
13588	EX_halipa(e)	Yes	hepta-acylated KDO(2)-lipid (A) exchange	[e] : halipa <==>													
4143	EX_hdca(e)	Yes	Hexadecanoate (n-C16:0) exchange	[e] : hdca <==>													
2040	EX_hdcea(e)	Yes	hexadecenoate (n-C16:1) exchange	[e] : hdcea <==>													
13686	EX_hg2(e)	Yes	Hg2+ exchange	[e] : hg2 <==>													
843	EX_his-L(e)	Yes	L-Histidine exchange	[e] : his-L <==>													
12043	EX_hom-L(e)	Yes	L-Homoserine exchange	[e] : hom-L <==>													
8158	EX_hxa(e)	Yes	Hexanoate (n-C6:0) exchange	[e] : hxa <==>													
844	EX_hxan(e)	Yes	Hypoxanthine exchange	[e] : hxan <==>													
2623	EX_idon-L(e)	Yes	L-Idonate exchange	[e] : idon-L <==>													
845	EX_ile-L(e)	Yes	L-Isoleucine exchange	[e] : ile-L <==>													
11256	EX_imp(e)	Yes	IMP exchange	[e] : imp <==>													
2624	EX_indole(e)	Yes	Indole exchange	[e] : indole <==>													
712	EX_inost(e)	Yes	myo-Inositol exchange	[e] : inost <==>													
759	EX_ins(e)	Yes	Inosine exchange	[e] : ins <==>													
12358	EX_isetac(e)	Yes	Isethionic acid exchange	[e] : isetac <==>													
846	EX_k(e)	Yes	K+ exchange	[e] : k <==>													
3075	EX_lac-D(e)	Yes	D-lactate exchange	[e] : lac-D <==>													
847	EX_lac-L(e)	Yes	L-Lactate exchange	[e] : lac-L <==>													
13212	EX_LalaDgluMdap(e)	Yes	"L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate exchange"	[e] : LalaDgluMdap <==>													
13211	EX_LalaDgluMdapDala(e)	Yes	"L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine exchange"	[e] : LalaDgluMdapDala <==>													
2032	EX_lcts(e)	Yes	Lactose exchange	[e] : lcts <==>										
848	EX_leu-L(e)	Yes	L-Leucine exchange	[e] : leu-L <==>										
13590	EX_lipa(e)	Yes	KDO(2)-lipid (A) exchange	[e] : lipa <==>										
13591	EX_lipa_cold(e)	Yes	cold adapted KDO(2)-lipid (A) exchange	[e] : lipa_cold <==>										
1072	EX_lys-L(e)	Yes	L-Lysine exchange	[e] : lys-L <==>										
8159	EX_lyx-L(e)	Yes	L-Lyxose exchange	[e] : lyx-L <==>										
849	EX_mal-L(e)	Yes	L-Malate exchange	[e] : mal-L <==>										
713	EX_malt(e)	Yes	Maltose exchange	[e] : malt <==>										
2637	EX_malthx(e)	Yes	Maltohexaose exchange	[e] : malthx <==>										
2638	EX_maltpt(e)	Yes	Maltopentaose exchange	[e] : maltpt <==>										
3253	EX_malttr(e)	Yes	Maltotriose exchange	[e] : malttr <==>										
2639	EX_maltttr(e)	Yes	Maltotetraose exchange	[e] : maltttr <==>										
714	EX_man(e)	Yes	D-Mannose exchange	[e] : man <==>										
2631	EX_man6p(e)	Yes	D-Mannose 6-phosphate exchange	[e] : man6p <==>										
8164	EX_manglyc(e)	Yes	2(alpha-D-Mannosyl)-D-glycerate exchange	[e] : manglyc <==>										
1457	EX_melib(e)	Yes	Melibiose exchange	[e] : melib <==>										
2632	EX_met-D(e)	Yes	D-Methionine exchange	[e] : met-D <==>													
1120	EX_met-L(e)	Yes	L-Methionine exchange	[e] : met-L <==>													
1121	EX_metox(e)	Yes	L-Methionine S-oxide exchange	[e] : metsox-S-L <==>													
11507	EX_met-r-ox-L(e)	Yes	L-methionine-R-sulfoxide exchange	[e] : metsox-R-L <==>													
6658	EX_mg2(e)	Yes	Mg exchange	[e] : mg2 <==>													
8156	EX_minohp(e)	Yes	myo-Inositol hexakisphosphate exchange	[e] : minohp <==>													
3094	EX_mmet(e)	Yes	S-Methyl-L-methionine exchange	[e] : mmet <==>													
715	EX_mn2(e)	Yes	Mn2+ exchange	[e] : mn2 <==>													
683	EX_mnl(e)	Yes	D-Mannitol exchange	[e] : mnl <==>													
716	EX_mobd(e)	Yes	Molybdate exchange	[e] : mobd <==>													
12359	EX_mso3(e)	Yes	methanesulfonate exchange	[e] : mso3 <==>													
13625	EX_n2o(e)	Yes	Nitrous oxide exchange	[e] : n2o <==>													
850	EX_na1(e)	Yes	Sodium exchange	[e] : na1 <==>													
2033	EX_nac(e)	Yes	Nicotinate exchange	[e] : nac <==>													
2034	EX_nad(e)	Yes	Nicotinamide adenine dinucleotide exchange	[e] : nad <==>													
892	EX_nh4(e)	Yes	Ammonia exchange	[e] : nh4 <==>													
5898	EX_ni2(e)	Yes	Ni2+ exchange	[e] : ni2 <==>													
2924	EX_nmn(e)	Yes	NMN exchange	[e] : nmn <==>													
6011	EX_no(e)	Yes	Nitric oxide exchange	[e] : no <==>													
1119	EX_no2(e)	Yes	Nitrite exchange	[e] : no2 <==>													
851	EX_no3(e)	Yes	Nitrate exchange	[e] : no3 <==>													
13589	EX_o16a4colipa(e)	Yes	(O16 antigen)x4 core oligosaccharide lipid A exchange	[e] : o16a4colipa <==>													
804	EX_o2(e)	Yes	O2 exchange	[e] : o2 <==>													
12318	EX_o2-(e)	Yes	Superoxide anion exchange	[e] : o2- <==>													
2035	EX_ocdca(e)	Yes	octadecanoate (n-C18:0) exchange	[e] : ocdca <==>													
4144	EX_ocdcea(e)	Yes	octadecenoate (n-C18:1) exchange	[e] : ocdcea <==>													
8163	EX_octa(e)	Yes	octanoate (n-C8:0) exchange	[e] : octa <==>													
852	EX_orn(e)	Yes	Ornithine exchange	[e] : orn <==>													
12297	EX_pacald(e)	Yes	Phenylacetaldehyde exchange	[e] : pacald <==>													
12298	EX_peamn(e)	Yes	Phenethylamine exchange	[e] : peamn <==>													
853	EX_phe-L(e)	Yes	L-Phenylalanine exchange	[e] : phe-L <==>													
7833	EX_pheme(e)	Yes	Protoheme exchange	[e] : pheme <==>													
101	EX_pi(e)	Yes	Phosphate exchange	[e] : pi <==>													
1616	EX_pnto-R(e)	Yes	(R)-Pantothenate exchange	[e] : pnto-R <==>													
2622	EX_pppn(e)	Yes	Phenylpropanoate exchange	[e] : pppn <==>													
8157	EX_ppt(e)	Yes	Phosphonate exchange	[e] : ppt <==>													
19735	EX_progly(e)	Yes	L-Prolinylglycine exchange	[e] : progly <==>													
854	EX_pro-L(e)	Yes	L-Proline exchange	[e] : pro-L <==>													
13952	EX_pser-L(e)	Yes	O-Phospho-L-serine exchange	[e] : pser-L <==>													
1617	EX_ptrc(e)	Yes	Putrescine exchange	[e] : ptrc <==>													
855	EX_pyr(e)	Yes	Pyruvate exchange	[e] : pyr <==>													
13955	EX_r5p(e)	Yes	alpha-D-Ribose 5-phosphate exchange	[e] : r5p <==>													
717	EX_rib-D(e)	Yes	D-Ribose exchange	[e] : rib-D <==>													
2036	EX_rmn(e)	Yes	L-Rhamnose exchange	[e] : rmn <==>													
718	EX_sbt-D(e)	Yes	D-Sorbitol exchange	[e] : sbt-D <==>													
4138	EX_ser-D(e)	Yes	D-Serine exchange	[e] : ser-D <==>													
1074	EX_ser-L(e)	Yes	L-Serine exchange	[e] : ser-L <==>													
14044	EX_skm(e)	Yes	Shikimate exchange	[e] : skm <==>													
13941	EX_so2(e)	Yes	sulfur dioxide exchange	[e] : so2 <==>													
8749	EX_so3(e)	Yes	Sulfite exchange	[e] : so3 <==>													
719	EX_so4(e)	Yes	Sulfate exchange	[e] : so4 <==>													
1618	EX_spmd(e)	Yes	Spermidine exchange	[e] : spmd <==>													
856	EX_succ(e)	Yes	Succinate exchange	[e] : succ <==>													
720	EX_sucr(e)	Yes	Sucrose exchange	[e] : sucr <==>													
13615	EX_sulfac(e)	Yes	sulfoacetate exchange	[e] : sulfac <==>													
2633	EX_tartr-L(e)	Yes	L-tartrate exchange	[e] : tartr-L <==>													
2634	EX_taur(e)	Yes	Taurine exchange	[e] : taur <==>													
13954	EX_tcynt(e)	Yes	Thiocyanate exchange	[e] : tcynt <==>													
1075	EX_thm(e)	Yes	Thiamin exchange	[e] : thm <==>													
857	EX_thr-L(e)	Yes	L-Threonine exchange	[e] : thr-L <==>													
13957	EX_thrp(e)	Yes	L-Threonine O-3-phosphate exchange	[e] : thrp <==>													
858	EX_thymd(e)	Yes	Thymidine exchange	[e] : thymd <==>													
2765	EX_tma(e)	Yes	Trimethylamine exchange	[e] : tma <==>													
2766	EX_tmao(e)	Yes	Trimethylamine N-oxide exchange	[e] : tmao <==>													
721	EX_tre(e)	Yes	Trehalose exchange	[e] : tre <==>										
1076	EX_trp-L(e)	Yes	L-Tryptophan exchange	[e] : trp-L <==>										
2635	EX_tsul(e)	Yes	Thiosulfate exchange	[e] : tsul <==>										
2037	EX_ttdca(e)	Yes	tetradecanoate (n-C14:0) exchange	[e] : ttdca <==>										
2589	EX_ttdcea(e)	Yes	tetradecenoate (n-C14:1) exchange	[e] : ttdcea <==>										
12286	EX_tym(e)	Yes	Tyramine exchange	[e] : tym <==>										
859	EX_tyr-L(e)	Yes	L-Tyrosine exchange	[e] : tyr-L <==>										
13945	EX_tyrp(e)	Yes	Phosphotyrosine exchange	[e] : tyrp <==>										
13946	EX_uacgam(e)	Yes	UDP-N-acetyl-D-glucosamine exchange	[e] : uacgam <==>										
13947	EX_udpacgal(e)	Yes	UDP-N-acetyl-D-galactosamine exchange	[e] : udpacgal <==>										
13948	EX_udpg(e)	Yes	UDPglucose exchange	[e] : udpg <==>										
13949	EX_udpgal(e)	Yes	UDPgalactose exchange	[e] : udpgal <==>										
13950	EX_udpglcur(e)	Yes	UDP-D-glucuronate exchange	[e] : udpglcur <==>										
10948	EX_ump(e)	Yes	UMP exchange	[e] : ump <==>										
860	EX_ura(e)	Yes	Uracil exchange	[e] : ura <==>										
2925	EX_urea(e)	Yes	Urea exchange	[e] : urea <==>										
861	EX_uri(e)	Yes	Uridine exchange	[e] : uri <==>													
862	EX_val-L(e)	Yes	L-Valine exchange	[e] : val-L <==>													
863	EX_xan(e)	Yes	Xanthine exchange	[e] : xan <==>													
12322	EX_xmp(e)	Yes	Xanthosine 5'-phosphate exchange	[e] : xmp <==>													
1622	EX_xtsn(e)	Yes	Xanthosine exchange	[e] : xtsn <==>													
684	EX_xyl-D(e)	Yes	D-Xylose exchange	[e] : xyl-D <==>													
8165	EX_xylu-L(e)	Yes	L-Xylulose exchange	[e] : xylu-L <==>													
722	EX_zn2(e)	Yes	Zinc exchange	[e] : zn2 <==>													
2547	F6PA	No	fructose 6-phosphate aldolase	[c] : f6p <==> dha + g3p	Glycolysis/Gluconeogenesis		( b0825  or  b3946 )	JLR	JLR- no longer putative	5.38114	6.58758	[c] : f6p[c] <==> dha[c] + g3p[c] 					
13360	F6PP	Yes	D-fructose 6-phosphate phosphatase	[c] : f6p + h2o --> fru + pi	Update		b0822	AMF	"enzyme acts on a number of other sugar phosphates, these reactions were shown to be substrates and were in the model

(glyc3p was not tested, but high activity was shown ot glyc1p and glyc2p, so the reaction G3PT was assigned to this gene)

sbt-d - not in network yet, but could be a signalling molecule (not sure of the source for this statement), so added this reaction
PMID: 15657928
AMF"	-2.35942	1.9257	[c] : f6p[c] + h2o[c] --> fru[c] + h[c] + pi[c] 					
19976	FACOAE100	Yes	fatty-acid-CoA thioesterase (decanoate)	[c] : dcacoa + h2o --> coa + dca + h	Update		b0452	AMF	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-5.85263	4.37924	[c] : dcacoa[c] + h2o[c] --> coa[c] + dca[c] + h[c] 					
20123	FACOAE120	Yes	fatty-acid-CoA thioesterase (dodecanoate)	[c] : ddcacoa + h2o --> coa + ddca + h	Update		b0452	AMF	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-5.85263	4.37924	[c] : ddcacoa[c] + h2o[c] --> coa[c] + ddca[c] + h[c] 					
13691	FACOAE140	Yes	fatty-acid-CoA thioesterase (tetradecanoate)	[c] : h2o + tdcoa --> coa + h + ttdca	Update		b0452	"EC 3.1.2.-
AMF"	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-5.85263	4.37924	[c] : h2o[c] + tdcoa[c] --> coa[c] + h[c] + ttdca[c] 					
19979	FACOAE141	Yes	fatty-acid-CoA thioesterase (tetradecenoate)	[c] : h2o + tdecoa --> coa + h + ttdcea	Update		b0452	"EC 3.1.2.-
AMF"	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-7.44622	5.04838	[c] : h2o[c] + tdecoa[c] --> coa[c] + h[c] + ttdcea[c] 					
13690	FACOAE160	Yes	fatty-acid-CoA thioesterase (hexadecanoate)	[c] : h2o + pmtcoa --> coa + h + hdca	Update		b0452	AMF	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-5.85263	4.37924	[c] : h2o[c] + pmtcoa[c] --> coa[c] + h[c] + hdca[c] 					
19980	FACOAE161	Yes	fatty-acid-CoA thioesterase (hexadecenoate)	[c] : h2o + hdcoa --> coa + h + hdcea	Update		b0452	"EC 3.1.2.-
AMF"	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-5.85263	4.37924	[c] : h2o[c] + hdcoa[c] --> coa[c] + h[c] + hdcea[c] 					
19975	FACOAE180	Yes	fatty-acid-CoA thioesterase (octadecanoate)	[c] : h2o + stcoa --> coa + h + ocdca	Update		b0452	AMF	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-5.85263	4.37924	[c] : h2o[c] + stcoa[c] --> coa[c] + h[c] + ocdca[c] 		
13689	FACOAE181	Yes	fatty-acid-CoA thioesterase (octadecenoate)	[c] : h2o + odecoa --> coa + h + ocdcea	Update		b0452	AMF	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-5.85263	4.37924	[c] : h2o[c] + odecoa[c] --> coa[c] + h[c] + ocdcea[c] 		
19978	FACOAE60	Yes	fatty-acid-CoA thioesterase (hexanoate)	[c] : h2o + hxcoa --> coa + h + hxa	Update		b0452	"EC 3.1.2.-
AMF"	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-5.85263	4.37924	[c] : h2o[c] + hxcoa[c] --> coa[c] + h[c] + hxa[c] 		
19977	FACOAE80	Yes	fatty-acid-CoA thioesterase (octanoate)	[c] : h2o + occoa --> coa + h + octa	Update		b0452	AMF	"there are 2 acyl-CoA thioesterases (tesA (I) which is periplasmic and tesB (II) which is cytoplasmic)

KO of both genes show no phenotype
ecocye:hioesterase II is the tesB gene product. It has broad substrate specificity, cleaving short- and long-chain (C6-C18) acyl-CoA esters as well as 3-hydroxyacyl-CoA esters. 

See PMID: 8098033 for characterization of tesA
AMF"	-5.85263	4.37924	[c] : h2o[c] + occoa[c] --> coa[c] + h[c] + octa[c] 		
10745	FACOAL100t2pp	Yes	fatty-acid-CoA ligase (decanoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + dca[p] + h[p] --> amp[c] + dcacoa[c] + h[c] + ppi[c]	Update	6.2.1.3	( b1805  or  b1701 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane  "	-2.74083	4.99608	[c] : atp[c] + coa[c] + dca[p] + h[p] --> amp[c] + dcacoa[c] + ppi[c] 		
10744	FACOAL120t2pp	Yes	fatty-acid-CoA ligase (dodecanoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + ddca[p] + h[p] --> amp[c] + ddcacoa[c] + h[c] + ppi[c]	Update	6.2.1.3	( b1701  or  b1805 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane   "	-2.74083	4.99608	[c] : atp[c] + coa[c] + ddca[p] + h[p] --> amp[c] + ddcacoa[c] + ppi[c] 		
10746	FACOAL140t2pp	Yes	fatty-acid-CoA ligase (tetradecanoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + h[p] + ttdca[p] --> amp[c] + h[c] + ppi[c] + tdcoa[c]	Update	6.2.1.3	( b1805  or  b1701 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane  "	-2.74083	4.99608	[c] : atp[c] + coa[c] + h[p] + ttdca[p] --> amp[c] + ppi[c] + tdcoa[c] 		
19972	FACOAL141t2pp	Yes	fatty-acid-CoA ligase (tetradecenoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + h[p] + ttdcea[p] --> amp[c] + h[c] + ppi[c] + tdecoa[c]	Update	6.2.1.3	( b1805  or  b1701 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane  "	-1.14725	5.59188	[c] : atp[c] + coa[c] + h[p] + ttdcea[p] --> amp[c] + ppi[c] + tdecoa[c] 		
10747	FACOAL160t2pp	Yes	fatty-acid-CoA ligase (hexadecanoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + h[p] + hdca[p] --> amp[c] + h[c] + pmtcoa[c] + ppi[c]	Update	6.2.1.3	( b1701  or  b1805 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane  "	-2.74083	4.99608	[c] : atp[c] + coa[c] + h[p] + hdca[p] --> amp[c] + pmtcoa[c] + ppi[c] 		
19973	FACOAL161t2pp	Yes	fatty-acid-CoA ligase (hexadecenoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + h[p] + hdcea[p] --> amp[c] + h[c] + hdcoa[c] + ppi[c]	Update	6.2.1.3	( b1805  or  b1701 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane  "	-2.74083	4.99608	[c] : atp[c] + coa[c] + h[p] + hdcea[p] --> amp[c] + hdcoa[c] + ppi[c] 		
10751	FACOAL180t2pp	Yes	fatty-acid-CoA ligase (octadecanoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + h[p] + ocdca[p] --> amp[c] + h[c] + ppi[c] + stcoa[c]	Update	6.2.1.3	( b1805  or  b1701 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane  "	-2.74083	4.99608	[c] : atp[c] + coa[c] + h[p] + ocdca[p] --> amp[c] + ppi[c] + stcoa[c] 		
10749	FACOAL181t2pp	Yes	fatty-acid-CoA ligase (octadecenoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + h[p] + ocdcea[p] --> amp[c] + h[c] + odecoa[c] + ppi[c]	Update	6.2.1.3	( b1805  or  b1701 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane  "	-2.74083	4.99608	[c] : atp[c] + coa[c] + h[p] + ocdcea[p] --> amp[c] + odecoa[c] + ppi[c] 		
13379	FACOAL60t2pp	Yes	fatty-acid-CoA ligase (hexanoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + h[p] + hxa[p] --> amp[c] + h[c] + hxcoa[c] + ppi[c]	Update	6.2.1.3	( b1805  or  b1701 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane  "	-2.74083	4.99608	[c] : atp[c] + coa[c] + h[p] + hxa[p] --> amp[c] + hxcoa[c] + ppi[c] 		
13378	FACOAL80t2pp	Yes	fatty-acid-CoA ligase (octanoate transport via vectoral Co-A coupling)	atp[c] + coa[c] + h[p] + octa[p] --> amp[c] + h[c] + occoa[c] + ppi[c]	Update	6.2.1.3	( b1805  or  b1701 )	"FadD - works primarily on C12-C18;  some transport/activity of smaller FA's (C10)
MKA
AMF - assumed that a proton is moved with or that the fatty acid is in the protonated form"	"Reaction Proceedes in a two step mechanism PMID: 15213221, highly unlikely that its reversible

FadD has preferentiality for the longer chained FA and is active during aerobic growth, FadK is preferential for shorter FA and is active under anaerobic conditions PMID: 15213221

enzyme transports FA across inner membrane (FadL across outer membrane) at the same time that the CoA is added. See PMID: 15067008

Transport of FA across the inner membrane is represented as a symport with a proton which is justified the protonated FA hypothesis given in PMID: 10328825 and also justifies the necessity of an electrochemical gradient needed for inner membrane transport.  Also can be consistent with the vectoral mechanism given in PMID: 15067008 which doesn't mention ionization state.
AMF

MKA - reaction represented as accomplished by FadD/FadK because they are required to liberate fatty acids from the cell membrane  "	-2.74083	4.99608	[c] : atp[c] + coa[c] + h[p] + octa[p] --> amp[c] + occoa[c] + ppi[c] 		
2560	FADRx	Yes	FAD reductase	[c] : fad + h + nadh --> fadh2 + nad	Update		b3844	"JLR

EC#:  1.6.8.1  MKA"	"Fre will catalyze 5 flavin reducing reactions
see, PMID:8436124 and PMID: 12177066
Fre will not perform FADRx2 only FADRs, see fontecave et al. and man louie et al.
PMID: 3305505 talks about the action of Fre as a ferric iron reductase
AMF

CysIJ will catalyze the NADPH dependent flavin reactions, see PMID: 7657631

SsuE See PMID: 10480865, ssue will act of FAD and riboflavin, but since ssud only uses fmnh2, only the fmnh2 generating reactions were added"	-11.6304	7.78548	[c] : fad[c] + h[c] + nadh[c] --> fadh2[c] + nad[c] 		
2559	FADRx2	Yes	FAD reductase	[c] : fad + h + nadph --> fadh2 + nadp	Update		( b2763  and  b2764 )	"JLR
EC: 1.6.8.1 via Ecocyc"	"Fre will catalyze 5 flavin reducing reactions
see, PMID:8436124 and PMID: 12177066
Fre will not perform FADRx2 only FADRs, see fontecave et al. and man louie et al.
PMID: 3305505 talks about the action of Fre as a ferric iron reductase
AMF

CysIJ will catalyze the NADPH dependent flavin reactions, see PMID: 7657631

SsuE See PMID: 10480865, ssue will act of FAD and riboflavin, but since ssud only uses fmnh2, only the fmnh2 generating reactions were added"	-11.6304	7.78548	[c] : fad[c] + h[c] + nadph[c] --> fadh2[c] + nadp[c] 		
12348	FALDH2	Yes	formaldehyde dehydrogenase	[c] : hmgth + nad <==> Sfglutth + h + nadh	Update		b0356	"AMF
Ec 1.1.1.284"	"AMF
PMID: 1731906"	5.16584	4.34649	[c] : hmgth[c] + nad[c] <==> h[c] + nadh[c] + Sfglutth[c] 					
12473	FALDtex	Yes	formaldehyde transport via diffusion (extracellular to periplasm)	fald[e] <==> fald[p]	"Transport, Outer Membrane"			"AMF
"	"assumed diffusion

(personal communication with Milton Saier believes it should diffuse as well or additionally move through GlpF in the inner membrane)"	0	0	[c] : fald[e] <==> fald[p] 					
12470	FALDtpp	Yes	formaldehyde transport via diffusion (periplasm)	fald[p] <==> fald[c]	"Tranpsort, Inner Membrane"			"AMF
"	"diffusion reaction

personal communication with Milton Saier believes it should diffuse as well or additionally move through GlpF."	0	0	[c] : fald[p] <==> fald[c] 					
12349	FALGTHLs	Yes	formaldehyde glutathione ligase (spontaneous)	[c] : fald + gthrd <==> hmgth	Update			"AMF
spontaneous reaction
PMID: 1731906"	"spontaneous reaction
PMID: 1731906
AMF"	10.4677	3.49958	[c] : fald[c] + gthrd[c] <==> hmgth[c] 					
268	FBA	No	fructose-bisphosphate aldolase	[c] : fdp <==> dhap + g3p	Glycolysis/Gluconeogenesis	4.1.2.13	( b2097  or  b2925  or  b1773 )			5.38114	6.58758	[c] : fdp[c] <==> dhap[c] + g3p[c] 					
263	FBP	No	fructose-bisphosphatase	[c] : fdp + h2o --> f6p + pi	Glycolysis/Gluconeogenesis	3.1.3.11	( b4232  or  b3925 )	SMP	"for GlpX, the physiological function is unknown
from PMID: 10986273
""Strains lacking FBPase I (e.g., Delta fbp glpX+ strains DF657 and JLD2404) grew normally on glucose or fructose medium but were unable to grow on minimal medium supplemented with glycerol or other gluconeogenic substrates, indicating that chromosomal glpX+ does not compensate for the loss of fbp expression.""

- so it is thought that GlpX probably has a different function/ or is regulated
AMF"	-2.35942	1.9257	[c] : fdp[c] + h2o[c] --> f6p[c] + h[c] + pi[c] 					
1199	FCI	No	L-fucose isomerase	[c] : fuc-L <==> fcl-L	Alternate Carbon Metabolism	5.3.1.25	b2802	JLR		0	0.5	[c] : fuc-L[c] <==> fcl-L[c] 					
1200	FCLK	No	L-fuculokinase	[c] : atp + fcl-L --> adp + fc1p + h	Alternate Carbon Metabolism	2.7.1.51	b2803	JLR- had to add a proton to make it balance		-3.46855	2.28701	[c] : atp[c] + fcl-L[c] --> adp[c] + fc1p[c] 					
1201	FCLPA	No	L-fuculose 1-phosphate aldolase	[c] : fc1p <==> dhap + lald-L	Alternate Carbon Metabolism	4.1.2.17	( b2800  or  b2738 )	JLR	"PMID: 7016842
AMF"	3.94566	8.98948	[c] : fc1p[c] <==> dhap[c] + lald-L[c] 					
1145	FCLT	No	Ferrochelatase	[c] : fe2 + ppp9 --> (2) h + pheme	Cofactor and Prosthetic Group Biosynthesis	4.99.1.1	b0475	"tv
added Fe2+ to reactants and 2H+ to products"	JLR- JSE model didn't have Fe2+	No energy	No energy	[c] : fe2[c] + ppp9[c] --> (2) h[c] + pheme[c] 					
13749	FDH4pp	Yes	formate dehydrogenase (quinone-8) (periplasm)	for[p] + (2) h[c] + q8[c] --> co2[c] + h[p] + q8h2[c]	Oxidative Phosphorylation	1.2.2.1	( ( b1474  and  b1475  and  b1476 )  or  ( b3892  and  b3893  and  b3894 ) )	"AMF
PMID: 11884747"	"Fdh-N activity characterized inPMID: 11884747
along with Nitrate reductase
this is a change from iJR904 stoic

Fdo (Fdh-O) shows that These three subunits exhibit a considerable degree of identity with those of FDH-N, as predicted from inspection of the respective fdoGHI and fdnGHI operon sequences (6, 35). The alpha  and beta  subunits exhibited up to 75% identity, whereas the gamma  subunits were 45% identical.
therefore Fdo was assigned the same reactions
PMID: 9852007

FdhF was assigned only to FHL
Since nitrate suppresses Fdh-H synthesis, this enzyme is thought to play a role in fermentation and is not believed to be actively involved in electron transfer to either of the respiratory nitrate reductases
PMID: 12923080

AMF"	-25.7635	21.3166	[c] : for[p] + (2) h[c] + q8[c] --> co2[c] + h[p] + q8h2[c] 					
13748	FDH5pp	Yes	Formate Dehydrogenase (menaquinone-8) (periplasm)	for[p] + (2) h[c] + mqn8[c] --> co2[c] + h[p] + mql8[c]	Oxidative Phosphorylation	1.2.2.1	( ( b1474  and  b1475  and  b1476 )  or  ( b3892  and  b3893  and  b3894 ) )	"AMF
PMID: 11884747"	"Fdh-N activity characterized inPMID: 11884747
along with Nitrate reductase
this is a change from iJR904 stoic

Fdo (Fdh-O) shows that These three subunits exhibit a considerable degree of identity with those of FDH-N, as predicted from inspection of the respective fdoGHI and fdnGHI operon sequences (6, 35). The alpha  and beta  subunits exhibited up to 75% identity, whereas the gamma  subunits were 45% identical.
therefore Fdo was assigned the same reactions
PMID: 9852007

FdhF was assigned only to FHL
Since nitrate suppresses Fdh-H synthesis, this enzyme is thought to play a role in fermentation and is not believed to be actively involved in electron transfer to either of the respiratory nitrate reductases
PMID: 12923080

AMF"	-24.3116	17.1416	[c] : for[p] + (2) h[c] + mqn8[c] --> co2[c] + h[p] + mql8[c] 					
12342	FDMO	Yes	FMNH2-dependent monooxygenase	[c] : fmnh2 + isetac + o2 --> fmn + gcald + h + h2o + so3	Update		b0935	"AMF
PMID: 10480865"	"this is a substrate of SsuD amoung many others, no pathway for the breakdown of other end prodcuts, so only a few were included.

This is involved in alternate sulfur sources

TauD may be able to act on thsi substrate effectively, but reaction was not entered

See PMID: 10480865
AMF"	No energy	No energy	[c] : fmnh2[c] + isetac[c] + o2[c] --> fmn[c] + gcald[c] + h2o[c] + so3[c] 					
12343	FDMO2	Yes	FMNH2-dependent monooxygenase (methanesulfonate)	[c] : fmnh2 + mso3 + o2 --> fald + fmn + h + h2o + so3	Update		b0935	"AMF
PMID: 10480865"	"this is a substrate of SsuD amoung many others, no pathway for the breakdown of other end prodcuts, so only a few were included.

This is involved in alternate sulfur sources

See PMID: 10480865
AMF"	No energy	No energy	[c] : fmnh2[c] + mso3[c] + o2[c] --> fald[c] + fmn[c] + h2o[c] + so3[c] 					
13604	FDMO3	Yes	FMNH2-dependent monooxygenase (ethanesulfonate)	[c] : ethso3 + fmnh2 + o2 --> acald + fmn + h + h2o + so3	Update		b0935	"AMF
PMID: 10480865"	"this is a substrate of SsuD amoung many others, no pathway for the breakdown of other end prodcuts, so only a few were included.

This is involved in alternate sulfur sources

TauD may be able to act on thsi substrate effectively, but reaction was not entered

See PMID: 10480865
AMF"	No energy	No energy	[c] : ethso3[c] + fmnh2[c] + o2[c] --> acald[c] + fmn[c] + h2o[c] + so3[c] 					
13605	FDMO4	Yes	FMNH2-dependent monooxygenase (butanesulfonate)	[c] : butso3 + fmnh2 + o2 --> btal + fmn + h + h2o + so3	Update		b0935	"AMF
PMID: 10480865"	"this is a substrate of SsuD amoung many others, no pathway for the breakdown of other end prodcuts, so only a few were included.

This is involved in alternate sulfur sources

TauD may be able to act on thsi substrate effectively, but reaction was not entered

See PMID: 10480865
AMF"	No energy	No energy	[c] : butso3[c] + fmnh2[c] + o2[c] --> btal[c] + fmn[c] + h2o[c] + so3[c] 					
13609	FDMO6	Yes	FMNH2-dependent monooxygenase (sulfoacetate)	[c] : fmnh2 + o2 + sulfac --> fmn + glx + h + h2o + so3	Update		b0935	"AMF
PMID: 10480865"	"this is a substrate of SsuD amoung many others, no pathway for the breakdown of other end prodcuts, so only a few were included.

This is involved in alternate sulfur sources

TauD may be able to act on thsi substrate effectively, but reaction was not entered

See PMID: 10480865
AMF"	No energy	No energy	[c] : fmnh2[c] + o2[c] + sulfac[c] --> fmn[c] + glx[c] + h2o[c] + so3[c] 					
8821	FE2abcpp	Yes	iron (II) transport via ABC system (periplasm)	atp[c] + fe2[p] + h2o[c] --> adp[c] + fe2[c] + h[c] + pi[c]	"Transport, Inner Membrane"		b3409		JLR- believed to be an ATPase enzyme.	-7.01673	1.48181	[c] : atp[c] + fe2[p] + h2o[c] --> adp[c] + fe2[c] + h[c] + pi[c] 					
14042	FE2t2pp	Yes	iron (II) transport in via proton symport (periplasm)	fe2[p] + h[p] --> fe2[c] + h[c]	"Transport, Inner Membrane"		b2392	AMF	"see PMID: 11466284
AMF"	0	0	[c] : fe2[p] + h[p] --> fe2[c] + h[c] 					
9069	FE2tex	Yes	iron (II) transport via diffusion (extracellular to periplasm)	fe2[e] <==> fe2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : fe2[e] <==> fe2[p] 					
9130	FE3DCITabcpp	Yes	iron transport from ferric-dicitrate via ABC system (periplasm)	atp[c] + fe3dcit[p] + h2o[c] --> adp[c] + (2) cit[c] + fe3[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b4290  and  b4289  and  b4288  and  b4287 )	"AMF
PMID: 7654405 states only iron gains access to the cytoplasm for ferric citrate reaction"	"structure of fe3dcit may include 2 fe atoms, most state that there is one fe ion

reaction made to import 1 fe atom into the cytoplasm - PMID: 7654405

PMID: 12948487
also chacterized on transportDB
http://tcdb.ucsd.edu/tcdb/tcfamilybrowse.php?tcname=3.A.1
"	No energy	No energy	[c] : atp[c] + fe3dcit[p] + h2o[c] --> adp[c] + (2) cit[c] + fe3[c] + h[c] + pi[c] 					
9119	FE3DCITtonex	Yes	ferric-dicitrate transport via ton system (extracellular)	fe3dcit[e] + h[p] --> fe3dcit[p] + h[c]	"Transport, Outer Membrane"		( b4291  and  ( b1252  and  b3005  and  b3006 ) )	"AMF - PMID:8405078 and PMID: 10209752
assumption of 1 proton transported across the membrane
"	"PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR"	0	0	[c] : fe3dcit[e] + h[p] --> fe3dcit[p] + h[c] 					
13872	FE3DHBZR	Yes	"release of Fe(III) from ferric 2,3-dihydroxybenzoylserine"	[c] : fe3dhbzs --> 23dhbzs + fe3	Update			AMF	"added to release fe3 from the carrier, not sure iof it is catalyzed by an enzyme
see PMID: 2139424"	No energy	No energy	[c] : fe3dhbzs[c] --> 23dhbzs[c] + fe3[c] 					
13871	FE3DHBZSabcpp	Yes	"ferric 2,3-dihydroxybenzoylserine transport via ABC system (periplasm)"	atp[c] + fe3dhbzs[p] + h2o[c] --> adp[c] + fe3dhbzs[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0592  and  b0588  and  b0590  and  b0589 )		"see PMID: 2139424
AMF"	-7.01673	1.48181	[c] : atp[c] + fe3dhbzs[p] + h2o[c] --> adp[c] + fe3dhbzs[c] + h[c] + pi[c] 					
13870	FE3DHBZStonex	Yes	"ferric 2,3-dihydroxybenzoylserine transport via ton system (extracellular)"	fe3dhbzs[e] + h[p] --> fe3dhbzs[p] + h[c]	"Transport, Outer Membrane"		( ( b0805  and  ( b1252  and  b3005  and  b3006 ) )  or  ( b2155  and  ( b1252  and  b3005  and  b3006 ) ) )	"AMF
assumption of 1 proton transported across the membrane"	"see PMID: 2139424
AMF"	0	0	[c] : fe3dhbzs[e] + h[p] --> fe3dhbzs[p] + h[c] 					
8772	FE3HOXabcpp	Yes	ferric-dicitrate transport via ABC system (periplasm)	atp[c] + fe3hox[p] + h2o[c] --> adp[c] + fe3hox[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0153  and  b0151  and  b0152 )		"There are other molecules that are transported by this complex, listed on transportDB
http://tcdb.ucsd.edu/tcdb/tcfamilybrowse.php?tcname=3.A.1

PMID: 14668326
"	-7.01673	1.48181	[c] : atp[c] + fe3hox[p] + h2o[c] --> adp[c] + fe3hox[c] + h[c] + pi[c] 					
10837	FE3HOXexs	Yes	Fe(III) hydroxamate Fe-loading reaction (spontaneaous)	[e] : fe3 + fe3hox-un --> fe3hox	Update			MKA - necessary rxn for siderophore's function	"reaction reflects function of siderophore 

Fe(III) hydroxamate is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  not produced by K-12 ecoli, but they can ingest it and utilize the Fe it traps.  then releases siderophore to collect more Fe

MKA

reaction is in network to reflact the recycling of siderophones and then becoming reactivated with Fe to be took up again into the system -  AMF"	No energy	No energy	[e] : fe3[e] + fe3hox-un[e] --> fe3hox[e] 					
10830	FE3HOXR1	Yes	Fe(III)hydroxamate reductase	[c] : fadh2 + (2) fe3hox --> fad + (2) fe2 + (2) fe3hox-un + (2) h	Update				"indirectly (?) reduced by activity of Fre   

Fe(III) hydroximate is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  not produced by K-12 ecoli, but they can ingest it and utilize the Fe it traps.  then releases siderophore to collect more Fe

MKA"	No energy	No energy	[c] : fadh2[c] + (2) fe3hox[c] --> fad[c] + (2) fe2[c] + (2) fe3hox-un[c] + (2) h[c] 					
10818	FE3HOXR2	Yes	Fe(III)hydroxamate reductase	[c] : (2) fe3hox + fmnh2 --> (2) fe2 + (2) fe3hox-un + fmn + (2) h	Update			"
MKA"	"any flavin (fadh2, fmnh2, rivlf) can act as e-donor;  
indirectly (?) reduced by activity of Fre 
MKA
"	No energy	No energy	[c] : (2) fe3hox[c] + fmnh2[c] --> (2) fe2[c] + (2) fe3hox-un[c] + fmn[c] + (2) h[c] 					
10831	FE3HOXR3	Yes	Fe(III)hydroxamate reductase	[c] : (2) fe3hox + rbflvrd --> (2) fe2 + (2) fe3hox-un + (2) h + ribflv	Update				"indirectly (?) reduced by activity of Fre 

Fe(III) hydroximate is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  not produced by K-12 ecoli, but they can ingest it and utilize the Fe it traps.  then releases siderophore to collect more Fe

MKA"	No energy	No energy	[c] : (2) fe3hox[c] + rbflvrd[c] --> (2) fe2[c] + (2) fe3hox-un[c] + (2) h[c] + ribflv[c] 					
9121	FE3HOXtonex	Yes	Fe(III)hydroxamine transport via ton system (extracellular)	fe3hox[e] + h[p] --> fe3hox[p] + h[c]	"Transport, Outer Membrane"		( b0150  and  ( b1252  and  b3005  and  b3006 ) )	"AMF - PMID:8405078 and PMID: 10209752
assumption of 1 proton transported across the membrane"	"PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR"	0	0	[c] : fe3hox[e] + h[p] --> fe3hox[p] + h[c] 					
11825	FE3HOXUtex	Yes	Fe(III)hydroxamate unloaded secretion	fe3hox-un[c] + h[p] --> fe3hox-un[p] + h[c]	Update			"presumed reaction - no transporters known.   symport/antiport unknown MKA AMF
"	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes
AMF"	0	0	[c] : fe3hox-un[c] + h[p] --> fe3hox-un[p] + h[c] 					
11826	FE3HOXUtpp	Yes	Fe(III)hydroxamate unloaded secretion (extracellular)	fe3hox-un[p] + h[p] --> fe3hox-un[e] + h[c]	Update			"presumed reaction - no transporters known.   symport/antiport unknown MKA AMF
"	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes
AMF"	0	0	[c] : fe3hox-un[p] + h[p] --> fe3hox-un[e] + h[c] 					
10829	FE3Ri	Yes	Fe(III) reduction	[c] : fadh2 + (2) fe3 --> fad + (2) fe2 + (2) h	Update		b3844	as reported on ecocyc - MKA	"PMID: 3305505 talks about the action of Fre as a ferric iron reductase

AMF
"	No energy	No energy	[c] : fadh2[c] + (2) fe3[c] --> fad[c] + (2) fe2[c] + (2) h[c] 					
13677	FE3tex	Yes	iron (III) transport via diffusion (extracellular to periplasm)	fe3[e] <==> fe3[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : fe3[e] <==> fe3[p] 					
8769	FECRMabcpp	Yes	ferrichrome transport via ABC system (periplasm)	atp[c] + fecrm[p] + h2o[c] --> adp[c] + fecrm[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0153  and  b0151  and  b0152 )		"There are other molecules that are transported by this complex, listed on transportDB
http://tcdb.ucsd.edu/tcdb/tcfamilybrowse.php?tcname=3.A.1

PMID: 14668326
"	-7.01673	1.48181	[c] : atp[c] + fecrm[p] + h2o[c] --> adp[c] + fecrm[c] + h[c] + pi[c] 					
10844	FECRMexs	Yes	ferrichrome Fe(III)-loading reaction (spontaneous)	[e] : fe3 + fecrm-un --> fecrm	Update			MKA - reaction intrinsinc to function of ferrichrome as a siderophore AMF	"spontaneous

reaction is in network to reflact the recycling of siderophones and then becoming reactivated with Fe to be took up again into the system -  AMF"	No energy	No energy	[e] : fe3[e] + fecrm-un[e] --> fecrm[e] 					
10839	FECRMR1	Yes	Ferrichrome reductase	[c] : fadh2 + (2) fecrm --> fad + (2) fe2 + (2) fecrm-un + (2) h	Update			MKA	"indirectly (?) reduced by activity of Fre   

ferrichrome is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  not produced by K-12 ecoli, but they can ingest it and utilize the Fe it traps.  then releases siderophore to collect more Fe

MKA"	No energy	No energy	[c] : fadh2[c] + (2) fecrm[c] --> fad[c] + (2) fe2[c] + (2) fecrm-un[c] + (2) h[c] 					
10841	FECRMR2	Yes	Ferrichrome reductase	[c] : (2) fecrm + fmnh2 --> (2) fe2 + (2) fecrm-un + fmn + (2) h	Update			"MKA
see FCRMRED1 for refferences"	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.

Ferrichrome is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Not produced by K-12, just ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA"	No energy	No energy	[c] : (2) fecrm[c] + fmnh2[c] --> (2) fe2[c] + (2) fecrm-un[c] + fmn[c] + (2) h[c] 					
10842	FECRMR3	Yes	Ferrichrome reductase	[c] : (2) fecrm + rbflvrd --> (2) fe2 + (2) fecrm-un + (2) h + ribflv	Update			"MKA
see FCRMRED1 for references"	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.

Ferrichrome is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Not produced by K-12.  Just ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA"	No energy	No energy	[c] : (2) fecrm[c] + rbflvrd[c] --> (2) fe2[c] + (2) fecrm-un[c] + (2) h[c] + ribflv[c] 					
9122	FECRMtonex	Yes	ferrichrome transport via ton system (extracellular)	fecrm[e] + h[p] --> fecrm[p] + h[c]	"Transport, Outer Membrane"		( b0150  and  ( b1252  and  b3005  and  b3006 ) )	"AMF - PMID:8405078 and PMID: 10209752
assumption of 1 proton transported across the membrane"	"PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR"	0	0	[c] : fecrm[e] + h[p] --> fecrm[p] + h[c] 					
11833	FECRMUtex	Yes	ferrichrome (minus Fe) secretion (to extracellular)	fecrm-un[p] + h[p] --> fecrm-un[e] + h[c]	Update			assuming transport is facilitated by proton exchange - actual secretion mech. uncharacterized.   MKA AMF	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes
AMF"	0	0	[c] : fecrm-un[p] + h[p] --> fecrm-un[e] + h[c] 					
11832	FECRMUtpp	Yes	ferrichrome (minus Fe) secretion (to periplasm)	fecrm-un[c] + h[p] --> fecrm-un[p] + h[c]	Update			assuming transport is facilitated by proton exchange - actual secretion mech. uncharacterized.   MKA AMF	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes
AMF"	0	0	[c] : fecrm-un[c] + h[p] --> fecrm-un[p] + h[c] 					
8768	FEENTERabcpp	Yes	Fe-enterobactin transport via ABC system (periplasm)	atp[c] + feenter[p] + h2o[c] --> adp[c] + feenter[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0592  and  b0588  and  b0590  and  b0589 )		"PMID: 7551033

also chacterized on transportDB
http://tcdb.ucsd.edu/tcdb/tcfamilybrowse.php?tcname=3.A.1
"	-7.01673	1.48181	[c] : atp[c] + feenter[p] + h2o[c] --> adp[c] + feenter[c] + h[c] + pi[c] 					
10834	FEENTERexs	Yes	enterobactin Fe(III) binding (spontaneous)	[e] : enter + fe3 --> feenter	Update			MKA AMF	"reaction reflects function of siderophore 

Enterobactor is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Only siderophore produced by K-12.  produce/ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA

reaction is in network to reflact the recycling of siderophones and then becoming reactivated with Fe to be took up again into the system -  AMF"	No energy	No energy	[e] : enter[e] + fe3[e] --> feenter[e] 					
10832	FEENTERR1	Yes	Fe-enterobactin reduction (Fe(III)-unloading)	[c] : fadh2 + (2) feenter --> (2) enter + fad + (2) fe2 + (2) h	Update			MKA 	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.

Enterobactor is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Only siderophore produced by K-12.  produce/ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA"	No energy	No energy	[c] : fadh2[c] + (2) feenter[c] --> (2) enter[c] + fad[c] + (2) fe2[c] + (2) h[c] 					
10827	FEENTERR2	Yes	Fe-enterobactin reduction (Fe(III)-unloading)	[c] : (2) feenter + fmnh2 --> (2) enter + (2) fe2 + fmn + (2) h	Update			MKA 	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.

Enterobactor is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Only siderophore produced by K-12.  produce/ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA


"	No energy	No energy	[c] : (2) feenter[c] + fmnh2[c] --> (2) enter[c] + (2) fe2[c] + fmn[c] + (2) h[c] 					
10833	FEENTERR3	Yes	Fe-enterobactin reduction (Fe(III)-unloading)	[c] : (2) feenter + rbflvrd --> (2) enter + (2) fe2 + (2) h + ribflv	Update			MKA 	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre - MKA"	No energy	No energy	[c] : (2) feenter[c] + rbflvrd[c] --> (2) enter[c] + (2) fe2[c] + (2) h[c] + ribflv[c] 					
11819	FEENTERtex	Yes	enterochelin transport (secretion periplasm)	enter[p] + h[p] --> enter[e] + h[c]	Update			"assumption of costing the cell 1 proton to pump out of periplasm, mechanism not known 
PMID: 12068807
"	"assumption of costing the cell 1 proton to pump it out of the periplasm, method not known

PMID: 12068807"	0	0	[c] : enter[p] + h[p] --> enter[e] + h[c] 					
9120	FEENTERtonex	Yes	Fe-enterobactin transport via ton system (extracellular)	feenter[e] + h[p] --> feenter[p] + h[c]	"Transport, Outer Membrane"		( b0584  and  ( b1252  and  b3005  and  b3006 ) )	"AMF - PMID:8405078 and PMID: 10209752
assumption of 1 proton transported across the membrane"	"PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR"	0	0	[c] : feenter[e] + h[p] --> feenter[p] + h[c] 					
11818	FEENTERtpp	Yes	enterochelin transport (secretion)	enter[c] + h[p] --> enter[p] + h[c]	Update		b0591	"export of enter to periplasm  AMF PMID: 12068807 
"	"PMID: 12068807 
states that this protein is responsible to pump enterobactin out of the cytoplasm, but it doesnt know the mechansim of how it leaves the periplasm
also the stoich of the reaction is not known"	0	0	[c] : enter[c] + h[p] --> enter[p] + h[c] 					
8771	FEOXAMabcpp	Yes	ferroxamine transport via ABC system (periplasm)	atp[c] + feoxam[p] + h2o[c] --> adp[c] + feoxam[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0153  and  b0151  and  b0152 )		"There are other molecules that are transported by this complex, listed on transportDB
http://tcdb.ucsd.edu/tcdb/tcfamilybrowse.php?tcname=3.A.1

PMID: 14668326
"	-7.01673	1.48181	[c] : atp[c] + feoxam[p] + h2o[c] --> adp[c] + feoxam[c] + h[c] + pi[c] 					
10852	FEOXAMexs	Yes	ferroxamine Fe3-loading reaction (spontaneous)	[e] : fe3 + feoxam-un --> feoxam	Update			spontaneous reaction in extracellular space	"spontanous - MKA

reaction is in network to reflact the recycling of siderophones and then becoming reactivated with Fe to be took up again into the system -  AMF"	No energy	No energy	[e] : fe3[e] + feoxam-un[e] --> feoxam[e] 					
10853	FEOXAMR1	Yes	ferroxamine reductase	[c] : fadh2 + (2) feoxam --> fad + (2) fe2 + (2) feoxam-un + (2) h	Update			MKA	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.  FAD may be prefered

ferroxamine is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Not produced by K-12, just ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA"	No energy	No energy	[c] : fadh2[c] + (2) feoxam[c] --> fad[c] + (2) fe2[c] + (2) feoxam-un[c] + (2) h[c] 					
10854	FEOXAMR2	Yes	ferroxamine reductase	[c] : (2) feoxam + fmnh2 --> (2) fe2 + (2) feoxam-un + fmn + (2) h	Update			see FEOXAMRED1 for references	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.  FAD may be prefered

ferroxamine is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Not produced by K-12, just ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA"	No energy	No energy	[c] : (2) feoxam[c] + fmnh2[c] --> (2) fe2[c] + (2) feoxam-un[c] + fmn[c] + (2) h[c] 					
10855	FEOXAMR3	Yes	ferroxamine reductase	[c] : (2) feoxam + rbflvrd --> (2) fe2 + (2) feoxam-un + (2) h + ribflv	Update			"see FEOXAMR1 for references

reaction also work w/ fad and fmn.  fad may be prefered
MKA"	"reaction can involve any flavin (FAD, FMN, Ribflv).  indirectly (?) catalyzed by Fre.  FAD may be prefered

ferroxamine is a siderophore - an iron-uptake molecule secreted by other micro-organisms.  Not produced by K-12, just ingest it and remove the Fe before re-secreting the siderophore to collect more Fe from the environment.

MKA"	No energy	No energy	[c] : (2) feoxam[c] + rbflvrd[c] --> (2) fe2[c] + (2) feoxam-un[c] + (2) h[c] + ribflv[c] 					
9124	FEOXAMtonex	Yes	ferroxamine transport via ton system (extracellular)	feoxam[e] + h[p] --> feoxam[p] + h[c]	"Transport, Outer Membrane"		( b0150  and  ( b1252  and  b3005  and  b3006 ) )	"AMF - PMID:8405078 and PMID: 10209752
assumption of 1 proton transported across the membrane"	"PMID: 8405078 and PMID: 10209752  gives information about energy dependent transport across the outer membrane associated with the Ton complex.  Actual number of protons translocated is unknown, assumed to be 1 across the inner membrane.

PMID: 7654405 - TonB related activities are impied but not entirely abolished by mutations in exbBD - which are included in GPR"	0	0	[c] : feoxam[e] + h[p] --> feoxam[p] + h[c] 					
11828	FEOXAMUtex	Yes	ferroxamine (minus Fe3) secretion (to extracellular)	feoxam-un[p] + h[p] --> feoxam-un[e] + h[c]	Update			"K-12 re-secrete siderophores, though exact mech has not been found.  using proton antiport to approximate energy requirement -  MKA AMF"	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes
AMF"	0	0	[c] : feoxam-un[p] + h[p] --> feoxam-un[e] + h[c] 					
11827	FEOXAMUtpp	Yes	ferroxamine (minus Fe3) secretion (to periplasm)	feoxam-un[c] + h[p] --> feoxam-un[p] + h[c]	Update			"K-12 re-secrete siderophores, though exact mech has not been found.  using proton antiport to approximate energy requirement -  MKA AMF"	"transport mechanism not know, but necessary - K-12 ecoli do not produce nor degrade aerobactin, just utilze Fe it sequesters.
may not use proton antiport - just put in system to approximate energy expense
MKA

transport mech unknown - proton antiport assumed for inner and outer membranes
AMF"	0	0	[c] : feoxam-un[c] + h[p] --> feoxam-un[p] + h[c] 					
13656	FEROpp	Yes	ferroxidase	[p] : (4) fe2 + (4) h + o2 --> (4) fe3 + (2) h2o	Update	1.16.3.1	b0123	AMF	"characterized in PMID: 15516598 
activated by CuII
AMF"	No energy	No energy	[p] : (4) fe2[p] + (4) h[p] + o2[p] --> (4) fe3[p] + (2) h2o[p] 					
2948	FFSD	No	beta-fructofuranosidase	[c] : h2o + suc6p --> fru + g6p	Alternate Carbon Metabolism	3.2.1.26		JLR	JLR- can't find gene 	-3.13375	2.90645	[c] : h2o[c] + suc6p[c] --> fru[c] + g6p[c] 					
1628	FHL	No	Formate-hydrogen lyase	[c] : for + h --> co2 + h2	Pyruvate Metabolism		( b4079  and  ( b2481  and  b2482  and  b2483  and  b2484  and  b2485  and  b2486  and  b2487  and  b2488  and  b2489  and  b2490 ) )	JLR- NH page 268	"JLR- NH page 268, also says that h2 production is probably consumed by other hydrogenase enzymes (pg 271). 

FHL_1.3 is active at pH 6.5 by the FdhF and hydrogenase 3 (hyc) complex (FHL-1) and active at pH 7.5 by complex with FdhF and hydrogenase 4 (FHL-2). FHL activity is also thought to be dependant on the F0F1-ATPase
PMID: 11959127
AMF

The sotichiometry for FHL_1.3 is taken from
PMID: 15848284
and doesn't give a stoich for FHL-2 complex"	2.1	1	[c] : for[c] + h[c] --> co2[c] + h2[c] 					
13411	FHL_1.3	Yes	Formate-hydrogen lyase (proton translocating)	for[c] + (2.3) h[c] --> co2[c] + (1.3) h[p] + h2[c]	Update		( b4079  and  ( b2719  and  b2720  and  b2721  and  b2722  and  b2723  and  b2724 ) )	AMF - stoich from PMID: 15848284	"FHL_1.3 is active at pH 6.5 by the FdhF and hydrogenase 3 (hyc) complex (FHL-1) and active at pH 7.5 by complex with FdhF and hydrogenase 4 (FHL-2). FHL activity is also thought to be dependant on the F0F1-ATPase
PMID: 11959127
AMF

The sotichiometry for FHL_1.3 is taken from
PMID: 15848284
and doesn't give a stoich for FHL-2 complex"	2.1	1	[c] : for[c] + (2.3) h[c] --> co2[c] + (1.3) h[p] + h2[c] 					
13850	FLDR	Yes	flavodoxin reductase (NADPH)	[c] : fldox + h + nadph --> fldrd + nadp	Update	1.18.1.2	b3924	AMF	"from ecocyc
Flavodoxin NADP+ reductase is a part of chains of redox reactions and in E. coli is also required for the activation of anaerobic ribonucleoside reductase, pyruvate-formate lyase and methionine synthase. It forms a multi-enzyme complex with flavodoxin and the appropriate activating enzyme. Ferredoxin does not substitute for flavodoxin in E. coli. The FN reductase uses noncovalently bound FAD as a cofactor. Flavodoxin contains FMN. [ Bianchi93  , Jenkins94  , Bianchi95  ]

AMF"	No energy	No energy	[c] : fldox[c] + h[c] + nadph[c] --> fldrd[c] + nadp[c] 					
49	FLVR	Yes	flavin reductase	[c] : h + nadph + ribflv --> nadp + rbflvrd	Update	1.5.1.30	( b3844  or  ( b2763  and  b2764 ) )	ecoli EC 1.6.8.1 - MKA	"Fre will catalyze 5 flavin reducing reactions
see, PMID:8436124 and PMID: 12177066
Fre will not perform FADRx2 only FADRs, see fontecave et al. and man louie et al.
PMID: 3305505 talks about the action of Fre as a ferric iron reductase
AMF

CysIJ will catalyze the NADPH dependent flavin reactions, see PMID: 7657631

SsuE See PMID: 10480865, ssue will act of FAD and riboflavin, but since ssud only uses fmnh2, only the fmnh2 generating reactions were added"	-4.65546	6.2976	[c] : h[c] + nadph[c] + ribflv[c] --> nadp[c] + rbflvrd[c] 					
7631	FLVR(NAD)	Yes	flavin reductase (NAD)	[c] : h + nadh + ribflv --> nad + rbflvrd	Update	1.5.1.30	b3844	"Added for Staph (SAB).  Annotation is not specific, so this reaction may or may not happen."	"Fre will catalyze 5 flavin reducing reactions
see, PMID:8436124 and PMID: 12177066
Fre will not perform FADRx2 only FADRs, see fontecave et al. and man louie et al.
PMID: 3305505 talks about the action of Fre as a ferric iron reductase
AMF

CysIJ will catalyze the NADPH dependent flavin reactions, see PMID: 7657631

SsuE See PMID: 10480865, ssue will act of FAD and riboflavin, but since ssud only uses fmnh2, only the fmnh2 generating reactions were added"	-4.65546	6.2976	[c] : h[c] + nadh[c] + ribflv[c] --> nad[c] + rbflvrd[c] 					
3857	FMETTRS	Yes	Methionyl-tRNA formyltransferase	[c] : 10fthf + mettrna --> fmettrna + h + thf	Update	2.1.2.9	b3288		Added to incorporate tRNA peptides into model	No energy	No energy	[c] : 10fthf[c] + mettrna[c] --> fmettrna[c] + h[c] + thf[c] 					
140	FMNAT	No	FMN adenylyltransferase	[c] : atp + fmn + h --> fad + ppi	Cofactor and Prosthetic Group Biosynthesis	2.7.7.2	b0025			-1.92466	3.75933	[c] : atp[c] + fmn[c] --> fad[c] + ppi[c] 					
2562	FMNRx	Yes	FMN reductase	[c] : fmn + h + nadh --> fmnh2 + nad	Update		( b3844  or  b0937 )	"JLR
EC# 1.6.8.1  - MKA"	"FAD prefered substrate of Fre
- rxns are mostly repressed in aerobic environment
MKA

rxn in CysI - PMID: 7657631 

agree w/ this
AMF

for SsuE See PMID: 10480865, ssue will act of FAD and riboflavin, but since ssud only uses fmnh2, only the fmnh2 generating reactions were added"	-11.6304	7.78548	[c] : fmn[c] + h[c] + nadh[c] --> fmnh2[c] + nad[c] 					
2561	FMNRx2	Yes	FMN reductase	[c] : fmn + h + nadph --> fmnh2 + nadp	Update		( b3844  or  b0937  or  ( b2763  and  b2764 ) )	"JLR

EC 1.6.8.1 according to EcoCyc  - MKA"	"Fre will catalyze 5 flavin reducing reactions
see, PMID:8436124 and PMID: 12177066
Fre will not perform FADRx2 only FADRs, see fontecave et al. and man louie et al.
PMID: 3305505 talks about the action of Fre as a ferric iron reductase
AMF

CysIJ will catalyze the NADPH dependent flavin reactions, see PMID: 7657631

SsuE See PMID: 10480865, ssue will act of FAD and riboflavin, but since ssud only uses fmnh2, only the fmnh2 generating reactions were added"	-11.6304	7.78548	[c] : fmn[c] + h[c] + nadph[c] --> fmnh2[c] + nadp[c] 					
13409	FORt2pp	Yes	"formate transport via proton symport (uptake only, periplasm)"	for[p] + h[p] --> for[c] + h[c]	"Transport, Inner Membrane"		( b0904  or  b2492 )	AMF	"state that formate is probably taken up by a proton gradient
PMID: 15848284

also, transport database states that uptake is probably by symport, but less sure about transport out, probably by antiport or excahange
http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=2.A.44

FocB is similar to FocA, so it is assigned the same function

AMF"	0	0	[c] : for[p] + h[p] --> for[c] + h[c] 					
9070	FORtex	Yes	formate transport via diffusion (extracellular to periplasm)	for[e] <==> for[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : for[e] <==> for[p] 					
13410	FORtppi	Yes	formate transport via diffusion (cytoplasm to periplasm)	for[c] --> for[p]	"Transport, Inner Membrane"		( b0904  or  b2492 )	AMF	"state that formate is probably taken up by a proton gradient
PMID: 15848284

also, transport database states that uptake is probably by symport, but less sure about transport out, probably by antiport or excahange
http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=2.A.44

FocB is similar to FocA, so it is assigned the same function

AMF"	0	0	[c] : for[c] --> for[p] 					
1183	FRD2	No	fumarate reductase	[c] : fum + mql8 --> mqn8 + succ	Citric Acid Cycle	1.3.99.1	( b4151  and  b4152  and  b4153  and  b4154 )	JLR- E.coli uses menaquinone and demethylmenaquinone instead of ubiquinone		7.36647	17.2766	[c] : fum[c] + mql8[c] --> mqn8[c] + succ[c] 					
1184	FRD3	No	fumarate reductase	[c] : 2dmmql8 + fum --> 2dmmq8 + succ	Citric Acid Cycle	1.3.99.1	( b4151  and  b4152  and  b4153  and  b4154 )	JLR- E.coli uses menaquinone and demethylmenaquinone instead of ubiquinone		2.29999	15.1108	[c] : 2dmmql8[c] + fum[c] --> 2dmmq8[c] + succ[c] 					
2820	FRUK	No	fructose-1-phosphate kinase	[c] : atp + f1p --> adp + fdp + h	Alternate Carbon Metabolism	2.7.1.56	b2168			-4.65732	2.09859	[c] : atp[c] + f1p[c] --> adp[c] + fdp[c] 					
10030	FRULYSDG	Yes	Fructoselysine phosphate deglycase	[c] : frulysp + h2o <==> g6p + lys-L	Update		b3371	"MKA
homologous to glucosamine G-P synthase
Km=0.4mM"	"MKA
PubMed ID:  12147680
AMF"	2.97656	2.87507	[c] : frulysp[c] + h2o[c] <==> g6p[c] + lys-L[c] 					
11867	FRULYSK	Yes	Fructoselysine Kinase	[c] : atp + frulys --> adp + frulysp + h	Update		b3374	"MKA
Km = 18 microM
part of Pfk-B / ribokinase family"	"PubMed ID:  12147680
MKA
AMF"	-4.65732	2.09859	[c] : atp[c] + frulys[c] --> adp[c] + frulysp[c] 					
10044	FRULYSt2rpp	Yes	Fructoselysine cationic transporter	frulys[p] + h[p] <==> frulys[c] + h[c]	Update		b3370	MKA	"assumed to be a symporter like other cationic amino acid transporteres

Pubmed ID: 12147680

AMF
MKA
"	0	0	[c] : frulys[p] + h[p] <==> frulys[c] + h[c] 					
10045	FRULYStex	Yes	fructoselysine transporter via diffusion (extracellular)	frulys[e] <==> frulys[p]	Update			MKA - mech of transport unknown	"MKA - assumed reaction, mech unknown
AMF - small molecule, diffusion assumed"	0	0	[c] : frulys[e] <==> frulys[p] 					
8825	FRUpts2pp	Yes	Fructose transport via PEP:Pyr PTS (f6p generating) (periplasm)	fru[p] + pep[c] --> f6p[c] + pyr[c]	"Transport, Inner Membrane"		( b1817  and  b1818  and  b1819  and  b2415  and  b2416 )	JLR		-10.1729	3.20748	[c] : fru[p] + pep[c] --> f6p[c] + pyr[c] 
8824	FRUptspp	Yes	D-fructose transport via PEP:Pyr PTS (periplasm)	fru[p] + pep[c] --> f1p[c] + pyr[c]	"Transport, Inner Membrane"		( b2167  and  b2169  and  b2415  and  b2416 )			-10.1729	3.20748	[c] : fru[p] + pep[c] --> f1p[c] + pyr[c] 
9071	FRUtex	Yes	D-fructose transport via diffusion (extracellular to periplasm)	fru[e] <==> fru[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : fru[e] <==> fru[p] 
9986	FRUURt2rpp	Yes	"D-fructuronate transport via proton symport, reversible (periplasm)"	fruur[p] + h[p] <==> fruur[c] + h[c]	Update		b4321	KA	"MKA

gntP does not encode a glucuronate transporter
PMID: 15516583 
AMF"	0	0	[c] : fruur[p] + h[p] <==> fruur[c] + h[c] 
9989	FRUURtex	Yes	D-fructuronate transport via diffusion (extracellular)	fruur[e] <==> fruur[p]	Update			MKA	assumed diffusion	0	0	[c] : fruur[e] <==> fruur[p] 
94	FTHFD	No	formyltetrahydrofolate deformylase	[c] : 10fthf + h2o --> for + h + thf	Folate Metabolism	3.5.1.10	b1232			-7.28786	4.08995	[c] : 10fthf[c] + h2o[c] --> for[c] + h[c] + thf[c] 
8826	FUCPt6_2pp	Yes	Fucose 1-phosphate transport via phosphate antiport (periplasm)	fuc1p-L[p] + (2) pi[c] --> fuc1p-L[c] + (2) pi[p]	"Transport, Inner Membrane"		b3666	JLR	"JLR- NH has it listed in a table on page 1137, but it lists Fucose 6P not 1P. I assumed it was a typo since 6P isn't in Kegg and can't be found on google."	0	0	[c] : fuc1p-L[p] + (2) pi[c] --> fuc1p-L[c] + (2) pi[p] 
9072	FUCPtex	Yes	L-fucose 1-phosphate transport via diffusion (extracellular to periplasm)	fuc1p-L[e] <==> fuc1p-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : fuc1p-L[e] <==> fuc1p-L[p] 
9073	FUCtex	Yes	L-fucose transport via diffusion (extracellular to periplasm)	fuc-L[e] <==> fuc-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : fuc-L[e] <==> fuc-L[p] 
8827	FUCtpp	Yes	L-fucose transport via proton symport (periplasm)	fuc-L[p] + h[p] <==> fuc-L[c] + h[c]	"Transport, Inner Membrane"		b2801	JLR		0	0	[c] : fuc-L[p] + h[p] <==> fuc-L[c] + h[c] 
542	FUM	No	fumarase	[c] : fum + h2o <==> mal-L	Citric Acid Cycle	4.2.1.2	( b1612  or  b4122  or  b1611 )			-0.278853	2.66722	[c] : fum[c] + h2o[c] <==> mal-L[c] 
8828	FUMt2_2pp	Yes	Fumarate transport via proton symport (2 H) (periplasm)	fum[p] + (2) h[p] --> fum[c] + (2) h[c]	"Transport, Inner Membrane"		b3528	JLR		0	0	[c] : fum[p] + (2) h[p] --> fum[c] + (2) h[c] 
8829	FUMt2_3pp	Yes	Fumarate transport via proton symport (3 H) (periplasm)	fum[p] + (3) h[p] --> fum[c] + (3) h[c]	"Transport, Inner Membrane"		( b4138  or  b4123  or  b0621 )	JLR	JLR- for DcuC the number of protons transported is assumed to be the same as for DcuAB.	0	0	[c] : fum[p] + (3) h[p] --> fum[c] + (3) h[c] 
9074	FUMtex	Yes	Fumarate transport via diffusion (extracellular to periplasm)	fum[e] <==> fum[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : fum[e] <==> fum[p] 
3534	G1PACT	No	glucosamine-1-phosphate N-acetyltransferase	[c] : accoa + gam1p --> acgam1p + coa + h	Cell Envelope Biosynthesis	2.3.1.157	b3730			-2.48774	5.01459	[c] : accoa[c] + gam1p[c] --> acgam1p[c] + coa[c] + h[c] 
9714	G1PPpp	Yes	Glucose-1-phosphatase	[p] : g1p + h2o --> glc-D + pi	Update	3.1.3.10	b1002	KC	in periplasm	-3.54819	2.12947	[p] : g1p[p] + h2o[p] --> glc-D[p] + h[p] + pi[p] 
12313	G1Ptex	Yes	D-glucose 1-phosphate transport via diffusion	g1p[e] <==> g1p[p]	"Transport, Outer Membrane"			AMF - assumed	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : g1p[e] <==> g1p[p] 		
2487	G1PTT	No	glucose-1-phosphate thymidylyltransferase	[c] : dttp + g1p + h --> dtdpglu + ppi	Cell Envelope Biosynthesis	2.7.7.24	( b2039  or  b3789 )	JLR		-1.12149	3.25471	[c] : dttp[c] + g1p[c] --> dtdpglu[c] + ppi[c] 		
1	G1SAT	Yes	glutamate-1-semialdehyde aminotransferase	[c] : glu1sa <==> 5aop	Cofactor and Prosthetic Group Biosynthesis	5.4.3.8	b0154		"assumed reversible reaction
AMF"	-2.42139	2.1337	[c] : glu1sa[c] <==> 5aop[c] 		
13817	G2PPpp	Yes	glycerol 2-phosphate phosphatase (periplasmic)	[p] : glyc2p + h2o --> glyc + pi	Update		b4055	AMF	"from PMID: 9011040
AMF
very general phosphatase - probably more substrates
"	-3.54819	2.12947	[p] : glyc2p[p] + h2o[p] --> glyc[p] + h[p] + pi[p] 		
19325	G3PAT120	Yes	glycerol-3-phosphate acyltransferase (C12:0)	[c] : ddcaACP + glyc3p --> 1ddecg3p + ACP	Glycerophospholipid Metabolism	2.3.1.15	b4041	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-3.97568	4.69324	[c] : ddcaACP[c] + glyc3p[c] --> 1ddecg3p[c] + ACP[c] 		
19232	G3PAT140	Yes	glycerol-3-phosphate acyltransferase (C14:0)	[c] : glyc3p + myrsACP --> 1tdecg3p + ACP	Glycerophospholipid Metabolism	2.3.1.15	b4041	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-3.97568	4.69324	[c] : glyc3p[c] + myrsACP[c] --> 1tdecg3p[c] + ACP[c] 		
19235	G3PAT141	Yes	glycerol-3-phosphate acyltransferase (C14:1)	[c] : glyc3p + tdeACP --> 1tdec7eg3p + ACP	Glycerophospholipid Metabolism	2.3.1.15	b4041	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-2.38209	5.32305	[c] : glyc3p[c] + tdeACP[c] --> 1tdec7eg3p[c] + ACP[c] 		
19233	G3PAT160	Yes	glycerol-3-phosphate acyltransferase (C16:0)	[c] : glyc3p + palmACP --> 1hdecg3p + ACP	Glycerophospholipid Metabolism	2.3.1.15	b4041	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-3.97568	4.69324	[c] : glyc3p[c] + palmACP[c] --> 1hdecg3p[c] + ACP[c] 		
19236	G3PAT161	Yes	glycerol-3-phosphate acyltransferase (C16:1)	[c] : glyc3p + hdeACP --> 1hdec9eg3p + ACP	Glycerophospholipid Metabolism	2.3.1.15	b4041	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-3.97568	4.69324	[c] : glyc3p[c] + hdeACP[c] --> 1hdec9eg3p[c] + ACP[c] 		
19234	G3PAT180	Yes	glycerol-3-phosphate acyltransferase (C18:0)	[c] : glyc3p + ocdcaACP --> 1odecg3p + ACP	Glycerophospholipid Metabolism	2.3.1.15	b4041	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-3.97568	4.69324	[c] : glyc3p[c] + ocdcaACP[c] --> 1odecg3p[c] + ACP[c] 		
19237	G3PAT181	Yes	glycerol-3-phosphate acyltransferase (C18:1)	[c] : glyc3p + octeACP --> 1odec11eg3p + ACP	Glycerophospholipid Metabolism	2.3.1.15	b4041	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-2.38209	5.32305	[c] : glyc3p[c] + octeACP[c] --> 1odec11eg3p[c] + ACP[c] 		
19998	G3PCabcpp	Yes	sn-glycerol-3-phosphocholine transport via ABC system (periplasm)	atp[c] + g3pc[p] + h2o[c] --> adp[c] + g3pc[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b3452  and  b3453  and  b3450  and  b3451 )	AMF	"PMID: 2842304
states transport of glycerol-phosphodiesters for the ugp system
AMF"	-7.01673	1.48181	[c] : atp[c] + g3pc[p] + h2o[c] --> adp[c] + g3pc[c] + h[c] + pi[c] 		
12259	G3PCtex	Yes	glycero-3-phosphocholine transport via diffusion (extracellular to periplasm)	g3pc[e] <==> g3pc[p]	"Transport, Outer Membrane"				Assumed diffusion	0	0	[c] : g3pc[e] <==> g3pc[p] 		
2838	G3PD2	No	glycerol-3-phosphate dehydrogenase (NADP)	[c] : glyc3p + nadp <==> dhap + h + nadph	Alternate Carbon Metabolism	1.1.1.94	b3608			4.73639	4.5435	[c] : glyc3p[c] + nadp[c] <==> dhap[c] + h[c] + nadph[c] 		
1866	G3PD5	No	glycerol-3-phosphate dehydrogenase (ubiquinone-8)	[c] : glyc3p + q8 --> dhap + q8h2	Oxidative Phosphorylation	1.1.99.5	( ( b2241  and  b2242  and  b2243 )  or  b3426 )	JLR		-18.6813	21.401	[c] : glyc3p[c] + q8[c] --> dhap[c] + q8h2[c] 		
3064	G3PD6	No	glycerol-3-phosphate dehydrogenase (menaquinone-8)	[c] : glyc3p + mqn8 --> dhap + mql8	Oxidative Phosphorylation	1.1.99.5	( b2241  and  b2242  and  b2243 )	JLR		-17.2294	17.2464	[c] : glyc3p[c] + mqn8[c] --> dhap[c] + mql8[c] 		
1968	G3PD7	No	glycerol-3-phosphate dehydrogenase (demethylmenaquinone-8)	[c] : 2dmmq8 + glyc3p --> 2dmmql8 + dhap	Oxidative Phosphorylation	1.1.99.5	( b2241  and  b2242  and  b2243 )	JLR		-12.163	15.0763	[c] : 2dmmq8[c] + glyc3p[c] --> 2dmmql8[c] + dhap[c] 		
19997	G3PEabcpp	Yes	sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)	atp[c] + g3pe[p] + h2o[c] --> adp[c] + g3pe[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b3452  and  b3453  and  b3450  and  b3451 )	AMF	"PMID: 2842304
states transport of glycerol-phosphodiesters for the ugp system
AMF"	-7.01673	1.48181	[c] : atp[c] + g3pe[p] + h2o[c] --> adp[c] + g3pe[c] + h[c] + pi[c] 		
12258	G3PEtex	Yes	glycero-3-phosphoethanolamine transport via diffusion (extracellular to periplasm)	g3pe[e] <==> g3pe[p]	"Transport, Outer Membrane"				Assumed diffusion	0	0	[c] : g3pe[e] <==> g3pe[p] 		
19999	G3PGabcpp	Yes	sn-glycerol-3-phosphoglycerol transport via ABC system (periplasm)	atp[c] + g3pg[p] + h2o[c] --> adp[c] + g3pg[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b3452  and  b3453  and  b3450  and  b3451 )	AMF	"PMID: 2842304
states transport of glycerol-phosphodiesters for the ugp system
AMF"	-7.01673	1.48181	[c] : atp[c] + g3pg[p] + h2o[c] --> adp[c] + g3pg[c] + h[c] + pi[c] 		
12257	G3PGtex	Yes	glycerophoglycerol transport via diffusion (extracellular to periplasm)	g3pg[e] <==> g3pg[p]	"Transport, Outer Membrane"				Assumed diffusion	0	0	[c] : g3pg[e] <==> g3pg[p] 		
20000	G3PIabcpp	Yes	sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)	atp[c] + g3pi[p] + h2o[c] --> adp[c] + g3pi[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b3452  and  b3453  and  b3450  and  b3451 )	AMF	"PMID: 2842304
states transport of glycerol-phosphodiesters for the ugp system
AMF"	-7.01673	1.48181	[c] : atp[c] + g3pi[p] + h2o[c] --> adp[c] + g3pi[c] + h[c] + pi[c] 		
12256	G3PItex	Yes	glycero-3-phospho-1-inositol transport via diffusion (extracellular to periplasm)	g3pi[e] <==> g3pi[p]	"Transport, Outer Membrane"			AMF	Assumed diffusion	0	0	[c] : g3pi[e] <==> g3pi[p] 		
20001	G3PSabcpp	Yes	sn-glycerol-3-phosphoserine transport via ABC system (periplasm)	atp[c] + g3ps[p] + h2o[c] --> adp[c] + g3ps[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b3452  and  b3453  and  b3450  and  b3451 )	AMF	"PMID: 2842304
states transport of glycerol-phosphodiesters for the ugp system
AMF"	-7.01673	1.48181	[c] : atp[c] + g3ps[p] + h2o[c] --> adp[c] + g3ps[c] + h[c] + pi[c] 		
12255	G3PStex	Yes	glycerophosphserine transport via diffusion (extracellular to periplasm)	g3ps[e] <==> g3ps[p]	"Transport, Outer Membrane"				Assumed diffusion	0	0	[c] : g3ps[e] <==> g3ps[p] 		
1822	G3PT	Yes	glycerol-3-phosphatase	[c] : glyc3p + h2o --> glyc + pi	Update		b0822	"EC 3.1.3.-
NCD"	"enzyme acts on a number of other sugar phosphates, these reactions were shown to be substrates and were in the model

(glyc3p was not tested, but high activity was shown ot glyc1p and glyc2p, so the reaction G3PT was assigned to this gene)

sbt-d - not in network yet, but could be a signalling molecule (not sure of the source for this statement), so added this reaction
PMID: 15657928
AMF"	-2.35942	1.9257	[c] : glyc3p[c] + h2o[c] --> glyc[c] + h[c] + pi[c] 		
3574	G5SADr	Yes	"L-glutamate 5-semialdehyde dehydratase, reversible"	[c] : glu5sa <==> 1pyr5c + h + h2o	Arginine and Proline Metabolism			"spontaneous conversion
NCD"	JLR- spontaneous reaction.  Before JSE model has the reaction encoded by proC perfoming the dehydration and reduction together.  Now they are in the model as two separate reactions. EcoCyc also notes that this reaction (G5SADs) is spontaneous.	-12.166	4.98868	[c] : glu5sa[c] <==> 1pyr5c[c] + h[c] + h2o[c] 		
315	G5SD	No	glutamate-5-semialdehyde dehydrogenase	[c] : glu5p + h + nadph --> glu5sa + nadp + pi	Arginine and Proline Metabolism	1.2.1.41	b0243			-0.164006	4.46406	[c] : glu5p[c] + nadph[c] --> glu5sa[c] + nadp[c] + pi[c] 		
246	G6PDA	No	glucosamine-6-phosphate deaminase	[c] : gam6p + h2o --> f6p + nh4	Alternate Carbon Metabolism	3.5.99.6	b0678	Previously EC 5.3.1.10		1.74379	4.70274	[c] : gam6p[c] + h2o[c] --> f6p[c] + nh4[c] 		
2941	G6PDH2r	No	glucose 6-phosphate dehydrogenase	[c] : g6p + nadp <==> 6pgl + h + nadph	Pentose Phosphate Pathway	1.1.1.49	b1852	"JLR - a reversible reaction that is otherwise identical to ZWF
"	"PMID: 1729252
AMF
not sure of reversibility
doesnt matter in that 6pgl is only used in one other reaction"	-1.97585	5.96383	[c] : g6p[c] + nadp[c] <==> 6pgl[c] + h[c] + nadph[c] 		
13217	G6PP	Yes	glucose-6-phosphate phosphatase	[c] : g6p + h2o --> glc-D + pi	Update	3.1.3.9	b0822	AMF	"enzyme acts on a number of other sugar phosphates, these reactions were shown to be substrates and were in the model

(glyc3p was not tested, but high activity was shown ot glyc1p and glyc2p, so the reaction G3PT was assigned to this gene)

sbt-d - not in network yet, but could be a signalling molecule (not sure of the source for this statement), so added this reaction
PMID: 15657928
AMF"	-2.35942	1.9257	[c] : g6p[c] + h2o[c] --> glc-D[c] + h[c] + pi[c] 		
8830	G6Pt6_2pp	Yes	Glucose-6-phosphate transport via phosphate antiport (periplasm)	g6p[p] + (2) pi[c] --> g6p[c] + (2) pi[p]	"Transport, Inner Membrane"		b3666	JLR		0	0	[c] : g6p[p] + (2) pi[c] --> g6p[c] + (2) pi[p] 		
9245	G6Ptex	Yes	glucose 6-phosphate transport via diffusion (extracellular to periplasm)	g6p[e] <==> g6p[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : g6p[e] <==> g6p[p] 					
12230	GAL1PPpp	Yes	D-galactose 1-phosphatase	[p] : gal1p + h2o --> gal + pi	Update	3.1.3.10	b1002	AMF	"from EcoCyc:
The enzyme also acts on D-galactose 1-phosphate, more slowly than on glucose-1-phosphate. The enzyme is stable at a wide range of pH conditions, and pH optima for hydrolysis of various substrates are discussed [ Cottrill02  ] .
"	-3.54819	2.12947	[p] : gal1p[p] + h2o[p] --> gal[p] + h[p] + pi[p] 					
12314	GAL1Ptex	Yes	D-galactose 1-phosphate transport via diffusion (extracellular to periplasm)	gal1p[e] <==> gal1p[p]	"Transport, Outer Membrane"			AMF	assumed diffusion	0	0	[c] : gal1p[e] <==> gal1p[p] 					
8831	GALabcpp	Yes	D-galactose transport via ABC system (periplasm)	atp[c] + gal[p] + h2o[c] --> adp[c] + gal[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b2149  and  b2150  and  b2148 )			-7.01673	1.48181	[c] : atp[c] + gal[p] + h2o[c] --> adp[c] + gal[c] + h[c] + pi[c] 					
12216	GALBDtex	Yes	beta D-galactose transport via diffusion (extracellular to periplasm)	gal-bD[e] <==> gal-bD[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : gal-bD[e] <==> gal-bD[p] 					
2292	GALCTD	No	galactarate dehydratase	[c] : galct-D --> 5dh4dglc + h2o	Alternate Carbon Metabolism	4.2.1.42	b3128	JLR		-9.58412	3.68395	[c] : galct-D[c] --> 5dh4dglc[c] + h2o[c] 					
2501	GALCTND	No	galactonate dehydratase	[c] : galctn-D --> 2dh3dgal + h2o	Alternate Carbon Metabolism	4.2.1.6	b4478	JLR		-9.58412	3.68395	[c] : galctn-D[c] --> 2dh3dgal[c] + h2o[c] 					
8832	GALCTNt2rpp	Yes	"D-galactonate transport via proton symport, reversible (periplasm)"	galctn-D[p] + h[p] <==> galctn-D[c] + h[c]	"Transport, Inner Membrane"		b3691	JLR		0	0	[c] : galctn-D[p] + h[p] <==> galctn-D[c] + h[c] 					
9078	GALCTNtex	Yes	D-galactonate transport via diffusion (extracellular to periplasm)	galctn-D[e] <==> galctn-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : galctn-D[e] <==> galctn-D[p] 					
8833	GALCTt2rpp	Yes	"D-galactarte transport via proton symport, reversible (periplasm)"	galct-D[p] + h[p] <==> galct-D[c] + h[c]	"Transport, Inner Membrane"		( b3127  or  b2789 )	JLR	"PMID: 10762278
it was shown that GudP can transport D-galactarate, because a strain that lacks galactarate permease, showed that this substrate is able to enter the cells by another permease, probably D-glucarate permease.

It is also thought that GarP can transport both glactarate and glucarate PMID: 9772162

because of this, glycerate was assigned to both transporters since E. coli can grow on the substrate.PMID: 10762278

AMF"	0	0	[c] : galct-D[p] + h[p] <==> galct-D[c] + h[c] 					
9077	GALCTtex	Yes	D-galactarte transport via diffusion (extracellular to periplasm)	galct-D[e] <==> galct-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : galct-D[e] <==> galct-D[p] 					
1170	GALKr	No	galactokinase	[c] : atp + gal <==> adp + gal1p + h	Alternate Carbon Metabolism	2.7.1.6	( b0757  or  b2045 )	JLR - added reversible form of GALK		-3.46855	2.28701	[c] : atp[c] + gal[c] <==> adp[c] + gal1p[c] 					
13600	GALM2pp	Yes	aldose-1-epimerase	[p] : gal-bD --> gal	Update	5.1.3.3	b0756	AMF	"PMID: 7966338
AMF
not sure of reversibility"	0	0.5	[p] : gal-bD[p] --> gal[p] 					
1198	GALS3	No	a-galactosidase (melibiose)	[c] : h2o + melib --> gal + glc-D	Alternate Carbon Metabolism	3.2.1.22	b4119	JLR		-1.3356	2.48536	[c] : h2o[c] + melib[c] --> gal[c] + glc-D[c] 					
13504	GALT1	Yes	galactosyltransferase I (LPS core synthesis)	[c] : gicolipa + udpg --> gagicolipa + h + udp	Lipopolysaccharide Biosynthesis / Recycling		b3628	AMF	"Look in figure 2 to see the order of outer core oligosaccharide biosynthesis reactions - WaaO study
PMID: 9765561

study on WaaR function
PMID: 10234827

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108
"	No energy	No energy	[c] : gicolipa[c] + udpg[c] --> gagicolipa[c] + udp[c] 					
8834	GALt2pp	Yes	D-galactose transport in via proton symport (periplasm)	gal[p] + h[p] --> gal[c] + h[c]	"Transport, Inner Membrane"		b2943			0	0	[c] : gal[p] + h[p] --> gal[c] + h[c] 					
9076	GALtex	Yes	D-galactose transport via diffusion (extracellular to periplasm)	gal[e] <==> gal[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : gal[e] <==> gal[p] 					
8835	GALTptspp	Yes	Galactitol transport via PEP:Pyr PTS (periplasm)	galt[p] + pep[c] --> galt1p[c] + pyr[c]	"Transport, Inner Membrane"		( b2094  and  b2093  and  b2092  and  b2415  and  b2416 )	JLR		-10.1729	3.20748	[c] : galt[p] + pep[c] --> galt1p[c] + pyr[c] 					
9079	GALTtex	Yes	Galactitol transport via diffusion (extracellular to periplasm)	galt[e] <==> galt[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : galt[e] <==> galt[p] 					
3040	GALUi	No	UTP-glucose-1-phosphate uridylyltransferase (irreversible)	[c] : g1p + h + utp --> ppi + udpg	Cell Envelope Biosynthesis	2.7.7.9	( b1236  or  b2042 )	JLR - added irreversible form of GALU	JLR-  (JSE model had galU and galF as one enzyme)	-1.12149	3.25471	[c] : g1p[c] + utp[c] --> ppi[c] + udpg[c] 					
8836	GALURt2rpp	Yes	"D-galacturonate transport via proton symport, reversible (periplasm)"	galur[p] + h[p] <==> galur[c] + h[c]	"Transport, Inner Membrane"		b3093	JLR		0	0	[c] : galur[p] + h[p] <==> galur[c] + h[c] 					
9080	GALURtex	Yes	D-galacturonate transport via diffusion (extracellular to periplasm)	galur[e] <==> galur[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : galur[e] <==> galur[p] 					
8837	GAMptspp	Yes	D-glucosamine transport via PEP:Pyr PTS (periplasm)	gam[p] + pep[c] --> gam6p[c] + pyr[c]	"Transport, Inner Membrane"		( b1817  and  b1818  and  b1819  and  b2415  and  b2416 )			-10.1729	3.20748	[c] : gam[p] + pep[c] --> gam6p[c] + pyr[c] 					
9081	GAMtex	Yes	D-glucosamine transport via diffusion (extracellular to periplasm)	gam[e] <==> gam[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : gam[e] <==> gam[p] 					
2841	GAPD	No	glyceraldehyde-3-phosphate dehydrogenase	[c] : g3p + nad + pi <==> 13dpg + h + nadh	Glycolysis/Gluconeogenesis	1.2.1.12	( b1779  or  ( b1416  and  b1417 ) )	SMP		0.164006	4.46406	[c] : g3p[c] + nad[c] + pi[c] <==> 13dpg[c] + nadh[c] 					
3637	GARFT	No	phosphoribosylglycinamide formyltransferase	[c] : 10fthf + gar <==> fgam + h + thf	Purine and Pyrimidine Biosynthesis	2.1.2.2	b2500		"JLR- NH page 568 indicates that the reaction is reversible, JSE has it as irreversible"	No energy	No energy	[c] : 10fthf[c] + gar[c] <==> fgam[c] + h[c] + thf[c] 					
3536	GART	No	GAR transformylase-T	[c] : atp + for + gar --> adp + fgam + h + pi	Purine and Pyrimidine Biosynthesis		b1849	"tv
JLR- EC is unassigned 2.1.2.-"		No energy	No energy	[c] : atp[c] + for[c] + gar[c] --> adp[c] + fgam[c] + h[c] + pi[c] 					
9082	GBBTNtex	Yes	gamma-butyrobetaine transport via diffusion (extracellular to periplasm)	gbbtn[e] <==> gbbtn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : gbbtn[e] <==> gbbtn[p] 					
1967	GCALDD	No	Glycolaldehyde dehydrogenase	[c] : gcald + h2o + nad --> glyclt + (2) h + nadh	Folate Metabolism	1.2.1.21	b1415	JLR		-9.85991	4.39284	[c] : gcald[c] + h2o[c] + nad[c] --> glyclt[c] + (2) h[c] + nadh[c] 					
2305	GDMANE	No	GDP-4-dehydro-6-deoxy-D-mannose epimerase	[c] : gdpddman --> gdpofuc	Cell Envelope Biosynthesis		b2052	JLR (EC 5.1.3.-  ; reaction number R03400)		0	0.5	[c] : gdpddman[c] --> gdpofuc[c] 					
13382	GDPDPK	Yes	GDP diphosphokinase	[c] : atp + gdp --> amp + h + ppgpp	Update		( b2784  or  b3650 )	AMF	"4 reactions are involved in the ppGpp biosynthesis pathway
ppGpp is a signalling molecule

gppA : PMID: 8394006
RelA: PMID: 2844820
"	-2.66537	2.19769	[c] : atp[c] + gdp[c] --> amp[c] + ppgpp[c] 					
13363	GDPMNH	Yes	GDP-mannose mannosyl hydrolase	[c] : gdpmann + h2o --> gdp + h + man	Update		b2051	AMF	"PMID: 7592609
AMF

 a novel enzyme that hydrolyzes GDP-mannose or GDP-glucose to GDP and the respective hexose

gdp-glucose wasnt added since it is not in the network"	-4.00343	2.86196	[c] : gdpmann[c] + h2o[c] --> gdp[c] + man[c] 					
9083	GDPtex	Yes	GDP transport via diffusion (extracellular to periplasm)	gdp[e] <==> gdp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : gdp[e] <==> gdp[p] 		
3537	GF6PTA	No	glutamine-fructose-6-phosphate transaminase	[c] : f6p + gln-L --> gam6p + glu-L	Cell Envelope Biosynthesis	2.6.1.16	b3729			-6.43682	5.46127	[c] : f6p[c] + gln-L[c] --> gam6p[c] + glu-L[c] 		
10471	GGGABADr	Yes	gamma-glutamyl-gamma aminobutyric acid dehydrogenase	[c] : ggbutal + h2o + nadp <==> gg4abut + (2) h + nadph	Update		b1300	"MKA
AMF PMID: 15590624 "	"exhibits ""wide"" aldehyde substrate specificity in vitro, but proximity of gene to putrescine operon suggests Glu-Butyraldehyde ---> Glu-Gaba may be intended substrate.  not known whether AldH catalyzes DH of other aldehydes in-vivo in a physiologically relevant manner.

PMID: 15590624 AMF"	-9.85991	4.39284	[c] : ggbutal[c] + h2o[c] + nadp[c] <==> gg4abut[c] + (2) h[c] + nadph[c] 		
11866	GGGABAH	Yes	gamma-glutamyl-gamma-aminobutyric acid hydrolase	[c] : gg4abut + h2o --> 4abut + glu-L	Update		b1298	"MKA
AMF PMID: 15590624 "	"PMID: 15590624 AMF

PuuD can also hydrolize gamma-glutamyl-g.-putrescine (gluptrc-y), but acts on gamma-glu-GABA 36X more efficiently than (gluptrc-y)

MKA"	-3.36489	3.34628	[c] : gg4abut[c] + h2o[c] --> 4abut[c] + glu-L[c] 		
10586	GGPTRCO	Yes	gamma glutamyl putrescine oxidase	[c] : ggptrc + h2o + o2 --> ggbutal + h2o2 + nh4	Update		b1301	"MKA
AMF"	PMID: 15590624 AMF	-18.53	2.13874	[c] : ggptrc[c] + h2o[c] + o2[c] --> ggbutal[c] + h2o2[c] + nh4[c] 		
10585	GGPTRCS	Yes	gamma glutamyl putrescine synthase	[c] : atp + glu-L + ptrc --> adp + ggptrc + h + pi	Update		b1297	"MKA
AMF"	"MKA

PMID: 15590624 AMF"	-3.65185	3.59073	[c] : atp[c] + glu-L[c] + ptrc[c] --> adp[c] + ggptrc[c] + h[c] + pi[c] 		
1584	GHMT2r	Yes	"glycine hydroxymethyltransferase, reversible"	[c] : ser-L + thf <==> gly + h2o + mlthf	Glycine and Serine Metabolism	2.1.2.1	b2551	NCD	"Glycine hydroxymethyltransferase catalyzes the reversible cleavage of 3-hydroxy amino acids (L-serine, L-threonine, allothreonine, 3-phenylserine) to glycine and an aldehyde. When serine is the amino acid tetrahydrofolate is also required. 
PMID: 3512553 from ecocyc
AMF"	-1.49023	6.62106	[c] : ser-L[c] + thf[c] <==> gly[c] + h2o[c] + mlthf[c] 		
186	GK1	No	guanylate kinase (GMP:ATP)	[c] : atp + gmp <==> adp + gdp	Nucleotide Salvage Pathway	2.7.4.8	b3648			0	0.5	[c] : atp[c] + gmp[c] <==> adp[c] + gdp[c] 		
13777	GLBRAN2	Yes	"1,4-alpha-glucan branching enzyme (glycogen -> bglycogen)"	[c] : glycogen --> bglycogen	Update	2.4.1.18	b3432	AMF	added to signify the branching action of gylcogen	0	0.5	[c] : glycogen[c] --> bglycogen[c] 		
13501	GLCabcpp	Yes	D-glucose transport via ABC system (periplasm)	atp[c] + glc-D[p] + h2o[c] --> adp[c] + glc-D[c] + h[c] + pi[c]	Update		( b2149  and  b2150  and  b2148 )	"AMF
JLR
"	"This reaction is only active at very low levels of glucose (micromolar levels)

The PTS systems is still the major transporter at millimolar levels
PMID: 8703508

AMF
JLR
"	-7.01673	1.48181	[c] : atp[c] + glc-D[p] + h2o[c] --> adp[c] + glc-D[c] + h[c] + pi[c] 		
13693	GLCATr	Yes	D-glucose O-acetyltransferase	[c] : accoa + glc-D <==> acglc-D + coa	Update	2.3.1.79	b0459	AMF	"from PMID: 1856235
no physiological role found yet, could be in responce to a detoxification of sugars

also acts on
mannose
fructose
galactose
which were not entered
AMF"	-3.97568	4.69324	[c] : accoa[c] + glc-D[c] <==> acglc-D[c] + coa[c] 		
8987	GLCDpp	Yes	Glucose dehydrogenase (ubiquinone-8 as acceptor) (periplasm)	glc-D[p] + h2o[p] + q8[c] --> glcn[p] + h[p] + q8h2[c]	Oxidative Phosphorylation		b0124	JLR-Combination of 1.1.99.17 and 3.1.1.17	JLR- not that the enzyme requires a cofactor that E. coli doesn't make ( so this enzyme is normally inactive)	-32.1464	23.274	[c] : glc-D[p] + h2o[p] + q8[c] --> glcn[p] + h[p] + q8h2[c] 		
8838	GLCNt2rpp	Yes	"D-gluconate transport via proton symport, reversible (periplasm)"	glcn[p] + h[p] <==> glcn[c] + h[c]	"Transport, Inner Membrane"		( b4321  or  b3415  or  b4476  or  b4265 )	JLR		0	0	[c] : glcn[p] + h[p] <==> glcn[c] + h[c] 		
9134	GLCNtex	Yes	D-gluconate transport via diffusion (extracellular to periplasm)	glcn[e] <==> glcn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glcn[e] <==> glcn[p] 		
735	GLCP	No	glycogen phosphorylase	[c] : glycogen + pi --> g1p	Glycolysis/Gluconeogenesis	2.4.1.1	( b3428  or  b3417 )			1.30826	5.15877	[c] : glycogen[c] + (2) h[c] + pi[c] --> g1p[c] 		
20122	GLCP2	Yes	glycogen phosphorylase	[c] : bglycogen + pi --> g1p	Glycolysis/Gluconeogenesis	2.4.1.1	( b3428  or  b3417 )	#N/A	#N/A	1.30826	5.15877	[c] : bglycogen[c] + (2) h[c] + pi[c] --> g1p[c] 		
8839	GLCptspp	Yes	D-glucose transport via PEP:Pyr PTS (periplasm)	glc-D[p] + pep[c] --> g6p[c] + pyr[c]	"Transport, Inner Membrane"		( ( b2417  and  b1101  and  b2415  and  b2416 )  or  ( b1817  and  b1818  and  b1819  and  b2415  and  b2416 )  or  ( b2417  and  b1621  and  b2415  and  b2416 ) )			-10.1729	3.20748	[c] : glc-D[p] + pep[c] --> g6p[c] + pyr[c] 					
2291	GLCRAL	No	5-dehydro-4-deoxyglucarate aldolase	[c] : 5dh4dglc --> 2h3oppan + pyr	Alternate Carbon Metabolism	4.1.2.20	b3126	JLR		2.91741	2.32549	[c] : 5dh4dglc[c] --> 2h3oppan[c] + pyr[c] 					
3197	GLCRD	No	glucarate dehydratase	[c] : glcr --> 5dh4dglc + h2o	Alternate Carbon Metabolism	4.2.1.40	( b2787  or  b2788 )	JLR	YgcY is putative	-9.58412	3.68395	[c] : glcr[c] --> 5dh4dglc[c] + h2o[c] 					
8840	GLCRt2rpp	Yes	"D-glucarate transport via proton symport, reversible (periplasm)"	glcr[p] + h[p] <==> glcr[c] + h[c]	"Transport, Inner Membrane"		( b3127  or  b2789 )	JLR	"PMID: 10762278
it was shown that GudP can transport D-galactarate, because a strain that lacks galactarate permease, showed that this substrate is able to enter the cells by another permease, probably D-glucarate permease.

It is also thought that GarP can transport both glactarate and glucarate PMID: 9772162

because of this, glycerate was assigned to both transporters since E. coli can grow on the substrate.PMID: 10762278

AMF"	0	0	[c] : glcr[p] + h[p] <==> glcr[c] + h[c] 					
9133	GLCRtex	Yes	D-glucarate transport via diffusion (extracellular to periplasm)	glcr[e] <==> glcr[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glcr[e] <==> glcr[p] 					
734	GLCS1	No	glycogen synthase (ADPGlc)	[c] : adpglc --> adp + glycogen + h	Glycolysis/Gluconeogenesis	2.4.1.21	b3429			-1.76351	5.45611	[c] : adpglc[c] --> adp[c] + glycogen[c] + h[c] 					
8841	GLCt2pp	Yes	D-glucose transport in via proton symport (periplasm)	glc-D[p] + h[p] --> glc-D[c] + h[c]	"Transport, Inner Membrane"		b2943			0	0	[c] : glc-D[p] + h[p] --> glc-D[c] + h[c] 					
9084	GLCtex	Yes	glucose transport via diffusion (extracellular to periplasm)	glc-D[e] <==> glc-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glc-D[e] <==> glc-D[p] 					
9118	GLCtexi	Yes	D-glucoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible	glc-D[e] --> glc-D[p]	"Transport, Outer Membrane"		b4036		"PMID: 7654405

LamB binds to the maltoheptanose compounds and facitlitaes their diffuction through the outer membrane

PMID: 127000071
outer membrane protein porin for maltose and maltooligosacharides

GLC transport was an association from the iJR904 model and was assumed to be transported by LamB as well"	0	0	[c] : glc-D[e] --> glc-D[p] 					
13503	GLCTR1	Yes	glucosyltransferase I (LPS core synthesis)	[c] : icolipa + udpg --> gicolipa + h + udp	Lipopolysaccharide Biosynthesis / Recycling		b3631	AMF	"Look in figure 2 to see the order of outer core oligosaccharide biosynthesis reactions - WaaO study
PMID: 9765561

study on WaaR function
PMID: 10234827

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108
"	No energy	No energy	[c] : icolipa[c] + udpg[c] --> gicolipa[c] + udp[c] 					
13505	GLCTR2	Yes	glucosyltransferase II (LPS core synthesis)	[c] : gagicolipa + udpg --> ggagicolipa + h + udp	Lipopolysaccharide Biosynthesis / Recycling		b3627	AMF	"Look in figure 2 to see the order of outer core oligosaccharide biosynthesis reactions - WaaO study
PMID: 9765561

study on WaaR function
PMID: 10234827

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108

"	No energy	No energy	[c] : gagicolipa[c] + udpg[c] --> ggagicolipa[c] + udp[c] 					
13506	GLCTR3	Yes	glucosyltransferase III (LPS core synthesis)	[c] : ggagicolipa + udpg --> gggagicolipa + h + udp	Lipopolysaccharide Biosynthesis / Recycling		b3626	AMF	"Look in figure 2 to see the order of outer core oligosaccharide biosynthesis reactions - WaaO study
PMID: 9765561

study on WaaR function
PMID: 10234827

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108
"	No energy	No energy	[c] : ggagicolipa[c] + udpg[c] --> gggagicolipa[c] + udp[c] 					
13806	GLCUR1Ptex	Yes	D-glucuronate 1-phosphate transport via diffusion (extracellular to periplasm)	glcur1p[e] <==> glcur1p[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glcur1p[e] <==> glcur1p[p] 					
8842	GLCURt2rpp	Yes	"D-glucuronate transport via proton symport, reversible (periplasm)"	glcur[p] + h[p] <==> glcur[c] + h[c]	"Transport, Inner Membrane"		( b3909  or  b3093 )	JLR		0	0	[c] : glcur[p] + h[p] <==> glcur[c] + h[c] 					
9135	GLCURtex	Yes	D-glucuronat transport via diffusion (extracellular to periplasm)	glcur[e] <==> glcur[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glcur[e] <==> glcur[p] 					
264	GLGC	No	glucose-1-phosphate adenylyltransferase	[c] : atp + g1p + h --> adpglc + ppi	Glycolysis/Gluconeogenesis	2.7.7.27	b3430	SMP		-1.12149	3.25471	[c] : atp[c] + g1p[c] --> adpglc[c] + ppi[c] 					
8843	GLNabcpp	Yes	L-glutamine transport via ABC system (periplasm)	atp[c] + gln-L[p] + h2o[c] --> adp[c] + gln-L[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0811  and  b0810  and  b0809 )			-7.01673	1.48181	[c] : atp[c] + gln-L[p] + h2o[c] --> adp[c] + gln-L[c] + h[c] + pi[c] 		
3539	GLNS	No	glutamine synthetase	[c] : atp + glu-L + nh4 --> adp + gln-L + h + pi	Glutamate metabolism	6.3.1.2	( b3870  or  b1297 )			-2.3237	3.22576	[c] : atp[c] + glu-L[c] + nh4[c] --> adp[c] + gln-L[c] + h[c] + pi[c] 		
9136	GLNtex	Yes	L-glutamine transport via diffusion (extracellular to periplasm)	gln-L[e] <==> gln-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : gln-L[e] <==> gln-L[p] 		
1030	GLNTRS	Yes	Glutaminyl-tRNA synthetase	[c] : atp + gln-L + trnagln --> amp + glntrna + ppi	Update	6.1.1.18	b0680		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + gln-L[c] + h[c] + trnagln[c] --> amp[c] + glntrna[c] + ppi[c] 		
1209	GLTPD	No	Galactitol-1-phosphate dehydrogenase	[c] : galt1p + nad <==> h + nadh + tag6p-D	Alternate Carbon Metabolism		b2091	"JLR- EC 1.1.1.251 generates the L-form of tagatose-6-phosphate, used this reaction because EcoCyc indicates that it generates the D-form"		3.78793	9.00908	[c] : galt1p[c] + nad[c] <==> h[c] + nadh[c] + tag6p-D[c] 		
2854	GLU5K	No	glutamate 5-kinase	[c] : atp + glu-L --> adp + glu5p	Arginine and Proline Metabolism	2.7.2.11	b0242			3.00718	2.24154	[c] : atp[c] + glu-L[c] + h[c] --> adp[c] + glu5p[c] 		
8844	GLUabcpp	Yes	L-glutamate transport via ABC system (periplasm)	atp[c] + glu-L[p] + h2o[c] --> adp[c] + glu-L[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0655  and  b0654  and  b0653  and  b0652 )			-7.01673	1.48181	[c] : atp[c] + glu-L[p] + h2o[c] --> adp[c] + glu-L[c] + h[c] + pi[c] 		
8845	GLUABUTt7pp	Yes	4-aminobutyrate/glutamate antiport (periplasm)	4abut[c] + glu-L[p] <==> 4abut[p] + glu-L[c]	Putative Transporters		b1492	JLR	JLR- XasA is the same as GadC	0	0	[c] : 4abut[c] + glu-L[p] <==> 4abut[p] + glu-L[c] 		
3540	GLUCYS	No	gamma-glutamylcysteine synthetase	[c] : atp + cys-L + glu-L --> adp + glucys + h + pi	Cofactor and Prosthetic Group Biosynthesis	6.3.2.2	b2688	NCD		-3.65185	3.59073	[c] : atp[c] + cys-L[c] + glu-L[c] --> adp[c] + glucys[c] + h[c] + pi[c] 		
2960	GLUDC	No	Glutamate Decarboxylase	[c] : glu-L + h --> 4abut + co2	Glutamate metabolism	4.1.1.15	( b3517  or  b1493 )	JLR- added h to balance		-4.96805	1.79669	[c] : glu-L[c] + h[c] --> 4abut[c] + co2[c] 		
2839	GLUDy	No	glutamate dehydrogenase (NADP)	[c] : glu-L + h2o + nadp <==> akg + h + nadph + nh4	Glutamate metabolism	1.4.1.4	b1761			6.72688	4.65726	[c] : glu-L[c] + h2o[c] + nadp[c] <==> akg[c] + h[c] + nadph[c] + nh4[c] 		
3541	GLUN	No	glutaminase	[c] : gln-L + h2o --> glu-L + nh4	Glutamate metabolism	3.5.1.2	( b1812  or  b0485  or  b1524 )		"JLR- JSE didn't have any genes assigned, there are two putative glutaminases so I assigned these genes to this reaction."	-4.69304	2.95123	[c] : gln-L[c] + h2o[c] --> glu-L[c] + nh4[c] 		
12262	GLUNpp	Yes	glutaminase	[p] : gln-L + h2o --> glu-L + nh4	Update	3.5.1.2	b2957	AMF	"moved to periplasm from PSORT and EcoCyc data
AMF

JLR:
 AnsB has some glutaminase activity"	-4.69304	2.95123	[p] : gln-L[p] + h2o[p] --> glu-L[p] + nh4[p] 		
3542	GLUPRT	No	glutamine phosphoribosyldiphosphate amidotransferase	[c] : gln-L + h2o + prpp --> glu-L + ppi + pram	Purine and Pyrimidine Biosynthesis	2.4.2.14	b2312			-12.6116	3.75316	[c] : gln-L[c] + h2o[c] + prpp[c] --> glu-L[c] + ppi[c] + pram[c] 		
478	GLUR	No	glutamate racemase	[c] : glu-D <==> glu-L	Cell Envelope Biosynthesis	5.1.1.3	b3967			0	0.5	[c] : glu-D[c] <==> glu-L[c] 		
3309	GLUSy	No	glutamate synthase (NADPH)	[c] : akg + gln-L + h + nadph --> (2) glu-L + nadp	Glutamate metabolism	1.4.1.13	( b3212  and  b3213 )			-11.4199	5.69483	[c] : akg[c] + gln-L[c] + h[c] + nadph[c] --> (2) glu-L[c] + nadp[c] 		
8846	GLUt2rpp	Yes	"L-glutamate transport via proton symport, reversible (periplasm)"	glu-L[p] + h[p] <==> glu-L[c] + h[c]	"Transport, Inner Membrane"		b4077	NCD		0	0	[c] : glu-L[p] + h[p] <==> glu-L[c] + h[c] 		
8847	GLUt4pp	Yes	Na+/glutamate symport (periplasm)	glu-L[p] + na1[p] --> glu-L[c] + na1[c]	"Transport, Inner Membrane"		b3653	JLR		0	0	[c] : glu-L[p] + na1[p] --> glu-L[c] + na1[c] 		
9137	GLUtex	Yes	L-glutamate transport via diffusion (extracellular to periplasm)	glu-L[e] <==> glu-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glu-L[e] <==> glu-L[p] 		
731	GLUTRR	No	glutamyl-tRNA reductase	[c] : glutrna + h + nadph --> glu1sa + nadp + trnaglu	Cofactor and Prosthetic Group Biosynthesis		b1210			5.99101	4.69803	[c] : glutrna[c] + h[c] + nadph[c] --> glu1sa[c] + nadp[c] + trnaglu[c] 		
1029	GLUTRS	No	Glutamyl-tRNA synthetase	[c] : atp + glu-L + trnaglu --> amp + glutrna + ppi	Cofactor and Prosthetic Group Biosynthesis	6.1.1.17	b2400			-4.72457	3.42862	[c] : atp[c] + glu-L[c] + h[c] + trnaglu[c] --> amp[c] + glutrna[c] + ppi[c] 		
2287	GLXCL	No	glyoxalate carboligase	[c] : (2) glx + h --> 2h3oppan + co2	Glyoxylate Metabolism	4.1.1.47	b0507	JLR		-7.40877	2.3118	[c] : (2) glx[c] + h[c] --> 2h3oppan[c] + co2[c] 		
9139	GLYALDtex	Yes	Glyceraldehyde transport via diffusion (extracellular to periplasm)	glyald[e] <==> glyald[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glyald[e] <==> glyald[p] 		
8848	GLYALDtpp	Yes	Glyceraldehyde facilitated diffusion (periplasm)	glyald[p] <==> glyald[c]	"Transport, Inner Membrane"		b3927	JLR		0	0	[c] : glyald[p] <==> glyald[c] 		
2805	GLYAT	Yes	glycine C-acetyltransferase	[c] : accoa + gly <==> 2aobut + coa	Glycine and Serine Metabolism	2.3.1.29	b3617		"2-Amino-3-ketobutyrate CoA ligase (AKB ligase) catalyzes the reversible cleavage/condensation reaction between 2-amino-3-ketobutyrate and glycine plus acetyl-CoA. PMID: 3117785 
AMF"	6.30295	4.26524	[c] : accoa[c] + gly[c] <==> 2aobut[c] + coa[c] 		
8849	GLYBabcpp	Yes	Glycine betaine transport via ABC system (periplasm)	atp[c] + glyb[p] + h2o[c] --> adp[c] + glyb[c] + h[c] + pi[c]	Putative Transporters		( b2128  and  b2129  and  b2130  and  b2131 )	JLR	JLR- EcoCyc lists that yehWXYZ form a putative ABC transporter 	-7.01673	1.48181	[c] : atp[c] + glyb[p] + h2o[c] --> adp[c] + glyb[c] + h[c] + pi[c] 		
8850	GLYBt2rpp	Yes	"Glycine betaine transport via proton symport, reversible (periplasm)"	glyb[p] + h[p] <==> glyb[c] + h[c]	Putative Transporters		b1801	JLR		0	0	[c] : glyb[p] + h[p] <==> glyb[c] + h[c] 		
9140	GLYBtex	Yes	Glycine betaine transport via diffusion (extracellular to periplasm)	glyb[e] <==> glyb[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glyb[e] <==> glyb[p] 		
13827	GLYC2Ptex	Yes	Glycerol-2-phosphate transport via diffusion (extracellular to periplasm)	glyc2p[e] <==> glyc2p[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glyc2p[e] <==> glyc2p[p] 		
8951	GLYC3Pabcpp	Yes	sn-Glycerol 3-phosphate transport via ABC system (periplasm)	atp[c] + glyc3p[p] + h2o[c] --> adp[c] + glyc3p[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b3452  and  b3453  and  b3450  and  b3451 )			-7.01673	1.48181	[c] : atp[c] + glyc3p[p] + h2o[c] --> adp[c] + glyc3p[c] + h[c] + pi[c] 		
8851	GLYC3Pt6pp	Yes	Glycerol-3-phosphate : phosphate antiporter (periplasm)	glyc3p[p] + pi[c] --> glyc3p[c] + pi[p]	"Transport, Inner Membrane"		b2240	JLR	"transports glycerol-3-phosphate into the cytoplasm and inorganic phosphate into the periplasm.
PMID: 12893936 
AMF"	0	0	[c] : glyc3p[p] + pi[c] --> glyc3p[c] + pi[p] 		
9142	GLYC3Ptex	Yes	Glycerol-3-phosphate transport via diffusion (extracellular to periplasm)	glyc3p[e] <==> glyc3p[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glyc3p[e] <==> glyc3p[p] 		
13582	GLYCAt2rpp	Yes	"D-glycerate transport via proton symport, reversible (periplasm)"	glyc-R[p] + h[p] <==> glyc-R[c] + h[c]	"Transport, Inner Membrane"		( b3127  or  b2789 )	AMF	"PMID: 10762278
it was shown that GudP can transport D-galactarate, because a strain that lacks galactarate permease, showed that this substrate is able to enter the cells by another permease, probably D-glucarate permease.

It is also thought that GarP can transport both glactarate and glucarate PMID: 9772162

because of this, glycerate was assigned to both transporters since E. coli can grow on the substrate.PMID: 10762278

AMF"	0	0	[c] : glyc-R[p] + h[p] <==> glyc-R[c] + h[c] 		
13583	GLYCAtex	Yes	D-glycerate transport via diffusion (extracellular to periplasm)	glyc-R[e] <==> glyc-R[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glyc-R[e] <==> glyc-R[p] 		
2133	GLYCDx	No	Glycerol dehydrogenase	[c] : glyc + nad --> dha + h + nadh	Alternate Carbon Metabolism	1.1.1.6	b3945	JLR	EcoCyc indicates this gene is cryptic	4.73639	4.5435	[c] : glyc[c] + nad[c] --> dha[c] + h[c] + nadh[c] 		
2288	GLYCK	No	glycerate kinase	[c] : atp + glyc-R --> 3pg + adp + h	Glyoxylate Metabolism	2.7.1.31	b0514	JLR	garK might make 2PG rather than 3PG	-4.65732	2.09859	[c] : atp[c] + glyc-R[c] --> 3pg[c] + adp[c] 		
6159	GLYCK2	Yes	glycerate kinase	[c] : atp + glyc-R --> 2pg + adp + h	Update	2.7.1.31	b3124	JLR	"garK makes 2pg, assumed that glxK still made 3pg."	-3.46855	2.28701	[c] : atp[c] + glyc-R[c] --> 2pg[c] + adp[c] 		
1568	GLYCL	No	Glycine Cleavage System	[c] : gly + nad + thf --> co2 + mlthf + nadh + nh4	Folate Metabolism		( b2904  and  b2903  and  b2905  and  b0116 )	JLR - Ecoli	JLR- NH pg 608 (note that EcoCyc uses NAD and ref as well).	2.24121	9.1054	[c] : gly[c] + nad[c] + thf[c] --> co2[c] + mlthf[c] + nadh[c] + nh4[c] 		
2127	GLYCLTDx	No	Glycolate dehydrogenase (NAD)	[c] : glx + h + nadh --> glyclt + nad	Glyoxylate Metabolism		( b3553  or  b1033 )	JLR	JLR- nadph is preferred 10:1 over nadh	-5.16584	4.34649	[c] : glx[c] + h[c] + nadh[c] --> glyclt[c] + nad[c] 		
2128	GLYCLTDy	No	Glycolate dehydrogenase (NADP)	[c] : glx + h + nadph --> glyclt + nadp	Glyoxylate Metabolism		( b1033  or  b3553 )	JLR		-5.16584	4.34649	[c] : glx[c] + h[c] + nadph[c] --> glyclt[c] + nadp[c] 		
8852	GLYCLTt2rpp	Yes	"glycolate transport via proton symport, reversible (periplasm)"	glyclt[p] + h[p] <==> glyclt[c] + h[c]	"Transport, Inner Membrane"		( b3603  or  b2975 )	JLR		0	0	[c] : glyclt[p] + h[p] <==> glyclt[c] + h[c] 		
8853	GLYCLTt4pp	Yes	glycolate transport via sodium symport (periplasm)	glyclt[p] + na1[p] --> glyclt[c] + na1[c]	Update		b4067	"JLR
2.A.21.7.2"	"Ref couldn't distinguish between a proton or a Na symporter, assumed Na based on sequence homology."	0	0	[c] : glyclt[p] + na1[p] --> glyclt[c] + na1[c] 		
9143	GLYCLTtex	Yes	glycolate transport via diffusion (extracellular to periplasm)	glyclt[e] <==> glyclt[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glyclt[e] <==> glyclt[p] 		
9141	GLYCtex	Yes	glycerol transport via diffusion (extracellular to periplasm)	glyc[e] <==> glyc[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : glyc[e] <==> glyc[p] 		
1981	GLYCTO2	No	Glycolate oxidase	[c] : glyclt + q8 --> glx + q8h2	Alternate Carbon Metabolism		( b2979  and  b4467  and  b4468 )	JLR- not sure about electron acceptor		-18.2519	21.36	[c] : glyclt[c] + q8[c] --> glx[c] + q8h2[c] 		
1982	GLYCTO3	No	Glycolate oxidase	[c] : glyclt + mqn8 --> glx + mql8	Alternate Carbon Metabolism		( b2979  and  b4467  and  b4468 )	JLR		-16.8	17.1956	[c] : glyclt[c] + mqn8[c] --> glx[c] + mql8[c] 		
1983	GLYCTO4	No	Glycolate oxidase	[c] : 2dmmq8 + glyclt --> 2dmmql8 + glx	Alternate Carbon Metabolism		( b2979  and  b4467  and  b4468 )	JLR		-11.7335	15.0181	[c] : 2dmmq8[c] + glyclt[c] --> 2dmmql8[c] + glx[c] 		
8854	GLYCtpp	Yes	glycerol transport via channel (periplasm)	glyc[c] <==> glyc[p]	"Transport, Inner Membrane"		b3927	NCD	"glycerol can freely diffuse through the membrane, but at a substantially smaller rate than the facilitated uptake of glycerol by the GlpF permease
AMF
JLR"	0	0	[c] : glyc[c] <==> glyc[p] 		
256	GLYK	No	glycerol kinase	[c] : atp + glyc --> adp + glyc3p + h	Alternate Carbon Metabolism	2.7.1.30	b3926			-4.65732	2.09859	[c] : atp[c] + glyc[c] --> adp[c] + glyc3p[c] 		
455	GLYOX	No	hydroxyacylglutathione hydrolase	[c] : h2o + lgt-S --> gthrd + h + lac-D	Methylglyoxal Metabolism	3.1.2.6	b0212	IF	This enzyme hasn't been studied in E.coli	-5.85263	4.37924	[c] : h2o[c] + lgt-S[c] --> gthrd[c] + h[c] + lac-D[c] 		
13597	GLYOX3	Yes	glyoxalase III	[c] : h2o + mthgxl --> h + lac-D	Update			"AMF
PMID: 7848303"	"not totaly sure of the reaction since gene has yet to be found
PMID: 7848303
AMF
"	-14.5963	2.61917	[c] : h2o[c] + mthgxl[c] --> h[c] + lac-D[c] 		
8855	GLYt2rpp	Yes	glycine reversible transport via proton symport (periplasm)	gly[p] + h[p] <==> gly[c] + h[c]	"Transport, Inner Membrane"		( b0007  or  b4208  or  b1801 )	NCD	"YeaV is putative

CycA mediates the uptake of L-alanine, D-alanine, glycine, D-serine, and Dcycloserine (Wargel et al. 1970; Cosloy 1973).....utilize H+ co-transport as the energy source (Swiss-Prot data base; http://www.expasy.org/sprot;
accession no. P39312). Together with fklB, cycA is thought to form the fklB-cycA operon, whose expression is regulated by the nitrogen assimilation control (Nac) protein
PMID: 15221223
AMF"	0	0	[c] : gly[p] + h[p] <==> gly[c] + h[c] 		
9138	GLYtex	Yes	Glycine transport via diffusion (extracellular to periplasm)	gly[e] <==> gly[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : gly[e] <==> gly[p] 		
1038	GLYTRS	Yes	Glycyl-tRNA synthetase	[c] : atp + gly + trnagly --> amp + glytrna + ppi	Update	6.1.1.14	( b3559  and  b3560 )		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + gly[c] + h[c] + trnagly[c] --> amp[c] + glytrna[c] + ppi[c] 		
2304	GMAND	No	GDP-D-mannose dehydratase	[c] : gdpmann --> gdpddman + h2o	Cell Envelope Biosynthesis	4.2.1.47	b2053	JLR	Ref says the gene is well established	-14.0592	3.01096	[c] : gdpmann[c] --> gdpddman[c] + h2o[c] 		
2550	GMHEPAT	No	D-glycero-D-manno-hepose 1-phosphate adenyltransferase	"[c] : atp + gmhep1p + h --> adphep-D,D + ppi"	Cell Envelope Biosynthesis		b3052	JLR Kegg RXN R05644		-1.12149	3.25471	"[c] : atp[c] + gmhep1p[c] --> adphep-D,D[c] + ppi[c] "		
3246	GMHEPK	No	D-glycero-D-manno-heptose 7-phosphate kinase	[c] : atp + gmhep7p --> adp + gmhep17bp + h	Cell Envelope Biosynthesis		b3052	JLR- Kegg RXN R05646		-3.46855	2.28701	[c] : atp[c] + gmhep7p[c] --> adp[c] + gmhep17bp[c] 		
2551	GMHEPPA	No	"D-glycero-D-manno-heptose 1,7-bisphosphate phosphatase"	[c] : gmhep17bp + h2o --> gmhep1p + pi	Cell Envelope Biosynthesis		b0200	JLR Kegg RXN R05647		-2.35942	1.9257	[c] : gmhep17bp[c] + h2o[c] --> gmhep1p[c] + h[c] + pi[c] 		
3543	GMPR	No	GMP reductase	[c] : gmp + (2) h + nadph --> imp + nadp + nh4	Purine and Pyrimidine Biosynthesis	1.7.1.7	b0104	EC- changed from 1.7.1.7		-8.647	5.44802	[c] : gmp[c] + (2) h[c] + nadph[c] --> imp[c] + nadp[c] + nh4[c] 		
2926	GMPS2	No	GMP synthase	[c] : atp + gln-L + h2o + xmp --> amp + glu-L + gmp + (2) h + ppi	Purine and Pyrimidine Biosynthesis	6.3.5.2	b2507	JLR		-7.5991	6.07762	[c] : atp[c] + gln-L[c] + h2o[c] + xmp[c] --> amp[c] + glu-L[c] + gmp[c] + h[c] + ppi[c] 		
12309	GMPtex	Yes	GMP transport via diffusion (extracellular to periplasm)	gmp[e] <==> gmp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : gmp[e] <==> gmp[p] 		
2843	GND	No	phosphogluconate dehydrogenase	[c] : 6pgc + nadp --> co2 + nadph + ru5p-D	Pentose Phosphate Pathway	1.1.1.44	b2029	"SMP
Note no proton generation by the the reaction"		1.76029	5.60794	[c] : 6pgc[c] + nadp[c] --> co2[c] + nadph[c] + ru5p-D[c] 		
251	GNK	No	gluconokinase	[c] : atp + glcn --> 6pgc + adp + h	Alternate Carbon Metabolism	2.7.1.12	( b4268  or  b3437 )			-4.65732	2.09859	[c] : atp[c] + glcn[c] --> 6pgc[c] + adp[c] 		
2303	GOFUCR	No	GDP-4-oxo-L-fucose reductase	[c] : gdpofuc + h + nadph --> gdpfuc + nadp	Cell Envelope Biosynthesis		b2052	JLR (EC 1.-.-.-; Reaction number R01950)		-1.77658	4.765	[c] : gdpofuc[c] + h[c] + nadph[c] --> gdpfuc[c] + nadp[c] 		
3242	GP4GH	No	Gp4G hydrolase	[c] : gp4g + h2o --> (2) gdp + (2) h	Nucleotide Salvage Pathway		b0049	JLR		-6.6688	3.75933	[c] : gp4g[c] + h2o[c] --> (2) gdp[c] 
2531	GPDDA1	No	Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)	[c] : g3pc + h2o --> chol + glyc3p + h	Glycerophospholipid Metabolism	3.1.4.46	b3449	JLR	"PMID: 2842304 For ugpQ enzyme:
""We showed that UgpQ-mediated hydrolysis must occur on the inner side of the cytoplasmic membrane... We were unable to characterize this protein on the biochemical level since cellular extracts did not exhibit enzyme activity. We presented evidence that this result is due to a physical dependency of the enzyme on the transport components.  Internal glycerophosphoryl diesters are not substrates of the ugpQ-encoded enzyme; they are hydrolyzed only when transported by the Ugp system.""
reactions were assigned only to upgQ, although from the evidence presented, a dependance of the other ugp genes could be made for the GPR
AMF"	-2.01149	2.78659	[c] : g3pc[c] + h2o[c] --> chol[c] + glyc3p[c] 
12250	GPDDA1pp	Yes	Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)	[p] : g3pc + h2o --> chol + glyc3p + h	Update	3.1.4.46	b2239	"JLR
"		-2.01149	2.78659	[p] : g3pc[p] + h2o[p] --> chol[p] + glyc3p[p] 
2532	GPDDA2	No	Glycerophosphodiester phosphodiesterase (Glycerophosphoethanolamine)	[c] : g3pe + h2o --> etha + glyc3p + h	Glycerophospholipid Metabolism	3.1.4.46	b3449	JLR	"PMID: 2842304 For ugpQ enzyme:
""We showed that UgpQ-mediated hydrolysis must occur on the inner side of the cytoplasmic membrane... We were unable to characterize this protein on the biochemical level since cellular extracts did not exhibit enzyme activity. We presented evidence that this result is due to a physical dependency of the enzyme on the transport components.  Internal glycerophosphoryl diesters are not substrates of the ugpQ-encoded enzyme; they are hydrolyzed only when transported by the Ugp system.""
reactions were assigned only to upgQ, although from the evidence presented, a dependance of the other ugp genes could be made for the GPR
AMF"	-2.01149	2.78659	[c] : g3pe[c] + h2o[c] --> etha[c] + glyc3p[c] 
9790	GPDDA2pp	Yes	Glycerophosphodiester phosphodiesterase (Glycerophosphoethanolamine)	[p] : g3pe + h2o --> etha + glyc3p + h	Update	3.1.4.46	b2239	"JLR
KC"		-2.01149	2.78659	[p] : g3pe[p] + h2o[p] --> etha[p] + glyc3p[p] 
3241	GPDDA3	No	Glycerophosphodiester phosphodiesterase (Glycerophosphoserine)	[c] : g3ps + h2o --> glyc3p + h + ser-L	Glycerophospholipid Metabolism	3.1.4.46	b3449	JLR	"PMID: 2842304 For ugpQ enzyme:
""We showed that UgpQ-mediated hydrolysis must occur on the inner side of the cytoplasmic membrane... We were unable to characterize this protein on the biochemical level since cellular extracts did not exhibit enzyme activity. We presented evidence that this result is due to a physical dependency of the enzyme on the transport components.  Internal glycerophosphoryl diesters are not substrates of the ugpQ-encoded enzyme; they are hydrolyzed only when transported by the Ugp system.""
reactions were assigned only to upgQ, although from the evidence presented, a dependance of the other ugp genes could be made for the GPR
AMF"	-2.01149	2.78659	[c] : g3ps[c] + h2o[c] --> glyc3p[c] + ser-L[c] 
9787	GPDDA3pp	Yes	Glycerophosphodiester phosphodiesterase (Glycerophosphoserine)	[p] : g3ps + h2o --> glyc3p + h + ser-L	Update	3.1.4.46	b2239	"JLR
KC"		-2.01149	2.78659	[p] : g3ps[p] + h2o[p] --> glyc3p[p] + ser-L[p] 
2533	GPDDA4	No	Glycerophosphodiester phosphodiesterase (Glycerophosphoglycerol)	[c] : g3pg + h2o --> glyc + glyc3p + h	Glycerophospholipid Metabolism	3.1.4.46	b3449	JLR	"PMID: 2842304 For ugpQ enzyme:
""We showed that UgpQ-mediated hydrolysis must occur on the inner side of the cytoplasmic membrane... We were unable to characterize this protein on the biochemical level since cellular extracts did not exhibit enzyme activity. We presented evidence that this result is due to a physical dependency of the enzyme on the transport components.  Internal glycerophosphoryl diesters are not substrates of the ugpQ-encoded enzyme; they are hydrolyzed only when transported by the Ugp system.""
reactions were assigned only to upgQ, although from the evidence presented, a dependance of the other ugp genes could be made for the GPR
AMF"	-2.01149	2.78659	[c] : g3pg[c] + h2o[c] --> glyc[c] + glyc3p[c] 
9788	GPDDA4pp	Yes	Glycerophosphodiester phosphodiesterase (Glycerophosphoglycerol)	[p] : g3pg + h2o --> glyc + glyc3p + h	Update	3.1.4.46	b2239	"JLR
KC"		-2.01149	2.78659	[p] : g3pg[p] + h2o[p] --> glyc[p] + glyc3p[p] 
2534	GPDDA5	No	Glycerophosphodiester phosphodiesterase (Glycerophosphoinositol)	[c] : g3pi + h2o --> glyc3p + h + inost	Glycerophospholipid Metabolism	3.1.4.46	b3449	JLR	"PMID: 2842304 For ugpQ enzyme:
""We showed that UgpQ-mediated hydrolysis must occur on the inner side of the cytoplasmic membrane... We were unable to characterize this protein on the biochemical level since cellular extracts did not exhibit enzyme activity. We presented evidence that this result is due to a physical dependency of the enzyme on the transport components.  Internal glycerophosphoryl diesters are not substrates of the ugpQ-encoded enzyme; they are hydrolyzed only when transported by the Ugp system.""
reactions were assigned only to upgQ, although from the evidence presented, a dependance of the other ugp genes could be made for the GPR
AMF"	-4.00343	2.86196	[c] : g3pi[c] + h2o[c] --> glyc3p[c] + inost[c] 
12251	GPDDA5pp	Yes	Glycerophosphodiester phosphodiesterase (Glycerophosphoinositol)	[p] : g3pi + h2o --> glyc3p + h + inost	Update	3.1.4.46	b2239	JLR		-4.00343	2.86196	[p] : g3pi[p] + h2o[p] --> glyc3p[p] + inost[p] 
109	GRTT	No	geranyltranstransferase	[c] : grdp + ipdp --> frdp + ppi	Cofactor and Prosthetic Group Biosynthesis	2.5.1.10	b0421			-14.4146	2.92602	[c] : grdp[c] + ipdp[c] --> frdp[c] + ppi[c] 
13840	GRXR	Yes	glutaredoxin reductase	[c] : grxox + (2) gthrd --> grxrd + gthox	Update	1.8.4.2		AMF	"not sure of gene association,
reaciton needed to re-reduce grx
AMF"	7.42557	8.06849	[c] : grxox[c] + (2) gthrd[c] --> grxrd[c] + gthox[c] 
2928	GSNK	No	guanosine kinase	[c] : atp + gsn --> adp + gmp + h	Nucleotide Salvage Pathway		b0477	JLR		-4.65732	2.09859	[c] : atp[c] + gsn[c] --> adp[c] + gmp[c] 
8856	GSNt2pp	Yes	guanosine transport in via proton symport (periplasm)	gsn[p] + h[p] --> gsn[c] + h[c]	"Transport, Inner Membrane"		b2964			0	0	[c] : gsn[p] + h[p] --> gsn[c] + h[c] 
9144	GSNtex	Yes	guanosine transport via diffusion (extracellular to periplasm)	gsn[e] <==> gsn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : gsn[e] <==> gsn[p] 
3310	GSPMDA	No	Glutathionylspermidine amidase	[c] : gtspmd + h2o --> gthrd + spmd	Arginine and Proline Metabolism	3.5.1.78	b2988	JLR		-3.36489	3.34628	[c] : gtspmd[c] + h2o[c] --> gthrd[c] + spmd[c] 		
3311	GSPMDS	No	Glutathionylspermidine synthetase	[c] : atp + gthrd + spmd --> adp + gtspmd + h + pi	Arginine and Proline Metabolism	6.3.1.8	b2988	JLR		-3.65185	3.59073	[c] : atp[c] + gthrd[c] + spmd[c] --> adp[c] + gtspmd[c] + h[c] + pi[c] 		
1655	GTHOr	No	glutathione oxidoreductase	[c] : gthox + h + nadph <==> (2) gthrd + nadp	Cofactor and Prosthetic Group Biosynthesis	1.8.1.7	b3500	JLR- added reversible form	JLR-  JSE model had 1 gthrd not 2	-3.15997	6.25689	[c] : gthox[c] + h[c] + nadph[c] <==> (2) gthrd[c] + nadp[c] 		
19630	GTHOXtex	Yes	glutathione (ox) transport via diffusion (extracellular to periplasm)	gthox[e] <==> gthox[p]	"Transport, Outer Membrane"			AMF	"assumed diffusion through the outer membrane, also supported in PMID: 16040611
AMF"	0	0	[c] : gthox[e] <==> gthox[p] 		
19632	GTHRDabc2pp	Yes	glutathione export via ABC system (cytoplasm to periplasm)	atp[c] + gthrd[c] + h2o[c] --> adp[c] + gthrd[p] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0886  and  b0887 )	AMF	"characterized in PMID: 16040611
AMF"	-7.01673	1.48181	[c] : atp[c] + gthrd[c] + h2o[c] --> adp[c] + gthrd[p] + h[c] + pi[c] 		
19622	GTHRDabcpp	Yes	Reduced glutathione via ABC system (periplasm)	atp[c] + gthrd[p] + h2o[c] --> adp[c] + gthrd[c] + h[c] + pi[c]	"Transport, Inner Membrane"		( b0829  and  b0830  and  b0831  and  b0832 )	AMF	"E. coli can utilize glutathione as a sole sulfur source
It is possibile that a nonspecific glutathione uptake system besides YliABCD and GGT exists in E. coli.
Charcterization of transporter.
PMID: 16109926
AMF"	-7.01673	1.48181	[c] : atp[c] + gthrd[p] + h2o[c] --> adp[c] + gthrd[c] + h[c] + pi[c] 		
19730	GTHRDHpp	Yes	glutathione hydralase (periplasmic)	[p] : gthrd + h2o --> cgly + glu-L	Update		b3447	AMF	"ggt catalyzes the transfer of gamma-glutamyl compounds to AA and can also hydrolyze a number of gamma-glutamyl compounds. see PMID: 8104180
AMF"	-3.36489	3.34628	[p] : gthrd[p] + h2o[p] --> cgly[p] + glu-L[p] 		
19623	GTHRDtex	Yes	glutathione transport via diffusion (extracellular to periplasm)	gthrd[e] <==> gthrd[p]	Update			AMF	"assumed diffusion through the outer membrane, also supported in PMID: 16040611
AMF"	0	0	[c] : gthrd[e] <==> gthrd[p] 		
3545	GTHS	No	glutathione synthetase	[c] : atp + glucys + gly --> adp + gthrd + h + pi	Cofactor and Prosthetic Group Biosynthesis	6.3.2.3	b2947	NCD		-3.65185	3.59073	[c] : atp[c] + glucys[c] + gly[c] --> adp[c] + gthrd[c] + h[c] + pi[c] 		
7819	GTPCI	No	GTP cyclohydrolase I	[c] : gtp + h2o --> ahdt + for + h	Cofactor and Prosthetic Group Biosynthesis	3.5.4.16	b2153	The reaction involves hydrolysis of two C-N bonds and isomerization of the pentose unit; the recyclization may be non-enzymic		-23.0541	8.56572	[c] : gtp[c] + h2o[c] --> ahdt[c] + for[c] + h[c] 		
2739	GTPCII2	No	GTP cyclohydrolase II (25drapp)	[c] : gtp + (3) h2o --> 25drapp + for + (2) h + ppi	Cofactor and Prosthetic Group Biosynthesis		b1277	JLR	JLR- added reaction and 25drapp to the database 25drapp is not the same as 25dhpp (check LIGAND and NH page 658)	-3.27811	10.0415	[c] : gtp[c] + (3) h2o[c] --> 25drapp[c] + for[c] + h[c] + ppi[c] 		
13384	GTPDPDP	Yes	"guanosine-5'-triphosphate,3'-diphosphate diphosphatase"	[c] : gdptp + h2o --> h + pi + ppgpp	Update	3.6.1.40	b3779	AMF	"4 reactions are involved in the ppGpp biosynthesis pathway
ppGpp is a signalling molecule

gppA : PMID: 8394006
RelA: PMID: 2844820
"	-7.01673	1.48181	[c] : gdptp[c] + h2o[c] --> h[c] + pi[c] + ppgpp[c] 		
169	GTPDPK	Yes	GTP diphosphokinase	[c] : atp + gtp --> amp + gdptp + h	Update	2.7.6.5	b2784		"4 reactions are involved in the ppGpp biosynthesis pathway
ppGpp is a signalling molecule

gppA : PMID: 8394006
RelA: PMID: 2844820
"	-2.66537	2.19769	[c] : atp[c] + gtp[c] --> amp[c] + gdptp[c] 		
12488	GTPHs	Yes	spontaneous GTP amine hydrolysis	[c] : gtp + h + h2o --> nh4 + xtp	Update			"MKA - spontaneous rxn
http://www.jbmb.or.kr/view_article.php3?cont=jbmb&kid=153&mid=10&pid=10
The mutation protection mechanisms are
caused by the incorporation into DNA of unwelcome
nucleotides that are formed spontaneously."	"PMID: 12297000
The mutation protection mechanisms are caused by the incorporation into DNA of unwelcome nucleotides that are formed spontaneously.
AMF
atphs reaction not mentioned specifically, but seems logical"	-5.6874	4.84135	[c] : gtp[c] + h[c] + h2o[c] --> nh4[c] + xtp[c] 		
9145	GTPtex	Yes	GTP transport via diffusion (extracellular to periplasm)	gtp[e] <==> gtp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : gtp[e] <==> gtp[p] 		
3312	GUAD	No	guanine deaminase	[c] : gua + h + h2o --> nh4 + xan	Nucleotide Salvage Pathway	3.5.4.3	b2883			-5.6874	4.84135	[c] : gua[c] + h[c] + h2o[c] --> nh4[c] + xan[c] 		
2808	GUAPRT	No	guanine phosphoribosyltransferase	[c] : gua + prpp --> gmp + ppi	Nucleotide Salvage Pathway	2.4.2.8	( b0238  or  b0125 )	"Guanine and 6-mercaptopurine can replace hypoxanthine

EC added (2.4.2.7 makes the same reaction) IT"		-3.6643	3.87109	[c] : gua[c] + prpp[c] --> gmp[c] + ppi[c] 		
8857	GUAt2pp	Yes	guanine transport in via proton symport (periplasm)	gua[p] + h[p] --> gua[c] + h[c]	Putative Transporters		b3654			0	0	[c] : gua[p] + h[p] --> gua[c] + h[c] 		
9146	GUAtex	Yes	Guanine transport via diffusion (extracellular to periplasm)	gua[e] <==> gua[p]	"Transport, Outer Membrane"		b0411		"assumed passive diffusion through the outer peptidoglycan layer

Tsx is responsible for the permeation of ribo- and deoxy-nucleosides, across the outer membrane of E. coli"	0	0	[c] : gua[e] <==> gua[p] 		
8988	GUAtpp	Yes	Guanine transport via diffusion (periplasm)	gua[p] <==> gua[c]	"Transport, Inner Membrane"			JLR	JLR- not sure about the reaction 	0	0	[c] : gua[p] <==> gua[c] 		
494	GUI1	No	glucuronate isomerase (D-glucuronate)	[c] : glcur <==> fruur	Alternate Carbon Metabolism	5.3.1.12	b3092			-0.246702	4.88847	[c] : glcur[c] <==> fruur[c] 		
495	GUI2	No	glucuronate isomerase (D-galacturonate)	[c] : galur <==> tagur	Alternate Carbon Metabolism	5.3.1.12	b3092			-0.246702	4.88847	[c] : galur[c] <==> tagur[c] 		
13794	GUR1PPpp	Yes	Glucuronate 1-phosphate phosphatase (periplasm)	[p] : glcur1p + h2o --> glcur + pi	Update			AMF	"assumed probable reactions, may be carried out by the Agp reaction - almost assigned to Agp reaction

needed to degrade 1-phosphates from UDP- hydrolase activity of UshA which is known to produce these products

AMF"	-3.54819	2.12947	[p] : glcur1p[p] + h2o[p] --> glcur[p] + h[p] + pi[p] 		
12231	H2O2tex	Yes	hydrogen peroxide transport via diffusion (external)	h2o2[e] <==> h2o2[p]	"Transport, Outer Membrane"			AMF	"assumed
"	0	0	[c] : h2o2[e] <==> h2o2[p] 		
9149	H2Otex	Yes	H2O transport via diffusion (extracellular to periplasm)	h2o[e] <==> h2o[p]	"Transport, Outer Membrane"		( b1377  or  b0929  or  b2215  or  b0241  or  b1319 )		"assumed passive diffusion through the outer peptidoglycan layer

this reaction is assigned to the general porins of the outer membrane - water filled porins - allow the transport of metabolites <600 Da

"	0	0	[c] : h2o[e] <==> h2o[p] 		
8858	H2Otpp	Yes	H2O transport via diffusion (periplasm)	h2o[p] <==> h2o[c]	"Transport, Inner Membrane"		b0875	"renamed from H20t5 to H2Ot
NCD"		0	0	[c] : h2o[p] <==> h2o[c] 		
5201	H2SO	Yes	Hydrogen sulfide oxidation	[c] : h2s + (2) o2 --> (2) h + so4	Update			"Spontaneous Reaction
JLR"	Reaction is spontaneous.	-190.25	1.58114	[c] : h2s[c] + (2) o2[c] --> (2) h[c] + so4[c] 		
8989	H2St1pp	Yes	h2s transport (periplasm)	h2s[c] --> h2s[p]	Update			JLR	"Ref. assumes that occurs via diffusion, no strong evidence"	0	0	[c] : h2s[c] --> h2s[p] 		
9150	H2Stex	Yes	h2s transport via diffusion (extracellular to periplasm)	h2s[e] <==> h2s[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : h2s[e] <==> h2s[p] 		
9148	H2tex	Yes	hydrogen transport via diffusion (extracellular to periplasm)	h2[e] <==> h2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : h2[e] <==> h2[p] 		
12330	H2tpp	Yes	hydrogen transport diffusion (periplasm)	h2[p] <==> h2[c]	Update				"assumed diffusion

Dr. Saier supports this assumption
7-8-05"	0	0	[c] : h2[p] <==> h2[c] 		
5392	HACD1i	Yes	3-hydroxyacyl-CoA dehydrogenase (acetoacetyl-CoA)	[c] : 3hbcoa + nad --> aacoa + h + nadh	Membrane Lipid Metabolism	1.1.1.35	( b3846  or  b2341 )	Same as EC 1.1.1.157		4.73639	4.5435	[c] : 3hbcoa[c] + nad[c] --> aacoa[c] + h[c] + nadh[c] 		
5394	HACD2i	Yes	3-hydroxyacyl-CoA dehydrogenase (3-oxohexanoyl-CoA)	[c] : 3hhcoa + nad --> 3ohcoa + h + nadh	Membrane Lipid Metabolism	1.1.1.35	( b3846  or  b2341 )			4.73639	4.5435	[c] : 3hhcoa[c] + nad[c] --> 3ohcoa[c] + h[c] + nadh[c] 					
5395	HACD3i	Yes	3-hydroxyacyl-CoA dehydrogenase (3-oxooctanoyl-CoA)	[c] : 3hocoa + nad --> 3oocoa + h + nadh	Membrane Lipid Metabolism	1.1.1.35	( b3846  or  b2341 )			4.73639	4.5435	[c] : 3hocoa[c] + nad[c] --> 3oocoa[c] + h[c] + nadh[c] 					
5396	HACD4i	Yes	3-hydroxyacyl-CoA dehydrogenase (3-oxodecanoyl-CoA)	[c] : 3hdcoa + nad --> 3odcoa + h + nadh	Membrane Lipid Metabolism	1.1.1.35	( b3846  or  b2341 )			4.73639	4.5435	[c] : 3hdcoa[c] + nad[c] --> 3odcoa[c] + h[c] + nadh[c] 					
5397	HACD5i	Yes	3-hydroxyacyl-CoA dehydrogenase (3-oxododecanoyl-CoA)	[c] : 3hddcoa + nad --> 3oddcoa + h + nadh	Membrane Lipid Metabolism	1.1.1.35	( b3846  or  b2341 )			4.73639	4.5435	[c] : 3hddcoa[c] + nad[c] --> 3oddcoa[c] + h[c] + nadh[c] 					
5398	HACD6i	Yes	3-hydroxyacyl-CoA dehydrogenase (3-oxotetradecanoyl-CoA)	[c] : 3htdcoa + nad --> 3otdcoa + h + nadh	Membrane Lipid Metabolism	1.1.1.35	( b3846  or  b2341 )			4.73639	4.5435	[c] : 3htdcoa[c] + nad[c] --> 3otdcoa[c] + h[c] + nadh[c] 					
5399	HACD7i	Yes	3-hydroxyacyl-CoA dehydrogenase (3-oxohexadecanoyl-CoA)	[c] : 3hhdcoa + nad --> 3ohdcoa + h + nadh	Membrane Lipid Metabolism	1.1.1.35	( b3846  or  b2341 )			4.73639	4.5435	[c] : 3hhdcoa[c] + nad[c] --> 3ohdcoa[c] + h[c] + nadh[c] 					
8137	HACD8i	Yes	3-hydroxyacyl-CoA dehydrogenase (3-oxooctadecanoyl-CoA)	[c] : 3hodcoa + nad --> 3oodcoa + h + nadh	Membrane Lipid Metabolism	1.1.1.35	( b3846  or  b2341 )	JLR		4.73639	4.5435	[c] : 3hodcoa[c] + nad[c] --> 3oodcoa[c] + h[c] + nadh[c] 					
1146	HBZOPT	No	Hydroxybenzoate octaprenyltransferase	[c] : 4hbz + octdp --> 3ophb + ppi	Cofactor and Prosthetic Group Biosynthesis		b4040	"tv
JLR - EC 2.5.1.-"		-19.3044	3.85522	[c] : 4hbz[c] + octdp[c] --> 3ophb[c] + ppi[c] 					
8859	HCINNMt2rpp	Yes	"3-hydroxycinnamic acid transport via proton symport, reversible (periplasm)"	3hcinnm[p] + h[p] <==> 3hcinnm[c] + h[c]	Putative Transporters		b0353	JLR	JLR- reference indicates in a figure that mhpT transports 3hcinnm	0	0	[c] : 3hcinnm[p] + h[p] <==> 3hcinnm[c] + h[c] 					
9024	HCINNMtex	Yes	3-hydroxycinnamic acid transport via diffusion (extracellular to periplasm)	3hcinnm[e] <==> 3hcinnm[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : 3hcinnm[e] <==> 3hcinnm[p] 					
917	HCO3E	No	HCO3 equilibration reaction	[c] : co2 + h2o <==> h + hco3	Unassigned	4.2.1.1	( b0339  or  b0126 )			-0.8	1	[c] : co2[c] + h2o[c] <==> h[c] + hco3[c] 					
1466	HCYSMT	Yes	homocysteine S-methyltransferase	[c] : amet + hcys-L --> ahcys + h + met-L	Update	2.1.1.10	b0261	NCD	"PMID: 9882684

 A mmuM metE metH triple mutant shows inability to grow on S-methylmethionine, in contrast to a metE metH double mutant or to wild type

AMF"	No energy	No energy	[c] : amet[c] + hcys-L[c] --> ahcys[c] + h[c] + met-L[c] 					
13675	HCYSMT2	Yes	Homocysteine Methyltransferase	[c] : hcys-L + mmet --> h + (2) met-L	Update		b0261		"PMID: 9882684

 A mmuM metE metH triple mutant shows inability to grow on S-methylmethionine, in contrast to a metE metH double mutant or to wild type

AMF"	No energy	No energy	[c] : hcys-L[c] + mmet[c] --> h[c] + (2) met-L[c] 					
13524	HDCAabcpp	Yes	hexadecanoate (n-C16:0) transport via ABC system (periplasm)	atp[c] + h2o[c] + hdca[c] --> adp[c] + h[c] + hdca[p] + pi[c]	Lipopolysaccharide Biosynthesis / Recycling		b0914	"AMF
assumed transport"	"PMID: 12045108 gives a reaview on LPS biosynthesis and states that it can transport PE

also, atpase acitvity was activated by kdo2-lipidA and other hexa-acylated compounds, also kd02-lipid4A could be transported by MsbA
PMID: 15052329

assuming that it transports hdca

AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + hdca[c] --> adp[c] + h[c] + hdca[p] + pi[c] 					
9241	HDCAtexi	Yes	Hexadecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)	hdca[e] --> hdca[p]	"Transport, Outer Membrane"		b2344		"Transport of C12 - C18 fatty acids are facilitated by the outer membrane FadL protein (PMID: 103228825), inner membrane transport and subsequently outer membrane can require FACOAL enzyme (PMID: 15067008)

smaller FA can also pass through, C6 - C11, but can also diffuse, so they weren't associated"	0	0	[c] : hdca[e] --> hdca[p] 					
19982	HDCEAtexi	Yes	Hexadecenoate transport via facilitated irreversible diffusion (extracellular to periplasm)	hdcea[e] --> hdcea[p]	"Transport, Outer Membrane"		b2344		"Transport of C12 - C18 fatty acids are facilitated by the outer membrane FadL protein (PMID: 103228825), inner membrane transport and subsequently outer membrane can require FACOAL enzyme (PMID: 15067008)

smaller FA can also pass through, C6 - C11, but can also diffuse, so they weren't associated"	0	0	[c] : hdcea[e] --> hdcea[p] 					
19990	HDCOAI	Yes	hexadecenoyl-coa cis-trans isomerization	[c] : hdcoa --> hdd2coa	Membrane Lipid Metabolism	5.3.3.8	b3846	"JLR
AMF"	"Evidence in PMID: 12535077
From Ecocyc: A reaction in beta-oxidation of fatty acids, required to feed unsaturated fatty acids into the main pathway.  Not sure of reaction reversibility.
AMF
FadJ might also carry out this reaction.  No evidence found for it yet though.
JLR
"	0	0.5	[c] : hdcoa[c] --> hdd2coa[c] 					
1021	HEMEOS	No	Heme O synthase	[c] : frdp + h2o + pheme --> hemeO + ppi	Cofactor and Prosthetic Group Biosynthesis		b0428			No energy	No energy	[c] : frdp[c] + h2o[c] + pheme[c] --> hemeO[c] + ppi[c] 					
13494	HEPK1	Yes	LPS heptose kinase I (LPS core synthesis)	[c] : atp + hhlipa --> adp + h + phhlipa	Lipopolysaccharide Biosynthesis / Recycling		b3630	AMF	"The sequence of HEPK1 --> HEPT3 --> HEPK2 is well established ( WaaPQY)

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108

see specifically PMID: 11054112
for WaaPQY"	-3.46855	2.28701	[c] : atp[c] + hhlipa[c] --> adp[c] + phhlipa[c] 					
13496	HEPK2	Yes	LPS heptose kinase II (LPS core synthesis)	[c] : atp + hphhlipa --> adp + h + phphhlipa	Lipopolysaccharide Biosynthesis / Recycling		b3625	AMF	"The sequence of HEPK1 --> HEPT3 --> HEPK2 is well established ( WaaPQY)

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108

see specifically PMID: 11054112
for WaaPQY"	-3.46855	2.28701	[c] : atp[c] + hphhlipa[c] --> adp[c] + phphhlipa[c] 					
13489	HEPT1	Yes	heptosyltransferase I (LPS core synthesis)	"[c] : adphep-L,D + lipa --> adp + h + hlipa"	Lipopolysaccharide Biosynthesis / Recycling		b3621	AMF	"Core LPS biosynthesis
see PMID: 12045108
for review

see PMID: 11054112
for WaaA, WaaC and WaaF reactions 

ADP-D-mannose can also serve as a surrogate substrate for WaaC
"	-0.675884	3.38607	"[c] : adphep-L,D[c] + lipa[c] --> adp[c] + hlipa[c] "					
13490	HEPT2	Yes	heptosyltransferase II (LPS core synthesis)	"[c] : adphep-L,D + hlipa --> adp + h + hhlipa"	Lipopolysaccharide Biosynthesis / Recycling		b3620	AMF	"Core LPS biosynthesis
see PMID: 12045108
for review

see PMID: 11054112
for WaaA, WaaC and WaaF reactions 

ADP-D-mannose can also serve as a surrogate substrate for WaaC
"	-0.675884	3.38607	"[c] : adphep-L,D[c] + hlipa[c] --> adp[c] + hhlipa[c] "					
13495	HEPT3	Yes	heptosyltransferase III (LPS core synthesis)	"[c] : adphep-L,D + phhlipa --> adp + h + hphhlipa"	Lipopolysaccharide Biosynthesis / Recycling		b3632	AMF	"The sequence of HEPK1 --> HEPT3 --> HEPK2 is well established ( WaaPQY)

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108

see specifically PMID: 11054112
for WaaPQY"	0.803173	2.08341	"[c] : adphep-L,D[c] + phhlipa[c] --> adp[c] + hphhlipa[c] "					
13507	HEPT4	Yes	heptosyltransferase IV (LPS core synthesis)	"[c] : adphep-L,D + gggagicolipa --> adp + colipa + h"	Lipopolysaccharide Biosynthesis / Recycling		b3623	AMF	"Look in figure 2 to see the order of outer core oligosaccharide biosynthesis reactions - WaaO study
PMID: 9765561

study on WaaR function
PMID: 10234827

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108
"	No energy	No energy	"[c] : adphep-L,D[c] + gggagicolipa[c] --> adp[c] + colipa[c] "					
2791	HETZK	No	hydroxyethylthiazole kinase	[c] : 4mhetz + atp --> 4mpetz + adp + h	Cofactor and Prosthetic Group Biosynthesis	2.7.1.50	b2104			-4.65732	2.09859	[c] : 4mhetz[c] + atp[c] --> 4mpetz[c] + adp[c] 					
2842	HEX1	No	hexokinase (D-glucose:ATP)	[c] : atp + glc-D --> adp + g6p + h	Glycolysis/Gluconeogenesis	2.7.1.1	b2388	"D-Glucose, D-mannose, D-fructose, sorbitol and D-glucosamine can act as acceptors; ITP and dATP can act as donors. The liver isoenzyme has sometimes been called glucokinase. Reaction also associated with EC 2.7.1.2"	"the reaction was completed in little more than 1 min with glucose as the substrate. Under the same assay conditions, phosphorylation of
mannose and galactose could be observed by TLC only after 30 min of incubation as faint spots of the respective phosphates. Phosphorylation of fructose could not be detected (Fig. 2).

PMID: 9023215
AMF
statement makes it seem like glucose is the only true physiological substrate"	-4.65732	2.09859	[c] : atp[c] + glc-D[c] --> adp[c] + g6p[c] 					
666	HEX4	Yes	hexokinase (D-mannose:ATP)	[c] : atp + man --> adp + h + man6p	Update	2.7.1.7		"D-Glucose, D-mannose, D-fructose, sorbitol and D-glucosamine can act as acceptors; ITP and dATP can act as donors. The liver isoenzyme has sometimes been called glucokinase.
also active in ecoli PMID: 4557975
"	"needed to utilize mannose from the wcaH enzyme

checked to see if glk is a probable enzyme, but it probably isn't, very little activity towards mannose
(see glk description)

states there is mamnokinase activity
PMID: 4557975"	-4.65732	2.09859	[c] : atp[c] + man[c] --> adp[c] + man6p[c] 					
669	HEX7	Yes	hexokinase (D-fructose:ATP)	[c] : atp + fru --> adp + f6p + h	Update	2.7.1.1	b0394	"D-Glucose, D-mannose, D-fructose, sorbitol and D-glucosamine can act as acceptors; ITP and dATP can act as donors. The liver isoenzyme has sometimes been called glucokinase.
Same as 2.7.1.4
"	"Mak activity is low in wild-type cells
could be thought as cryptic from the same ref
PMID: 11361065
AMF"	-4.65732	2.09859	[c] : atp[c] + fru[c] --> adp[c] + f6p[c] 					
19996	HEXt2rpp	Yes	"hexanoate transport via proton symport, reversible (periplasm)"	h[p] + hxa[p] <==> h[c] + hxa[c]	Putative Transporters		b2223	JLR	"JLR-based on Saier's database
see PMID: 3025185 for realated SCFA metabolism
AMF"	0	0	[c] : h[p] + hxa[p] <==> h[c] + hxa[c] 					
13654	HG2abcpp	Yes	Mercury (Hg+2) ABC transporter (periplasm)	atp[c] + h2o[c] + hg2[c] --> adp[c] + h[c] + hg2[p] + pi[c]	"Transport, Inner Membrane"		b3469	AMF	"characterized in PMID: 10660539
ATP-dependent efflux
The activity was specific for Pb(II), Cd(II), Zn(II), and Hg(II), with the highest activity obtained when the metals were present as thiolate complexes of cysteine or glutathione.

AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + hg2[c] --> adp[c] + h[c] + hg2[p] + pi[c] 					
13683	HG2tex	Yes	mercury (Hg+2) transport via diffusion (extracellular to periplasm)	hg2[e] <==> hg2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : hg2[e] <==> hg2[p] 					
8860	HISabcpp	Yes	L-histidine transport via ABC system (periplasm)	atp[c] + h2o[c] + his-L[p] --> adp[c] + h[c] + his-L[c] + pi[c]	"Transport, Inner Membrane"		( b2309  and  b2307  and  b2306  and  b2308 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + his-L[p] --> adp[c] + h[c] + his-L[c] + pi[c] 					
8861	HISt2rpp	Yes	L-histidine reversible transport via proton symport (periplasm)	h[p] + his-L[p] <==> h[c] + his-L[c]	"Transport, Inner Membrane"		b0112	NCD		0	0	[c] : h[p] + his-L[p] <==> h[c] + his-L[c] 		
340	HISTD	No	histidinol dehydrogenase	[c] : h2o + histd + (2) nad --> (3) h + his-L + (2) nadh	Histidine Metabolism	1.1.1.23	b2020		JLR- JSE model uses 3 NAD/NADH instead of 2.  Neidhardt indicates that it is 2 as does EcoCyc.	-10.6681	9.12058	[c] : h2o[c] + histd[c] + (2) nad[c] --> (4) h[c] + his-L[c] + (2) nadh[c] 		
9152	HIStex	Yes	L-histidine transport via diffusion (extracellular to periplasm)	his-L[e] <==> his-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : his-L[e] <==> his-L[p] 		
2863	HISTP	No	histidinol-phosphatase	[c] : h2o + hisp --> histd + pi	Histidine Metabolism	3.1.3.15	b2022			3.61464	3.99246	[c] : h2o[c] + hisp[c] --> histd[c] + pi[c] 		
1035	HISTRS	Yes	Histidyl-tRNA synthetase	[c] : atp + his-L + trnahis --> amp + histrna + ppi	Update	6.1.1.21	b2514		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + his-L[c] + trnahis[c] --> amp[c] + histrna[c] + ppi[c] 		
7715	HKNDDH	No	"2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase"	[c] : h2o + hkndd --> h + op4en + succ	Alternate Carbon Metabolism		b0349	JLR- Kegg reaction 02603		-13.2725	2.78576	[c] : h2o[c] + hkndd[c] --> h[c] + op4en[c] + succ[c] 		
7716	HKNTDH	No	2-hydroxy-6-ketononotrienedioate hydrolase	[c] : h2o + hkntd --> fum + h + op4en	Alternate Carbon Metabolism		b0349	JLR- see PMID 9603882 and PMID 9098055		-13.2725	2.78576	[c] : h2o[c] + hkntd[c] --> fum[c] + h[c] + op4en[c] 		
4	HMBS	No	hydroxymethylbilane synthase	[c] : h2o + (4) ppbng --> hmbil + (4) nh4	Cofactor and Prosthetic Group Biosynthesis	4.3.1.8	b3805			-14.9756	9.31077	[c] : h2o[c] + (4) ppbng[c] --> hmbil[c] + (4) nh4[c] 		
128	HMPK1	No	hydroxymethylpyrimidine kinase (ATP)	[c] : 4ahmmp + atp --> 4ampm + adp + h	Cofactor and Prosthetic Group Biosynthesis	2.7.1.49	( b2103  or  b2418 )		"see PMID: 15150256
AMF
"	-4.65732	2.09859	[c] : 4ahmmp[c] + atp[c] --> 4ampm[c] + adp[c] 		
13873	HOMt2pp	Yes	L-homoserineserine efflux via proton symport	h[p] + hom-L[c] --> h[c] + hom-L[p]	"Transport, Inner Membrane"		( b0813  or  b3824 )		"RhtA charcterized in PMID: 12648727
RhtA could also transport other AA, listed in ref

RhtC and RhtB characterized in PMID: 10386596
AMF"	0	0	[c] : h[p] + hom-L[c] --> h[c] + hom-L[p] 		
13875	HOMtex	Yes	L-homoserine transport via diffusion (extracellular to periplasm)	hom-L[e] <==> hom-L[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : hom-L[e] <==> hom-L[p] 		
2367	HOPNTAL	No	4-hydroxy-2-oxopentanoate aldolase	[c] : 4h2opntn --> acald + pyr	Alternate Carbon Metabolism		b0352	JLR (Kegg reaction R00750)		2.91741	2.32549	[c] : 4h2opntn[c] --> acald[c] + pyr[c] 		
1834	HPPK2	No	6-hydroxymethyl-dihydropterin pyrophosphokinase	[c] : 6hmhpt + atp --> 6hmhptpp + amp + h	Cofactor and Prosthetic Group Biosynthesis		b0142	JLR- Neidhardt pg 667	"JLR- had to add 6hmhptpp to database, different then 2ahhmd (ketone vs. OH).  "	-4.65732	2.09859	[c] : 6hmhpt[c] + atp[c] --> 6hmhptpp[c] + amp[c] 		
7714	HPPPNDO	No	"2,3-dihydroxypheylpropionate 1,2-dioxygenase"	[c] : dhpppn + o2 --> h + hkndd	Alternate Carbon Metabolism	1.13.11.16	b0348	JLR-		-69.9514	13.2166	[c] : dhpppn[c] + o2[c] --> h[c] + hkndd[c] 		
8862	HPPPNt2rpp	Yes	"3-(3-hydroxyphenyl)propionate transport via proton symport, reversible (periplasm)"	3hpppn[p] + h[p] <==> 3hpppn[c] + h[c]	Putative Transporters		b0353	JLR	JLR- reference refers to unpublished data indicating that mhpT transports 3hpppn	0	0	[c] : 3hpppn[p] + h[p] <==> 3hpppn[c] + h[c] 		
9025	HPPPNtex	Yes	3-(3-hydroxyphenyl)propionate transport via diffusion (extracellular to periplasm)	3hpppn[e] <==> 3hpppn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : 3hpppn[e] <==> 3hpppn[p] 		
2546	HPYRI	No	hydroxypyruvate isomerase	[c] : hpyr <==> 2h3oppan	Alternate Carbon Metabolism	5.3.1.22	b0508	JLR		0.429448	2.63724	[c] : hpyr[c] <==> 2h3oppan[c] 		
2132	HPYRRx	No	Hydroxypyruvate reductase (NADH)	[c] : h + hpyr + nadh --> glyc-R + nad	Alternate Carbon Metabolism		( b1033  or  b3553 )	JLR	JLR- nadph is preferred 10:1 over nadh	-4.73639	4.5435	[c] : h[c] + hpyr[c] + nadh[c] --> glyc-R[c] + nad[c] 		
2130	HPYRRy	No	Hydroxypyruvate reductase (NADPH)	[c] : h + hpyr + nadph --> glyc-R + nadp	Alternate Carbon Metabolism		( b1033  or  b3553 )	JLR		-4.73639	4.5435	[c] : h[c] + hpyr[c] + nadph[c] --> glyc-R[c] + nadp[c] 		
2868	HSDy	No	homoserine dehydrogenase (NADPH)	[c] : hom-L + nadp <==> aspsa + h + nadph	Threonine and Lysine Metabolism	1.1.1.3	( b3940  or  b0002 )			5.16584	4.34649	[c] : hom-L[c] + nadp[c] <==> aspsa[c] + h[c] + nadph[c] 		
361	HSK	No	homoserine kinase	[c] : atp + hom-L --> adp + h + phom	Threonine and Lysine Metabolism	2.7.1.39	b0003			-4.65732	2.09859	[c] : atp[c] + hom-L[c] --> adp[c] + phom[c] 		
368	HSST	No	homoserine O-succinyltransferase	[c] : hom-L + succoa --> coa + suchms	Methionine Metabolism	2.3.1.46	b4013			-3.97568	4.69324	[c] : hom-L[c] + succoa[c] --> coa[c] + suchms[c] 		
342	HSTPT	No	histidinol-phosphate transaminase	[c] : glu-L + imacp --> akg + hisp	Histidine Metabolism	2.6.1.9	b2021			0	0.5	[c] : glu-L[c] + imacp[c] --> akg[c] + hisp[c] 		
9147	Htex	Yes	proton transport via diffusion (extracellular to periplasm)	h[e] <==> h[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : h[e] <==> h[p] 		
14003	HXAND	Yes	hypoxanthine dehydrogenase	[c] : h2o + hxan + nad --> h + nadh + xan	Update		( b2866  and  b2867  and  b2868 )	"AMF
PMID: 10986234
not sure of NADH usage"	"pathway in PMID: 10986234
does not mention an electron acceptor (NAD) in the paper, so further charcterization is needed, but reaction is outlined
AMF"	2.95959	6.17887	[c] : h2o[c] + hxan[c] + nad[c] --> h[c] + nadh[c] + xan[c] 		
9153	HXAtex	Yes	Hexanoate transport via diffusion (extracellular to periplasm)	hxa[e] <==> hxa[p]	"Transport, Outer Membrane"				"assumed passive diffusion through the outer peptidoglycan layer

can also pass through FadL
"	0	0	[c] : hxa[e] <==> hxa[p] 		
19995	HXCT	Yes	Acetyl-CoA:hexanoate-CoA transferase	[c] : accoa + hxa --> ac + hxcoa	Alternate Carbon Metabolism	2.8.3.8	( b2221  and  b2222 )	AMF	"JLR- see NH21 for info on regulation

From ecocyc: The growth of E. coli on short-chain fatty acids (C3-C6) requires the activation of the acids to their respective thioesters. This activation is catalyzed by acetoacetyl-CoA transferase. [ Sramek75  ]
also, see PMID: 3025185
AMF"	0	0.5	[c] : accoa[c] + hxa[c] --> ac[c] + hxcoa[c] 		
441	HXPRT	No	hypoxanthine phosphoribosyltransferase (Hypoxanthine)	[c] : hxan + prpp --> imp + ppi	Nucleotide Salvage Pathway	2.4.2.8	( b0238  or  b0125 )	Guanine (see GUAPRT) and 6-mercaptopurine can replace hypoxanthine		-3.6643	3.87109	[c] : hxan[c] + prpp[c] --> imp[c] + ppi[c] 		
8991	HYD1pp	Yes	hydrogenase (ubiquinone-8: 2 protons) (periplasm)	(2) h[c] + h2[c] + q8[c] --> (2) h[p] + q8h2[c]	Oxidative Phosphorylation	1.18.99.1	( ( b0972  and  b0973  and  b0974 )  or  ( b2994  and  b2997 )  or  ( b2719  and  b2720  and  b2721  and  b2722  and  b2723  and  b2724 ) )	JLR- ubiquinone-8 specific		-27.8635	21.3049	[c] : (2) h[c] + h2[c] + q8[c] --> (2) h[p] + q8h2[c] 		
8992	HYD2pp	Yes	Hydrogenase (menaquinone8: 2 protons) (periplasm)	(2) h[c] + h2[c] + mqn8[c] --> (2) h[p] + mql8[c]	Oxidative Phosphorylation	1.18.99.1	( ( b0972  and  b0973  and  b0974 )  or  ( b2994  and  b2997 ) )	JLR		-26.4116	17.1271	[c] : (2) h[c] + h2[c] + mqn8[c] --> (2) h[p] + mql8[c] 		
8993	HYD3pp	Yes	Hydrogenase (Demethylmenaquinone-8: 2 protons) (periplasm)	2dmmq8[c] + (2) h[c] + h2[c] --> 2dmmql8[c] + (2) h[p]	Oxidative Phosphorylation	1.18.99.1	( ( b0972  and  b0973  and  b0974 )  or  ( b2994  and  b2997 ) )	JLR		-21.3451	14.9396	[c] : 2dmmq8[c] + (2) h[c] + h2[c] --> 2dmmql8[c] + (2) h[p] 		
1732	HYPOE	No	hypothetical enyme	[c] : h2o + pyam5p --> pi + pydam	Cofactor and Prosthetic Group Biosynthesis			NCD		-2.35942	1.9257	[c] : h2o[c] + pyam5p[c] --> h[c] + pi[c] + pydam[c] 		
9154	HYXNtex	Yes	Hypoxanthine transport via diffusion (extracellular to periplasm)	hxan[e] <==> hxan[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : hxan[e] <==> hxan[p] 		
8994	HYXNtpp	Yes	Hypoxanthine transport (periplasm)	hxan[p] <==> hxan[c]	"Transport, Inner Membrane"			tv	JLR- not sure about the reaction 	0	0	[c] : hxan[p] <==> hxan[c] 		
288	ICDHyr	No	isocitrate dehydrogenase (NADP)	[c] : icit + nadp <==> akg + co2 + nadph	Citric Acid Cycle	1.1.1.42	b1136	Two reactions (ICDH1 and ICDH2) for isocitrate dehydrogenase		-0.231652	5.1204	[c] : icit[c] + nadp[c] <==> akg[c] + co2[c] + nadph[c] 		
38	ICHORS	Yes	isochorismate synthase	[c] : chor <==> ichor	Cofactor and Prosthetic Group Biosynthesis	5.4.99.6	b2265		"from ecocyc:
Unlike the entC enzyme, the menF enzyme catalyzes an irreversible reaction. [  Daruwala97  , Daruwala96  , Muller96  ]
AMF"	0	0.5	[c] : chor[c] <==> ichor[c] 		
1351	ICHORSi	No	Isochorismate Synthase	[c] : chor --> ichor	Cofactor and Prosthetic Group Biosynthesis		b0593	JLR- added irreversible form of ICHORS	"from ecocyc:
Unlike the entC enzyme, the menF enzyme catalyzes an irreversible reaction. [  Daruwala97  , Daruwala96  , Muller96  ]
AMF"	0	0.5	[c] : chor[c] --> ichor[c] 		
44	ICHORT	No	isochorismatase	[c] : h2o + ichor --> 23ddhb + pyr	Cofactor and Prosthetic Group Biosynthesis	3.3.2.1	b0595		"JLR- JSE has it as reversible, EcoCyc indicates irreversible

EntB,D,F,E may work as a large complex - MKA
http://biocyc.org/ECOLI/new-image?type=PATHWAY&object=ENTBACSYN-PWY"	-11.5085	3.80635	[c] : h2o[c] + ichor[c] --> 23ddhb[c] + pyr[c] 		
546	ICL	No	Isocitrate lyase	[c] : icit --> glx + succ	Anaplerotic reactions	4.1.3.1	b4015	"IF
"		2.44073	2.95322	[c] : icit[c] --> glx[c] + succ[c] 		
2125	IDOND	No	L-idonate 5-dehydrogenase	[c] : 5dglcn + h + nadh <==> idon-L + nad	Alternate Carbon Metabolism		b4267	JLR		-4.73639	4.5435	[c] : 5dglcn[c] + h[c] + nadh[c] <==> idon-L[c] + nad[c] 		
2126	IDOND2	No	L-indonate 5-dehydrogenase (NADP)	[c] : 5dglcn + h + nadph --> idon-L + nadp	Alternate Carbon Metabolism		b4267	JLR		-4.73639	4.5435	[c] : 5dglcn[c] + h[c] + nadph[c] --> idon-L[c] + nadp[c] 		
8863	IDONt2rpp	Yes	"L-idonate transport via proton symport, reversible (periplasm)"	h[p] + idon-L[p] <==> h[c] + idon-L[c]	"Transport, Inner Membrane"		b4265	JLR		0	0	[c] : h[p] + idon-L[p] <==> h[c] + idon-L[c] 		
9155	IDONtex	Yes	L-idonate transport via diffusion (extracellular to periplasm)	idon-L[e] <==> idon-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : idon-L[e] <==> idon-L[p] 		
1020	IG3PS	No	Imidazole-glycerol-3-phosphate synthase	[c] : gln-L + prlp --> aicar + eig3p + glu-L + h	Histidine Metabolism		( b2023  and  b2025 )	Essential in L-histidine synthesis: No definite EC number assigned: EC 2.4.2.-; HisF cyclase		-22.0155	7.42913	[c] : gln-L[c] + prlp[c] --> aicar[c] + eig3p[c] + glu-L[c] + h[c] 		
341	IGPDH	No	imidazoleglycerol-phosphate dehydratase	[c] : eig3p --> h2o + imacp	Histidine Metabolism	4.2.1.19	b2022			-9.58412	3.68395	[c] : eig3p[c] --> h2o[c] + imacp[c] 		
334	IGPS	No	indole-3-glycerol-phosphate synthase	[c] : 2cpr5p + h --> 3ig3p + co2 + h2o	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.1.1.48	b1262			-17.8662	9.04226	[c] : 2cpr5p[c] + h[c] --> 3ig3p[c] + co2[c] + h2o[c] 		
8864	ILEabcpp	Yes	L-isoleucine transport via ABC system (periplasm)	atp[c] + h2o[c] + ile-L[p] --> adp[c] + h[c] + ile-L[c] + pi[c]	"Transport, Inner Membrane"		( b3454  and  b3455  and  b3457  and  b3460  and  b3456 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + ile-L[p] --> adp[c] + h[c] + ile-L[c] + pi[c] 		
8865	ILEt2rpp	Yes	L-isoleucine reversible transport via proton symport (periplasm)	h[p] + ile-L[p] <==> h[c] + ile-L[c]	"Transport, Inner Membrane"		b0401	NCD	"JLR- h/na symporter not known, Lactobacillus has a proton symport rxn."	0	0	[c] : h[p] + ile-L[p] <==> h[c] + ile-L[c] 		
319	ILETA	No	isoleucine transaminase	[c] : akg + ile-L <==> 3mop + glu-L	"Valine, Leucine, and Isoleucine Metabolism"	2.6.1.42	b3770			0	0.5	[c] : akg[c] + ile-L[c] <==> 3mop[c] + glu-L[c] 					
9156	ILEtex	Yes	L-isoleucine transport via diffusion (extracellular to periplasm)	ile-L[e] <==> ile-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ile-L[e] <==> ile-L[p] 					
1025	ILETRS	Yes	Isoleucyl-tRNA synthetase	[c] : atp + ile-L + trnaile --> amp + iletrna + ppi	Update	6.1.1.5	b0026		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + ile-L[c] + trnaile[c] --> amp[c] + iletrna[c] + ppi[c] 					
399	IMPC	No	IMP cyclohydrolase	[c] : h2o + imp <==> fprica	Purine and Pyrimidine Biosynthesis	3.5.4.10	b4006			No energy	No energy	[c] : h2o[c] + imp[c] <==> fprica[c] 					
400	IMPD	No	IMP dehydrogenase	[c] : h2o + imp + nad --> h + nadh + xmp	Purine and Pyrimidine Biosynthesis	1.1.1.205	b2508			2.95959	6.17887	[c] : h2o[c] + imp[c] + nad[c] --> h[c] + nadh[c] + xmp[c] 					
12310	IMPtex	Yes	IMP transport via diffusion (extracellular to periplasm)	imp[e] <==> imp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : imp[e] <==> imp[p] 					
8866	INDOLEt2pp	Yes	"Indole transport via proton symport, irreversible (periplasm)"	h[c] + indole[c] --> h[p] + indole[p]	Update		( b3265  and  b3266 )	JLR		0	0	[c] : h[c] + indole[c] --> h[p] + indole[p] 					
8867	INDOLEt2rpp	Yes	"Indole transport via proton symport, reversible (periplasm)"	h[p] + indole[p] <==> h[c] + indole[c]	"Transport, Inner Membrane"		b3161	JLR		0	0	[c] : h[p] + indole[p] <==> h[c] + indole[c] 					
9157	INDOLEtex	Yes	Indole transport via diffusion (extracellular to periplasm)	indole[e] <==> indole[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : indole[e] <==> indole[p] 					
12326	INOSTt4pp	Yes	Na+/myo-inositol symporter (periplasm)	inost[p] + na1[p] --> inost[c] + na1[c]	Update		b3679	AMF - assumed stoichiometry	"assigned from http://www.membranetransport.org/

perdicted transporter, stoichiometry is unknown

"	0	0	[c] : inost[p] + na1[p] --> inost[c] + na1[c] 					
6177	INSH	Yes	Inosine hydrolase	[c] : h2o + ins --> hxan + rib-D	Update	3.2.2.8	b0030	JLR		-2.26379	3.60328	[c] : h2o[c] + ins[c] --> hxan[c] + rib-D[c] 					
1082	INSK	No	insosine kinase	[c] : atp + ins --> adp + h + imp	Nucleotide Salvage Pathway	2.7.1.73	b0477	JLR		-4.65732	2.09859	[c] : atp[c] + ins[c] --> adp[c] + imp[c] 					
8868	INSt2pp	Yes	inosine transport in via proton symport (periplasm)	h[p] + ins[p] --> h[c] + ins[c]	"Transport, Inner Membrane"		b2964			0	0	[c] : h[p] + ins[p] --> h[c] + ins[c] 					
8869	INSt2rpp	Yes	"inosine transport in via proton symport, reversible (periplasm)"	h[p] + ins[p] <==> h[c] + ins[c]	"Transport, Inner Membrane"		b2406	JLR		0	0	[c] : h[p] + ins[p] <==> h[c] + ins[c] 					
9159	INStex	Yes	inosine transport via diffusion (extracellular to periplasm)	ins[e] <==> ins[p]	"Transport, Outer Membrane"		b0411		"assumed passive diffusion through the outer peptidoglycan layer

Tsx is responsible for the permeation of ribo- and deoxy-nucleosides, across the outer membrane of E. coli"	0	0	[c] : ins[e] <==> ins[p] 					
9158	INSTtex	Yes	inositol transport via diffusion (extracellular to periplasm)	inost[e] <==> inost[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : inost[e] <==> inost[p] 					
107	IPDDI	Yes	isopentenyl-diphosphate D-isomerase	[c] : ipdp <==> dmpp	Cofactor and Prosthetic Group Biosynthesis	5.3.3.2	b2889		"in neidhardt pg. 640
assumed reversibility
AMF"	1.59359	2.51164	[c] : ipdp[c] <==> dmpp[c] 		
3442	IPDPS	No	1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (ipdp)	[c] : h + h2mb4p + nadh --> h2o + ipdp + nad	Cofactor and Prosthetic Group Biosynthesis		b0029	JLR- unsure about cofactor stoichiometry	"JLR- these reactions are not biochemically verified, the cofactors required are unknown"	-17.4294	4.73543	[c] : h[c] + h2mb4p[c] + nadh[c] --> h2o[c] + ipdp[c] + nad[c] 		
318	IPMD	No	3-isopropylmalate dehydrogenase	[c] : 3c2hmp + nad --> 3c4mop + h + nadh	"Valine, Leucine, and Isoleucine Metabolism"	1.1.1.85	b0073		JLR- IPMD and OMCDC are in JSE as one reaction.  Included the two separate reactions in this model.	4.73639	4.5435	[c] : 3c2hmp[c] + nad[c] --> 3c4mop[c] + h[c] + nadh[c] 		
322	IPPMIa	No	3-isopropylmalate dehydratase	[c] : 3c2hmp <==> 2ippm + h2o	"Valine, Leucine, and Isoleucine Metabolism"	4.2.1.33	( b0071  and  b0072 )		JLR- reactions IPPMIa and IPPMIb were combined in JSE model.  Included the two separate reactions.	0.190448	3.32787	[c] : 3c2hmp[c] <==> 2ippm[c] + h2o[c] 		
323	IPPMIb	No	2-isopropylmalate hydratase	[c] : 2ippm + h2o <==> 3c3hmp	"Valine, Leucine, and Isoleucine Metabolism"	4.2.1.33	( b0071  and  b0072 )	"Part of IPPMI (3-isopropylmalate dehydrogenase) enzyme
added EC -NCD
"	JLR- reactions IPPMIa and IPPMIb were combined in JSE model.  Included the two separate reactions.	-0.190448	3.32787	[c] : 2ippm[c] + h2o[c] <==> 3c3hmp[c] 		
2858	IPPS	No	2-isopropylmalate synthase	[c] : 3mob + accoa + h2o --> 3c3hmp + coa + h	"Valine, Leucine, and Isoleucine Metabolism"	4.1.3.12	b0074			-6.34865	5.63823	[c] : 3mob[c] + accoa[c] + h2o[c] --> 3c3hmp[c] + coa[c] + h[c] 		
12344	ISETACabcpp	Yes	isethionate transport via ABC system (periplasm)	atp[c] + h2o[c] + isetac[p] --> adp[c] + h[c] + isetac[c] + pi[c]	Update		( ( b0365  and  b0366  and  b0367 )  or  ( b0936  and  b0933  and  b0934 ) )	AMF	"Botht the ssu and the tau transporters will transport this, amound many others

see PMID:10781534

for a good diagram
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + isetac[p] --> adp[c] + h[c] + isetac[c] + pi[c] 		
12345	ISETACtex	Yes	isethionate transport via diffusion (extracellular to periplasm)	isetac[e] <==> isetac[p]	"Transport, Outer Membrane"			AMF	"assumed diffusion
"	0	0	[c] : isetac[e] <==> isetac[p] 		
8870	Kabcpp	Yes	Potassium ABC transporter (periplasm)	atp[c] + h2o[c] + k[p] --> adp[c] + h[c] + k[c] + pi[c]	"Transport, Inner Membrane"		( b0698  and  b0697  and  b0696 )	JLR		-7.01673	1.48181	[c] : atp[c] + h2o[c] + k[p] --> adp[c] + h[c] + k[c] + pi[c] 		
79	KARA1	Yes	"ketol-acid reductoisomerase (2,3-dihydroxy-3-methylbutanoate)"	[c] : 23dhmb + nadp <==> alac-S + h + nadph	"Valine, Leucine, and Isoleucine Metabolism"	1.1.1.86	b3774	reversible form of AHAI	"reversible reactions
NH pg 447
JLR
AMF"	4.73639	4.5435	[c] : 23dhmb[c] + nadp[c] <==> alac-S[c] + h[c] + nadph[c] 		
80	KARA2	Yes	ketol-acid reductoisomerase (2-Acetolactate)	[c] : 2ahbut + h + nadph <==> 23dhmp + nadp	"Valine, Leucine, and Isoleucine Metabolism"	1.1.1.86	b3774		"reversible reactions
NH pg 447
JLR
AMF
"	-4.73639	4.5435	[c] : 2ahbut[c] + h[c] + nadph[c] <==> 23dhmp[c] + nadp[c] 		
3373	KAS14	No	beta-ketoacyl-ACP synthase	[c] : acACP + h + malACP --> ACP + actACP + co2	Membrane Lipid Metabolism	2.3.1.41	( b2323  or  b1095 )	"tv
AMF"		1.3349	4.20263	[c] : acACP[c] + h[c] + malACP[c] --> ACP[c] + actACP[c] + co2[c] 		
2936	KAS15	No	beta-ketoacyl-ACP synthase (2)	[c] : accoa + h + malACP --> actACP + co2 + coa	Membrane Lipid Metabolism		b1091	"tv
AMF"		1.3349	4.20263	[c] : accoa[c] + h[c] + malACP[c] --> actACP[c] + co2[c] + coa[c] 		
5407	KAT1	Yes	3-ketoacyl-CoA thiolase	[c] : aacoa + coa --> (2) accoa	Membrane Lipid Metabolism	2.3.1.16	( b3845  or  b2342 )	JC		-5.82626	4.21018	[c] : aacoa[c] + coa[c] --> (2) accoa[c] 		
5409	KAT2	Yes	3-ketoacyl-CoA thiolase	[c] : 3ohcoa + coa --> accoa + btcoa	Membrane Lipid Metabolism	2.3.1.16	( b3845  or  b2342 )	JC		-5.82626	4.21018	[c] : 3ohcoa[c] + coa[c] --> accoa[c] + btcoa[c] 		
5410	KAT3	Yes	3-ketoacyl-CoA thiolase	[c] : 3oocoa + coa --> accoa + hxcoa	Membrane Lipid Metabolism	2.3.1.16	( b3845  or  b2342 )	JC		-5.82626	4.21018	[c] : 3oocoa[c] + coa[c] --> accoa[c] + hxcoa[c] 		
5411	KAT4	Yes	3-ketoacyl-CoA thiolase	[c] : 3odcoa + coa --> accoa + occoa	Membrane Lipid Metabolism	2.3.1.16	( b3845  or  b2342 )	JC		-5.82626	4.21018	[c] : 3odcoa[c] + coa[c] --> accoa[c] + occoa[c] 					
5412	KAT5	Yes	3-ketoacyl-CoA thiolase	[c] : 3oddcoa + coa --> accoa + dcacoa	Membrane Lipid Metabolism	2.3.1.16	( b3845  or  b2342 )	JC		-5.82626	4.21018	[c] : 3oddcoa[c] + coa[c] --> accoa[c] + dcacoa[c] 					
5413	KAT6	Yes	3-ketoacyl-CoA thiolase	[c] : 3otdcoa + coa --> accoa + ddcacoa	Membrane Lipid Metabolism	2.3.1.16	( b3845  or  b2342 )	JC		-5.82626	4.21018	[c] : 3otdcoa[c] + coa[c] --> accoa[c] + ddcacoa[c] 					
5414	KAT7	Yes	3-ketoacyl-CoA thiolase	[c] : 3ohdcoa + coa --> accoa + tdcoa	Membrane Lipid Metabolism	2.3.1.16	( b3845  or  b2342 )	JC		-5.82626	4.21018	[c] : 3ohdcoa[c] + coa[c] --> accoa[c] + tdcoa[c] 					
8139	KAT8	Yes	3-ketoacyl-CoA thiolase	[c] : 3oodcoa + coa --> accoa + pmtcoa	Membrane Lipid Metabolism	2.3.1.16	( b3845  or  b2342 )	JLR		-5.82626	4.21018	[c] : 3oodcoa[c] + coa[c] --> accoa[c] + pmtcoa[c] 					
1861	KDOCT2	No	3-deoxy-manno-octulosonate cytidylyltransferase	[c] : ctp + kdo --> ckdo + ppi	Cell Envelope Biosynthesis	2.7.7.38	b0918	JLR- makes the ring form of kdo		-6.58198	3.68078	[c] : ctp[c] + kdo[c] --> ckdo[c] + ppi[c] 					
1163	KDOPP	No	3-deoxy-manno-octulosonate-8-phosphatase	[c] : h2o + kdo8p --> kdo + pi	Cell Envelope Biosynthesis	3.1.3.45	b3198	tv		-3.85076	7.64993	[c] : h2o[c] + kdo8p[c] --> h[c] + kdo[c] + pi[c] 					
1162	KDOPS	No	3-deoxy -D-manno-octulosonic -acid 8-phosphate synthase	[c] : ara5p + h2o + pep --> kdo8p + pi	Cell Envelope Biosynthesis	4.1.2.16	b1215	"TDV (5-31-2004)
new EC from Kegg: 2.5.1.55"		-13.9584	7.41722	[c] : ara5p[c] + h2o[c] + pep[c] --> h[c] + kdo8p[c] + pi[c] 					
2503	KG6PDC	No	3-keto-L-gulonate 6-phosphate decarboxylase	[c] : 3dhgulnp + h --> co2 + xu5p-L	Alternate Carbon Metabolism		( b4196  or  b3581 )	JLR		-2.9761	2.37286	[c] : 3dhgulnp[c] + h[c] --> co2[c] + xu5p-L[c] 					
8953	Kt2pp	Yes	potassium transport in via proton symport (periplasm)	h[p] + k[p] --> h[c] + k[c]	Update		( b3747  or  b1250 )	TC: 9.A.5.1.1 	"Added from PMID: 11682179

A single component system with a low rate of K+ uptake, Kup, becomes important at low pH when the activity of TrkA is insuficient, and when Kdp, known to be the high affinity K+ uptake system, is not induced.
AMF
"	0	0	[c] : h[p] + k[p] --> h[c] + k[c] 					
8871	Kt2rpp	Yes	potassium reversible transport  via proton symport (periplasm)	h[p] + k[p] <==> h[c] + k[c]	"Transport, Inner Membrane"		( b3849  or  b1363 )	JLR	"From the transport DB:

http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=2.A.38

The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD+-binding protein, and TrkE, an ATP-binding protein. The peripheral membrane proteins are thought to function in regulation rather than energy coupling. TrkE maps to the sapABCDF operon which encodes an ABC transporter (TC #3.A.1.5.5), and the SapD ATP binding cassette (ABC) protein of E. coli can stimulate K+ uptake via either TrkH or TrkG (Harms et al., 2001). Therefore, SapD is probably TrkE. ATP binding to SapD, rather than ATP hydrolysis, appears to activate. Thus, the pmf drives transport while ATP binding activates transport. At least one other ATP-activating protein is probably present in the E. coli cell (Harms et al., 2001).

Thus, TrkA and Trke (SapD) are not accociated to these systems since in the case of SapD, it is not critical.  TrkA may be needed however, further evaluation is needed."	0	0	[c] : h[p] + k[p] <==> h[c] + k[c] 					
13868	Kt3pp	Yes	potassium transport out via proton antiport (periplasm)	h[p] + k[c] --> h[c] + k[p]	"Tranpsort, Inner Membrane"		( b0047  or  b3350 )		"PMID: 10092637
potassium efflux - regulated

entered in network since it didnt allow protons to be freely pumped out to generate ATP"	0	0	[c] : h[p] + k[c] --> h[c] + k[p] 					
9160	Ktex	Yes	potassium transport via diffusion (extracellular to periplasm)	k[e] <==> k[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : k[e] <==> k[p] 					
13509	LA4NTpp	Yes	"4-amino-4-deoxy-L-arabinotransferase (LPS lipid A modification, periplasmic face of membrane))"	[p] : colipa + uLa4n --> acolipa + udcpp	Lipopolysaccharide Biosynthesis / Recycling		b2257	AMF	"latest article with an update for all these reactions is given in figure and text of PMID: 15695810

there are probably a number of different Lipid A varieties that can be arabinated by ArnT

AMF"	No energy	No energy	[p] : colipa[p] + h[p] + uLa4n[p] --> acolipa[p] + udcpp[p] 					
202	LACZ	No	b-galactosidase	[c] : h2o + lcts --> gal + glc-D	Alternate Carbon Metabolism	3.2.1.23	b0344	Some enzymes in this group hydrolyse a-L-arabinosides; some animal enzymes also hydrolyse b-D-fucosides and b-D-glucosides; cf. EC 3.2.1.108 lactase		-3.32755	3.07096	[c] : h2o[c] + lcts[c] --> gal[c] + glc-D[c] 					
12249	LACZpp	Yes	b-galactosidase	[p] : h2o + lcts --> gal + glc-D	Update	3.2.1.108	b2132	"Some enzymes in this group hydrolyse a-L-arabinosides; some animal enzymes also hydrolyse b-D-fucosides and b-D-glucosides; cf. EC 3.2.1.108 lactase
"	"periplasmic
"	-3.32755	3.07096	[p] : h2o[p] + lcts[p] --> gal[p] + glc-D[p] 					
12682	LADGMDH	Yes	L-alanyl-gamma-D-glutamyl-meso-diaminopimelate hydrolase	[c] : LalaDgluMdap + h2o --> 26dap-M + LalaDglu	Murein Recycling		b1326	AMF	"PMID: 12511517
AMF

nice figure in  PMID: 15901686"	-3.36489	3.34628	[c] : h2o[c] + LalaDgluMdap[c] --> 26dap-M[c] + LalaDglu[c] 		
20016	LALDO2x	Yes	D-Lactaldehyde:NAD+ 1-oxidoreductase	[c] : h + mthgxl + nadh --> lald-D + nad	Update	1.1.1.21	b3945	AMF	"PMID: 10049880
overexpressed gldA shown to act on mthgxyl with NADH, proposed to generate R-lactaldehyde (D- form)
AMF
"	-4.73639	4.5435	[c] : h[c] + mthgxl[c] + nadh[c] --> lald-D[c] + nad[c] 		
12685	LALGP	Yes	L-alanyl-gamma-L-glutamate peptidase	[c] : LalaLglu + h2o --> ala-L + glu-L	Murein Recycling		b0237	"AMF
PMID: 11747447"	"PMID: 11747447
this enolase can act on a number of different dipeptide substrates, see citation for ref
AMF

nice figure in  PMID: 15901686"	-3.36489	3.34628	[c] : h2o[c] + LalaLglu[c] --> ala-L[c] + glu-L[c] 		
2949	LCADi	No	lactaldehyde dehydrogenase	[c] : h2o + lald-L + nad --> (2) h + lac-L + nadh	Alternate Carbon Metabolism	1.2.1.21	b1415	JLR- added irreversible form of LCAD	"iJR904 had reversible version associated with (aldA, aldB, aldH, adhC, and adhE).  No evidence for these except of aldA."	-9.85991	4.39284	[c] : h2o[c] + lald-L[c] + nad[c] --> (2) h[c] + lac-L[c] + nadh[c] 		
20017	LCARR	Yes	"lacaldehyde reductase (R-propane-1,2-diol forming)"	[c] : h + lald-D + nadh <==> 12ppd-R + nad	Update	1.1.1.77		"JLR
AMF"	"PMID: 10049880
gene not identified, but a native E. coli unknown gene is proposed to carry out this reaction.  The gene is not fucO, it is specific to lald-L.
AMF
"	-5.16584	4.34649	[c] : h[c] + lald-D[c] + nadh[c] <==> 12ppd-R[c] + nad[c] 		
1203	LCARS	Yes	"lacaldehyde reductase (S-propane-1,2-diol forming)"	[c] : h + lald-L + nadh <==> 12ppd-S + nad	Alternate Carbon Metabolism	1.1.1.77	b2799	JLR	"PMID: 7016842
see also related enzymes in PMID: 10049880
FucO is specific for lald-L (S- form)
AMF"	-5.16584	4.34649	[c] : h[c] + lald-L[c] + nadh[c] <==> 12ppd-S[c] + nad[c] 		
13765	LCTSt3ipp	Yes	Lactose transport via proton aniport (periplasm)	h[p] + lcts[c] --> h[c] + lcts[p]	"Transport, Inner Membrane"		( b0070  or  b2170  or  b1528 )	AMF	"PMID: 10438792
charcetizes that SotB (ydeA) can export arabinose

PMID: 10671456 
states that SotB (ydea) xan export arabinose, but SotA exports arabinose

SetB, SetA functions are give in PMID: 10209755

AMF"	0	0	[c] : h[p] + lcts[c] --> h[c] + lcts[p] 		
9163	LCTStex	Yes	Lactose transport via diffusion (extracellular to periplasm)	lcts[e] <==> lcts[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : lcts[e] <==> lcts[p] 		
8872	LCTStpp	Yes	Lactose transport via proton symport (periplasm)	h[p] + lcts[p] <==> h[c] + lcts[c]	"Transport, Inner Membrane"		b0343	JLR		0	0	[c] : h[p] + lcts[p] <==> h[c] + lcts[c] 		
293	LDH_D	No	D-lactate dehydrogenase	[c] : lac-D + nad <==> h + nadh + pyr	Pyruvate Metabolism	1.1.1.28	( b2133  or  b1380 )	See also LDL_L		4.73639	4.5435	[c] : lac-D[c] + nad[c] <==> h[c] + nadh[c] + pyr[c] 		
2944	LDH_D2	No	D-lactate dehydrogenase	[c] : lac-D + q8 --> pyr + q8h2	Oxidative Phosphorylation	1.1.2.4	b2133	JLR		-18.6813	21.401	[c] : lac-D[c] + q8[c] --> pyr[c] + q8h2[c] 		
8873	LEUabcpp	Yes	L-leucine transport via ABC system (periplasm)	atp[c] + h2o[c] + leu-L[p] --> adp[c] + h[c] + leu-L[c] + pi[c]	"Transport, Inner Membrane"		( ( b3454  and  b3455  and  b3457  and  b3460  and  b3456 )  or  ( b3454  and  b3455  and  b3457  and  b3458  and  b3456 ) )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + leu-L[p] --> adp[c] + h[c] + leu-L[c] + pi[c] 		
8874	LEUt2rpp	Yes	L-leucine reversible transport via proton symport (periplasm)	h[p] + leu-L[p] <==> h[c] + leu-L[c]	"Transport, Inner Membrane"		b0401	NCD	"JLR- h/na symporter not known, Lactobacillus has a proton symport rxn."	0	0	[c] : h[p] + leu-L[p] <==> h[c] + leu-L[c] 		
1049	LEUTAi	No	leucine transaminase (irreversible)	[c] : 4mop + glu-L --> akg + leu-L	"Valine, Leucine, and Isoleucine Metabolism"	2.6.1.42	( b3770  or  b4054 )	JLR- added irreversible form of LEUTA .  Used 2.6.1.42 as the EC instead of 2.6.1.6 (they have the same reaction).	"biosynthetic direction favored
NH pg 447
JLR
AMF"	0	0.5	[c] : 4mop[c] + glu-L[c] --> akg[c] + leu-L[c] 		
9164	LEUtex	Yes	L-leucine transport via diffusion (extracellular to periplasm)	leu-L[e] <==> leu-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : leu-L[e] <==> leu-L[p] 		
2915	LEUTRS	Yes	Leucyl-tRNA synthetase	[c] : atp + leu-L + trnaleu --> amp + leutrna + ppi	Update	6.1.1.4	b0642		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + leu-L[c] + trnaleu[c] --> amp[c] + leutrna[c] + ppi[c] 		
457	LGTHL	No	lactoylglutathione lyase	[c] : gthrd + mthgxl --> lgt-S	Methylglyoxal Metabolism	4.4.1.5	b1651	IF		-8.74367	4.5065	[c] : gthrd[c] + mthgxl[c] --> lgt-S[c] 					
13510	LIPAabcpp	Yes	lipid A transport via ABC system (periplasm)	atp[c] + h2o[c] + lipa[c] --> adp[c] + h[c] + lipa[p] + pi[c]	Lipopolysaccharide Biosynthesis / Recycling		b0914		"PMID: 12045108 gives a reaview on LPS biosynthesis and states that it can transport PE

also, atpase acitvity was activated by kdo2-lipidA and other hexa-acylated compounds, also kd02-lipid4A could be transported by MsbA.
states that it can transport pretty much all lipids
PMID: 15052329

AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + lipa[c] --> adp[c] + h[c] + lipa[p] + pi[c] 					
13511	LIPACabcpp	Yes	lipid (cold) A transport via ABC system (periplasm)	atp[c] + h2o[c] + lipa_cold[c] --> adp[c] + h[c] + lipa_cold[p] + pi[c]	Lipopolysaccharide Biosynthesis / Recycling		b0914		"PMID: 12045108 gives a reaview on LPS biosynthesis and states that it can transport PE

also, atpase acitvity was activated by kdo2-lipidA and other hexa-acylated compounds, also kd02-lipid4A could be transported by MsbA.
states that it can transport pretty much all lipids
PMID: 15052329

AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + lipa_cold[c] --> adp[c] + h[c] + lipa_cold[p] + pi[c] 					
13527	LIPAHT2ex	Yes	core oligosaccharide lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)	[e] : colipa + h + hdca --> h2o + hacolipa	Lipopolysaccharide Biosynthesis / Recycling		b0622	AMF	"CrcA has its active site on the outside of the outer membrane

PMID: 11013210 shows that CrcA can act on a number of different Lipid A molecules and precursors, the two reactions chosen were arbritrary, lipa was proven to be a substrate, colipa was speculated as one"	No energy	No energy	[e] : colipa[e] + h[e] + hdca[e] --> h2o[e] + hacolipa[e] 					
13528	LIPAHTex	Yes	Lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)	[e] : h + hdca + lipa --> h2o + halipa	Lipopolysaccharide Biosynthesis / Recycling		b0622	AMF	"CrcA has its active site on the outside of the outer membrane

PMID: 11013210 shows that CrcA can act on a number of different Lipid A molecules and precursors, the two reactions chosen were arbritrary, lipa was proven to be a substrate, colipa was speculated as one"	3.8689	2.44385	[e] : h[e] + hdca[e] + lipa[e] --> h2o[e] + halipa[e] 					
13526	LIPAtex	Yes	lipid A transport via vector (periplasm to extracellular)	lipa[p] --> lipa[e]	Lipopolysaccharide Biosynthesis / Recycling			"AMF
not sure how it travels across the periplam or flipped to outer serface of the membrane"	"this reaction is needed to have the LPS lipid A derivative presented to the outer membrane surface - both moved across the periplasm and flipped across the outer membrane

not sure on the method of transport

this paper talks about the possibility of the transport PMID: 15576375

AMF"	0	0	[c] : lipa[p] --> lipa[e] 					
4628	L-LACD2	No	L-Lactate dehydrogenase (ubiquinone)	[c] : lac-L + q8 --> pyr + q8h2	Oxidative Phosphorylation	1.1.2.3	b3605	JLR	"Actual electron acceptor is FMN, since enzyme is induced during aerobic growth and during anaerobic growth with nitrate and TMAO assumed that it eventually goes to quinone and menaquinone.  Not sure about reversibility."	-18.6813	21.401	[c] : lac-L[c] + q8[c] --> pyr[c] + q8h2[c] 					
4627	L-LACD3	No	L-Lactate dehydrogenase (menaquinone)	[c] : lac-L + mqn8 --> mql8 + pyr	Oxidative Phosphorylation	1.1.2.3	b3605	JLR	"Actual electron acceptor is FMN, since enzyme is induced during aerobic growth and during anaerobic growth with nitrate and TMAO assumed that it eventually goes to quinone and menaquinone.   Not sure about reversibility."	-17.2294	17.2464	[c] : lac-L[c] + mqn8[c] --> mql8[c] + pyr[c] 					
8875	L-LACt2rpp	Yes	L-lactate reversible transport via proton symport (periplasm)	h[p] + lac-L[p] <==> h[c] + lac-L[c]	"Transport, Inner Membrane"		( b3603  or  b2975 )	NCD		0	0	[c] : h[p] + lac-L[p] <==> h[c] + lac-L[c] 					
9162	L-LACtex	Yes	L-lactate transport via diffusion (extracellular to periplasm)	lac-L[e] <==> lac-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : lac-L[e] <==> lac-L[p] 					
1256	LPADSS	No	Lipid A disaccaride synthase	[c] : lipidX + u23ga --> h + lipidAds + udp	Cell Envelope Biosynthesis	2.4.1.182	b0182	tv		-2.66783	3.32261	[c] : lipidX[c] + u23ga[c] --> lipidAds[c] + udp[c] 					
20095	LPLIPAL1A120pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphotidate, n-C12:0) (periplasm)"	[p] : 1ddecg3p + h2o --> ddca + glyc3p + h	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1ddecg3p[p] + h2o[p] --> ddca[p] + glyc3p[p] + h[p] 					
20098	LPLIPAL1A140pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphotidate, n-C14:0) (periplasm)"	[p] : 1tdecg3p + h2o --> glyc3p + h + ttdca	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1tdecg3p[p] + h2o[p] --> glyc3p[p] + h[p] + ttdca[p] 					
20099	LPLIPAL1A141pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphotidate, n-C14:1) (periplasm)"	[p] : 1tdec7eg3p + h2o --> glyc3p + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-3.47054	3.44311	[p] : 1tdec7eg3p[p] + h2o[p] --> glyc3p[p] + h[p] + ttdcea[p] 					
20100	LPLIPAL1A160pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphotidate, n-C16:0) (periplasm)"	[p] : 1hdecg3p + h2o --> glyc3p + h + hdca	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1hdecg3p[p] + h2o[p] --> glyc3p[p] + h[p] + hdca[p] 					
20097	LPLIPAL1A161pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphotidate, n-C16:1) (periplasm)"	[p] : 1hdec9eg3p + h2o --> glyc3p + h + hdcea	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1hdec9eg3p[p] + h2o[p] --> glyc3p[p] + h[p] + hdcea[p] 					
20101	LPLIPAL1A180pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphotidate, n-C18:0) (periplasm)"	[p] : 1odecg3p + h2o --> glyc3p + h + ocdca	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1odecg3p[p] + h2o[p] --> glyc3p[p] + h[p] + ocdca[p] 		
20102	LPLIPAL1A181pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphotidate, n-C18:1) (periplasm)"	[p] : 1odec11eg3p + h2o --> glyc3p + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1odec11eg3p[p] + h2o[p] --> glyc3p[p] + h[p] + ocdcea[p] 		
20103	LPLIPAL1E120pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C12:0) (periplasm)"	[p] : 1agpe120 + h2o --> ddca + g3pe + h	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpe120[p] + h2o[p] --> ddca[p] + g3pe[p] + h[p] 		
20104	LPLIPAL1E140pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C14:0) (periplasm)"	[p] : 1agpe140 + h2o --> g3pe + h + ttdca	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpe140[p] + h2o[p] --> g3pe[p] + h[p] + ttdca[p] 		
20105	LPLIPAL1E141pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C14:1) (periplasm)"	[p] : 1agpe141 + h2o --> g3pe + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpe141[p] + h2o[p] --> g3pe[p] + h[p] + ttdcea[p] 		
20106	LPLIPAL1E160pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C16:0) (periplasm)"	[p] : 1agpe160 + h2o --> g3pe + h + hdca	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpe160[p] + h2o[p] --> g3pe[p] + h[p] + hdca[p] 		
20107	LPLIPAL1E161pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C16:1) (periplasm)"	[p] : 1agpe161 + h2o --> g3pe + h + hdcea	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpe161[p] + h2o[p] --> g3pe[p] + h[p] + hdcea[p] 		
20108	LPLIPAL1E180pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C18:0) (periplasm)"	[p] : 1agpe180 + h2o --> g3pe + h + ocdca	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpe180[p] + h2o[p] --> g3pe[p] + h[p] + ocdca[p] 		
20109	LPLIPAL1E181pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C18:1) (periplasm)"	[p] : 1agpe181 + h2o --> g3pe + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpe181[p] + h2o[p] --> g3pe[p] + h[p] + ocdcea[p] 		
20117	LPLIPAL1G120pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C12:0) (periplasm)"	[p] : 1agpg120 + h2o --> ddca + g3pg + h	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpg120[p] + h2o[p] --> ddca[p] + g3pg[p] + h[p] 		
20111	LPLIPAL1G140pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C14:0) (periplasm)"	[p] : 1agpg140 + h2o --> g3pg + h + ttdca	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpg140[p] + h2o[p] --> g3pg[p] + h[p] + ttdca[p] 		
20112	LPLIPAL1G141pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C14:1) (periplasm)"	[p] : 1agpg141 + h2o --> g3pg + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpg141[p] + h2o[p] --> g3pg[p] + h[p] + ttdcea[p] 		
20113	LPLIPAL1G160pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C16:0) (periplasm)"	[p] : 1agpg160 + h2o --> g3pg + h + hdca	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpg160[p] + h2o[p] --> g3pg[p] + h[p] + hdca[p] 		
20114	LPLIPAL1G161pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C16:1) (periplasm)"	[p] : 1agpg161 + h2o --> g3pg + h + hdcea	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpg161[p] + h2o[p] --> g3pg[p] + h[p] + hdcea[p] 		
20115	LPLIPAL1G180pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C18:0) (periplasm)"	[p] : 1agpg180 + h2o --> g3pg + h + ocdca	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpg180[p] + h2o[p] --> g3pg[p] + h[p] + ocdca[p] 		
20116	LPLIPAL1G181pp	Yes	"Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C18:1) (periplasm)"	[p] : 1agpg181 + h2o --> g3pg + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.5	b0494	AMF	"PMID: 10423542
Enzyme also has shown both protease I and thioesterase I activities, not sure of specificity of protease substrates and not sure of acyl-CoA compounds in the periplasm.
See also, PMID: 1864840
AMF
"	-1.87695	2.35514	[p] : 1agpg181[p] + h2o[p] --> g3pg[p] + h[p] + ocdcea[p] 		
19911	LPLIPAL2A120	Yes	"Lysophospholipase L2 (2-acylglycerophosphotidate, n-C12:0)"	[c] : 2ddecg3p + h2o --> ddca + glyc3p + h	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed toact on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).  These reactions were not added.
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2ddecg3p[c] + h2o[c] --> ddca[c] + glyc3p[c] + h[c] 		
19912	LPLIPAL2A140	Yes	"Lysophospholipase L2 (2-acylglycerophosphotidate, n-C14:0)"	[c] : 2tdecg3p + h2o --> glyc3p + h + ttdca	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed toact on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).  These reactions were not added.
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2tdecg3p[c] + h2o[c] --> glyc3p[c] + h[c] + ttdca[c] 		
19915	LPLIPAL2A141	Yes	"Lysophospholipase L2 (2-acylglycerophosphotidate, n-C14:1)"	[c] : 2tdec7eg3p + h2o --> glyc3p + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed toact on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).  These reactions were not added.
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-3.47054	3.44311	[c] : 2tdec7eg3p[c] + h2o[c] --> glyc3p[c] + h[c] + ttdcea[c] 		
19913	LPLIPAL2A160	Yes	"Lysophospholipase L2 (2-acylglycerophosphotidate, n-C16:0)"	[c] : 2hdecg3p + h2o --> glyc3p + h + hdca	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed toact on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).  These reactions were not added.
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2hdecg3p[c] + h2o[c] --> glyc3p[c] + h[c] + hdca[c] 		
19916	LPLIPAL2A161	Yes	"Lysophospholipase L2 (2-acylglycerophosphotidate, n-C16:1)"	[c] : 2hdec9eg3p + h2o --> glyc3p + h + hdcea	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed toact on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).  These reactions were not added.
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2hdec9eg3p[c] + h2o[c] --> glyc3p[c] + h[c] + hdcea[c] 		
19914	LPLIPAL2A180	Yes	"Lysophospholipase L2 (2-acylglycerophosphotidate, n-C18:0)"	[c] : 2odecg3p + h2o --> glyc3p + h + ocdca	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed toact on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).  These reactions were not added.
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2odecg3p[c] + h2o[c] --> glyc3p[c] + h[c] + ocdca[c] 		
19917	LPLIPAL2A181	Yes	"Lysophospholipase L2 (2-acylglycerophosphotidate, n-C18:1)"	[c] : 2odec11eg3p + h2o --> glyc3p + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed toact on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).  These reactions were not added.
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2odec11eg3p[c] + h2o[c] --> glyc3p[c] + h[c] + ocdcea[c] 		
19965	LPLIPAL2ATE120	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C12:0)"	[c] : 2agpe120 + pg120 --> apg120 + g3pe	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpe120[c] + pg120[c] --> apg120[c] + g3pe[c] 		
19966	LPLIPAL2ATE140	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C14:0)"	[c] : 2agpe140 + pg140 --> apg140 + g3pe	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpe140[c] + pg140[c] --> apg140[c] + g3pe[c] 		
19969	LPLIPAL2ATE141	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C14:1)"	[c] : 2agpe141 + pg141 --> apg141 + g3pe	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpe141[c] + pg141[c] --> apg141[c] + g3pe[c] 		
19967	LPLIPAL2ATE160	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C16:0)"	[c] : 2agpe160 + pg160 --> apg160 + g3pe	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpe160[c] + pg160[c] --> apg160[c] + g3pe[c] 		
19970	LPLIPAL2ATE161	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C16:1)"	[c] : 2agpe161 + pg161 --> apg161 + g3pe	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpe161[c] + pg161[c] --> apg161[c] + g3pe[c] 		
19968	LPLIPAL2ATE180	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C18:0)"	[c] : 2agpe180 + pg180 --> apg180 + g3pe	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpe180[c] + pg180[c] --> apg180[c] + g3pe[c] 		
19971	LPLIPAL2ATE181	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C18:1)"	[c] : 2agpe181 + pg181 --> apg181 + g3pe	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpe181[c] + pg181[c] --> apg181[c] + g3pe[c] 		
19955	LPLIPAL2ATG120	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C12:0)"	[c] : 2agpg120 + pg120 --> apg120 + g3pg	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpg120[c] + pg120[c] --> apg120[c] + g3pg[c] 		
19958	LPLIPAL2ATG140	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C14:0)"	[c] : 2agpg140 + pg140 --> apg140 + g3pg	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpg140[c] + pg140[c] --> apg140[c] + g3pg[c] 		
19960	LPLIPAL2ATG141	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C14:1)"	[c] : 2agpg141 + pg141 --> apg141 + g3pg	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpg141[c] + pg141[c] --> apg141[c] + g3pg[c] 		
19961	LPLIPAL2ATG160	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C16:0)"	[c] : 2agpg160 + pg160 --> apg160 + g3pg	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpg160[c] + pg160[c] --> apg160[c] + g3pg[c] 		
19963	LPLIPAL2ATG161	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C16:1)"	[c] : 2agpg161 + pg161 --> apg161 + g3pg	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpg161[c] + pg161[c] --> apg161[c] + g3pg[c] 		
19962	LPLIPAL2ATG180	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C18:0)"	[c] : 2agpg180 + pg180 --> apg180 + g3pg	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpg180[c] + pg180[c] --> apg180[c] + g3pg[c] 		
19964	LPLIPAL2ATG181	Yes	"Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C18:1)"	[c] : 2agpg181 + pg181 --> apg181 + g3pg	Glycerophospholipid Metabolism		b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	0	0.5	[c] : 2agpg181[c] + pg181[c] --> apg181[c] + g3pg[c] 		
19868	LPLIPAL2E120	Yes	"Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C12:0)"	[c] : 2agpe120 + h2o --> ddca + g3pe + h	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpe120[c] + h2o[c] --> ddca[c] + g3pe[c] + h[c] 		
19899	LPLIPAL2E140	Yes	"Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C14:0)"	[c] : 2agpe140 + h2o --> g3pe + h + ttdca	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpe140[c] + h2o[c] --> g3pe[c] + h[c] + ttdca[c] 		
19902	LPLIPAL2E141	Yes	"Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C14:1)"	[c] : 2agpe141 + h2o --> g3pe + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-3.47054	3.44311	[c] : 2agpe141[c] + h2o[c] --> g3pe[c] + h[c] + ttdcea[c] 		
19900	LPLIPAL2E160	Yes	"Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C16:0)"	[c] : 2agpe160 + h2o --> g3pe + h + hdca	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpe160[c] + h2o[c] --> g3pe[c] + h[c] + hdca[c] 		
19903	LPLIPAL2E161	Yes	"Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C16:1)"	[c] : 2agpe161 + h2o --> g3pe + h + hdcea	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpe161[c] + h2o[c] --> g3pe[c] + h[c] + hdcea[c] 		
19901	LPLIPAL2E180	Yes	"Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C18:0)"	[c] : 2agpe180 + h2o --> g3pe + h + ocdca	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpe180[c] + h2o[c] --> g3pe[c] + h[c] + ocdca[c] 		
19904	LPLIPAL2E181	Yes	"Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C18:1)"	[c] : 2agpe181 + h2o --> g3pe + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpe181[c] + h2o[c] --> g3pe[c] + h[c] + ocdcea[c] 		
19879	LPLIPAL2G120	Yes	"Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C12:0)"	[c] : 2agpg120 + h2o --> ddca + g3pg + h	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpg120[c] + h2o[c] --> ddca[c] + g3pg[c] + h[c] 		
19905	LPLIPAL2G140	Yes	"Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C14:0)"	[c] : 2agpg140 + h2o --> g3pg + h + ttdca	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpg140[c] + h2o[c] --> g3pg[c] + h[c] + ttdca[c] 		
19908	LPLIPAL2G141	Yes	"Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C14:1)"	[c] : 2agpg141 + h2o --> g3pg + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-3.47054	3.44311	[c] : 2agpg141[c] + h2o[c] --> g3pg[c] + h[c] + ttdcea[c] 		
19906	LPLIPAL2G160	Yes	"Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C16:0)"	[c] : 2agpg160 + h2o --> g3pg + h + hdca	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpg160[c] + h2o[c] --> g3pg[c] + h[c] + hdca[c] 		
19909	LPLIPAL2G161	Yes	"Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C16:1)"	[c] : 2agpg161 + h2o --> g3pg + h + hdcea	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpg161[c] + h2o[c] --> g3pg[c] + h[c] + hdcea[c] 		
19907	LPLIPAL2G180	Yes	"Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:0)"	[c] : 2agpg180 + h2o --> g3pg + h + ocdca	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpg180[c] + h2o[c] --> g3pg[c] + h[c] + ocdca[c] 		
19910	LPLIPAL2G181	Yes	"Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:1)"	[c] : 2agpg181 + h2o --> g3pg + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.5	b3825	AMF	"PMID: 3908447
characterizes the enzyme to act on 2-acyl glycerophosphoethanolamine and -choline, but will not act on diacylphospholipids.  Assumed to act on -glycerol and -OH.
The enzyme also catalyzes the transfer of an acyl group from a lysophospholipid to phosphatidylglycerol for the formation of acyl phosphatidylglycerol (shown to be a small component on the membrane).
no specific mention of which side of the inner membrane the active site of the PldB enzyme is on.
AMF"	-1.87695	2.35514	[c] : 2agpg181[c] + h2o[c] --> g3pg[c] + h[c] + ocdcea[c] 		
13924	LSERDHr	Yes	L-serine dehydrogenase	[c] : nadp + ser-L <==> 2amsa + h + nadph	Update		b1539	"AMF
PMID: 12535615"	"reaction is characterized in PMID: 12535615

to act on L and D-serine, L-allo-threonine, D-threonine, and hydroxyisobutyrate

reaversibility is not for sure know, but hints that it may be"	5.16584	4.34649	[c] : nadp[c] + ser-L[c] <==> 2amsa[c] + h[c] + nadph[c] 		
8876	LYSabcpp	Yes	L-lysine transport via ABC system (periplasm)	atp[c] + h2o[c] + lys-L[p] --> adp[c] + h[c] + lys-L[c] + pi[c]	"Transport, Inner Membrane"		( b2310  and  b2307  and  b2306  and  b2308 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + lys-L[p] --> adp[c] + h[c] + lys-L[c] + pi[c] 		
362	LYSDC	No	lysine decarboxylase	[c] : h + lys-L --> 15dap + co2	Threonine and Lysine Metabolism	4.1.1.18	( b0186  or  b4131 )			-4.96805	1.79669	[c] : h[c] + lys-L[c] --> 15dap[c] + co2[c] 		
8877	LYSt2rpp	Yes	L-lysine reversible transport via proton symport (periplasm)	h[p] + lys-L[p] <==> h[c] + lys-L[c]	"Transport, Inner Membrane"		b2156	NCD		0	0	[c] : h[p] + lys-L[p] <==> h[c] + lys-L[c] 		
9165	LYStex	Yes	L-lysine transport via diffusion (extracellular to periplasm)	lys-L[e] <==> lys-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : lys-L[e] <==> lys-L[p] 		
2918	LYSTRS	Yes	Lysyl-tRNA synthetase	[c] : atp + lys-L + trnalys --> amp + lystrna + ppi	Update	6.1.1.6	( b2890  or  b4129 )		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + lys-L[c] + trnalys[c] --> amp[c] + lystrna[c] + ppi[c] 		
6227	LYXI	Yes	Lyxose isomerase	[c] : lyx-L --> xylu-L	Update		b3903	JLR	Lyxose can be used as a carbon source if the lyx gene becomes non-cryptic.	-0.246702	4.88847	[c] : lyx-L[c] --> xylu-L[c] 		
8878	LYXt2pp	Yes	L-Lyxose transport via proton symport (periplasm)	h[p] + lyx-L[p] --> h[c] + lyx-L[c]	Update		b3907	JLR	Lyxose can be used as a carbon source if the lyx gene becomes non-cryptic.	0	0	[c] : h[p] + lyx-L[p] --> h[c] + lyx-L[c] 		
9166	LYXtex	Yes	L-Lyxose transport via diffusion (extracellular to periplasm)	lyx-L[e] <==> lyx-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : lyx-L[e] <==> lyx-L[p] 		
2837	M1PD	No	mannitol-1-phosphate 5-dehydrogenase	[c] : mnl1p + nad <==> f6p + h + nadh	Alternate Carbon Metabolism	1.1.1.17	b3600		JLR - mannitol 6P is equal to mannitol 1P.	3.78793	9.00908	[c] : mnl1p[c] + nad[c] <==> f6p[c] + h[c] + nadh[c] 		
1347	MACPD	No	Malonyl-ACP decarboxylase	[c] : h + malACP --> acACP + co2	Membrane Lipid Metabolism		b2323	JLR		-4.49136	1.66176	[c] : h[c] + malACP[c] --> acACP[c] + co2[c] 		
2717	MALS	No	malate synthase	[c] : accoa + glx + h2o --> coa + h + mal-L	Anaplerotic reactions	4.1.3.2	( b4014  or  b2976 )	IF		-8.77004	4.9584	[c] : accoa[c] + glx[c] + h2o[c] --> coa[c] + h[c] + mal-L[c] 		
8879	MALt2_2pp	Yes	Malate transport via proton symport (2 H) (periplasm)	(2) h[p] + mal-L[p] --> (2) h[c] + mal-L[c]	"Transport, Inner Membrane"		b3528	JLR		0	0	[c] : (2) h[p] + mal-L[p] --> (2) h[c] + mal-L[c] 		
8880	MALt2_3pp	Yes	Malate transport via proton symport (3 H) (periplasm)	(3) h[p] + mal-L[p] --> (3) h[c] + mal-L[c]	"Transport, Inner Membrane"		( b4138  or  b4123 )	JLR		0	0	[c] : (3) h[p] + mal-L[p] --> (3) h[c] + mal-L[c] 
8881	MALTabcpp	Yes	maltose transport via ABC system (periplasm)	atp[c] + h2o[c] + malt[p] --> adp[c] + h[c] + malt[c] + pi[c]	"Transport, Inner Membrane"		( b4034  and  b4033  and  b4032  and  b4035 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + malt[p] --> adp[c] + h[c] + malt[c] + pi[c] 
13692	MALTATr	Yes	maltose O-acetyltransferase	[c] : accoa + malt <==> acmalt + coa	Update	2.3.1.79	b0459	AMF	"from PMID: 1856235
no physiological role found yet, could be in responce to a detoxification of sugars

also acts on
mannose
fructose
galactose
which were not entered
AMF"	-1.98374	4.73838	[c] : accoa[c] + malt[c] <==> acmalt[c] + coa[c] 
9167	MALtex	Yes	Malate transport via diffusion (extracellular to periplasm)	mal-L[e] <==> mal-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : mal-L[e] <==> mal-L[p] 
8882	MALTHXabcpp	Yes	maltohexaose transport via ABC system (periplasm)	atp[c] + h2o[c] + malthx[p] --> adp[c] + h[c] + malthx[c] + pi[c]	"Transport, Inner Membrane"		( b4034  and  b4033  and  b4032  and  b4035 )	JLR		-7.01673	1.48181	[c] : atp[c] + h2o[c] + malthx[p] --> adp[c] + h[c] + malthx[c] + pi[c] 
9116	MALTHXtexi	Yes	maltohexaose transport via diffusion (extracellular to periplasm) irreversible	malthx[e] --> malthx[p]	"Transport, Outer Membrane"		b4036		"PMID: 7654405

LamB binds to the maltoheptanose compounds and facitlitaes their diffuction through the outer membrane

PMID: 127000071
outer membrane protein porin for maltose and maltooligosacharides"	0	0	[c] : malthx[e] --> malthx[p] 
8883	MALTPTabcpp	Yes	maltopentaose transport via ABC system (periplasm)	atp[c] + h2o[c] + maltpt[p] --> adp[c] + h[c] + maltpt[c] + pi[c]	"Transport, Inner Membrane"		( b4034  and  b4033  and  b4032  and  b4035 )	JLR		-7.01673	1.48181	[c] : atp[c] + h2o[c] + maltpt[p] --> adp[c] + h[c] + maltpt[c] + pi[c] 
8884	MALTptspp	Yes	maltose transport via PEP:Pyr PTS (periplasm)	malt[p] + pep[c] --> malt6p[c] + pyr[c]	"Transport, Inner Membrane"		( b2417  and  b1621  and  b2415  and  b2416 )			-10.1729	3.20748	[c] : malt[p] + pep[c] --> malt6p[c] + pyr[c] 
9115	MALTPTtexi	Yes	maltopentaoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible	maltpt[e] --> maltpt[p]	"Transport, Outer Membrane"		b4036		"PMID: 7654405

LamB binds to the maltoheptanose compounds and facitlitaes their diffuction through the outer membrane

PMID: 127000071
outer membrane protein porin for maltose and maltooligosacharides"	0	0	[c] : maltpt[e] --> maltpt[p] 
9117	MALTtexi	Yes	maltoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible	malt[e] --> malt[p]	"Transport, Outer Membrane"		b4036		"PMID: 7654405

LamB binds to the maltoheptanose compounds and facitlitaes their diffuction through the outer membrane

PMID: 127000071
outer membrane protein porin for maltose and maltooligosacharides"	0	0	[c] : malt[e] --> malt[p] 
8885	MALTTRabcpp	Yes	Maltotriose transport via ABC system (periplasm)	atp[c] + h2o[c] + malttr[p] --> adp[c] + h[c] + malttr[c] + pi[c]	"Transport, Inner Membrane"		( b4034  and  b4033  and  b4032  and  b4035 )	JLR		-7.01673	1.48181	[c] : atp[c] + h2o[c] + malttr[p] --> adp[c] + h[c] + malttr[c] + pi[c] 
9113	MALTTRtexi	Yes	Maltotriose transport via diffusion (extracellular to periplasm) irreversible	malttr[e] --> malttr[p]	"Transport, Outer Membrane"		b4036		"PMID: 7654405

LamB binds to the maltoheptanose compounds and facitlitaes their diffuction through the outer membrane

PMID: 127000071
outer membrane protein porin for maltose and maltooligosacharides"	0	0	[c] : malttr[e] --> malttr[p] 
8886	MALTTTRabcpp	Yes	maltotetraose transport via ABC system (periplasm)	atp[c] + h2o[c] + maltttr[p] --> adp[c] + h[c] + maltttr[c] + pi[c]	"Transport, Inner Membrane"		( b4034  and  b4033  and  b4032  and  b4035 )	JLR		-7.01673	1.48181	[c] : atp[c] + h2o[c] + maltttr[p] --> adp[c] + h[c] + maltttr[c] + pi[c] 
9114	MALTTTRtexi	Yes	maltotetraoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible	maltttr[e] --> maltttr[p]	"Transport, Outer Membrane"		b4036		"PMID: 7654405

LamB binds to the maltoheptanose compounds and facitlitaes their diffuction through the outer membrane

PMID: 127000071
outer membrane protein porin for maltose and maltooligosacharides"	0	0	[c] : maltttr[e] --> maltttr[p] 
2536	MAN1PT2	No	mannose-1-phosphate guanylyltransferase (GDP)	[c] : gdp + h + man1p --> gdpmann + pi	Cell Envelope Biosynthesis	2.7.7.22	b2049	JLR	Ref says the gene is well established	0.455245	3.06551	[c] : gdp[c] + man1p[c] --> gdpmann[c] + h[c] + pi[c] 
244	MAN6PI	No	mannose-6-phosphate isomerase	[c] : man6p <==> f6p	Alternate Carbon Metabolism	5.3.1.8	b1613			-0.246702	4.88847	[c] : man6p[c] <==> f6p[c] 
8887	MAN6Pt6_2pp	Yes	Mannose-6-phosphate transport via phosphate antiport (periplasm)	man6p[p] + (2) pi[c] --> man6p[c] + (2) pi[p]	"Transport, Inner Membrane"		b3666	JLR		0	0	[c] : man6p[p] + (2) pi[c] --> man6p[c] + (2) pi[p] 					
9170	MAN6Ptex	Yes	Mannose 6-phosphate transport via diffusion (extracellular to periplasm)	man6p[e] <==> man6p[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : man6p[e] <==> man6p[p] 					
2284	MANAO	No	Mannonate oxidoreductase	[c] : mana + nad <==> fruur + h + nadh	Alternate Carbon Metabolism	1.1.1.57	b4323	JLR		3.78793	9.00908	[c] : mana[c] + nad[c] <==> fruur[c] + h[c] + nadh[c] 					
8889	MANGLYCptspp	Yes	2-O-alpha-mannosyl-D-glycerate transport via PEP:Pyr PTS (periplasm)	manglyc[p] + pep[c] --> man6pglyc[c] + pyr[c]	Update		( b0731  and  b2415  and  b2416 )	JLR	"The exact location of the phosphate is unknown, however, they don't believe it is on the glycerate group."	-10.1729	3.20748	[c] : manglyc[p] + pep[c] --> man6pglyc[c] + pyr[c] 					
11505	MANGLYCtex	Yes	2-O-alpha-mannosyl-D-glycerate transport via diffusion (extracellular to periplasm)	manglyc[e] <==> manglyc[p]	"Transport, Outer Membrane"				"assumed passive diffusion through outer peptidoglican barrier



modified by MKA, 4/26/05
(was previously manglyc[e] <==> man6pglyc[p])"	0	0	[c] : manglyc[e] <==> manglyc[p] 					
6180	MANPGH	Yes	2-O-alpha-mannosyl-6-phosphate-D-glycerate hydrolase	[c] : h2o + man6pglyc --> glyc-R + man6p	Update		b0732	JLR	"The actual substrate and product are unknown and assumed.  See MANGLYCpts.

PUTATIVE
"	-3.32755	3.07096	[c] : h2o[c] + man6pglyc[c] --> glyc-R[c] + man6p[c] 					
8890	MANptspp	Yes	D-mannose transport via PEP:Pyr PTS (periplasm)	man[p] + pep[c] --> man6p[c] + pyr[c]	"Transport, Inner Membrane"		( b1817  and  b1818  and  b1819  and  b2415  and  b2416 )			-10.1729	3.20748	[c] : man[p] + pep[c] --> man6p[c] + pyr[c] 					
9169	MANtex	Yes	D-mannose transport via diffusion (extracellular to periplasm)	man[e] <==> man[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : man[e] <==> man[p] 					
2660	MCITD	No	2-methylcitrate dehydratase	[c] : 2mcit --> 2mcacn + h2o	Alternate Carbon Metabolism	4.2.1.79	b0334	JLR		1.64172	4.4688	[c] : 2mcit[c] --> 2mcacn[c] + h2o[c] 					
2659	MCITL2	No	methylisocitrate lyase	[c] : micit <==> pyr + succ	Alternate Carbon Metabolism	4.1.3.30	b0331	JLR		1.55901	3.22422	[c] : micit[c] <==> pyr[c] + succ[c] 					
2250	MCITS	No	2-methylcitrate synthase	[c] : h2o + oaa + ppcoa --> 2mcit + coa + h	Alternate Carbon Metabolism	4.1.3.31	b0333	"NCD
new EC is 2.3.3.5 - NCD"		-7.41164	5.71005	[c] : h2o[c] + oaa[c] + ppcoa[c] --> 2mcit[c] + coa[c] + h[c] 					
3441	MCOATA	No	Malonyl-CoA-ACP transacylase	[c] : ACP + malcoa <==> coa + malACP	Membrane Lipid Metabolism	2.3.1.39	b1092	tv		0	0.5	[c] : ACP[c] + malcoa[c] <==> coa[c] + malACP[c] 					
13722	MCPST	Yes	3-mercaptopyruvate sulfurtransferase	[c] : cyan + mercppyr --> h + pyr + tcynt	Update	2.8.1.2	b2521	"MM
AMF"	"described in PMID: 12499560
AMF
"	No energy	No energy	[c] : cyan[c] + mercppyr[c] --> pyr[c] + tcynt[c] 					
18723	MCTP1App	Yes	murein crosslinking transpeptidase 1A:(A2pm->D-ala) (periplasm)	[p] : murein5p5p --> ala-D + murein5px4p	Murein Biosynthesis		( b0084  or  b0635  or  b3396  or  b0149 )	"AMF
links the peptides of a 2 murein unit (A2pm->D-ala)
3.4.-.-"	"MrcA and MrcB (best characeterized) are bifunctional transglycosylase and transpeptidase forming enzymes
PMID: 3906031
together they are lethal for a double deletion
PMID: 10542235

MrdA and FtsI are part of the cell cycle proteins and are predicted to be DD-transpeptidases
PMID: 10542235
Also, pbpC is thought to be a transglycolase only"	No energy	No energy	[p] : murein5p5p[p] --> ala-D[p] + murein5px4p[p] 					
18728	MCTP1Bpp	Yes	murein crosslinking transpeptidase 1B:(A2pm->A2pm) (periplasm)	[p] : murein5p5p --> alaala + murein5px3p	Murein Biosynthesis		( b0149  or  b3396 )	"AMF
links the peptides of a 2 murein unit (A2pm->A2pm)
3.4.-.-"	"MrcA and MrcB (best characeterized) are bifunctional transglycosylase and transpeptidase forming enzymes
PMID: 3906031
together they are lethal for a double deletion
PMID: 10542235

MrdA and FtsI are part of the cell cycle proteins and are predicted to be DD-transpeptidases
PMID: 10542235
Also, pbpC is thought to be a transglycolase only"	No energy	No energy	[p] : murein5p5p[p] --> alaala[p] + murein5px3p[p] 					
18726	MCTP2App	Yes	murein crosslinking transpeptidase 1A:(A2pm->D-ala) (periplasm)	[p] : murein5p5p5p --> (2) ala-D + murein5px4px4p	Murein Biosynthesis		( b0084  or  b0635  or  b3396  or  b0149 )	"AMF
this reaction is the net result of two consectutive linkings involving 3 different chains
links the peptides of a 2 murein unit (A2pm->D-ala)
3.4.-.-"	"MrcA and MrcB (best characeterized) are bifunctional transglycosylase and transpeptidase forming enzymes
PMID: 3906031
together they are lethal for a double deletion
PMID: 10542235

MrdA and FtsI are part of the cell cycle proteins and are predicted to be DD-transpeptidases
PMID: 10542235
Also, pbpC is thought to be a transglycolase only"	No energy	No energy	[p] : murein5p5p5p[p] --> (2) ala-D[p] + (3) h[p] + murein5px4px4p[p] 					
18731	MDDCP1pp	Yes	"murein D,D-carboxypeptidase (murein5px4p) (periplasm)"	[p] : h2o + murein5px4p --> ala-D + murein4px4p	Murein Biosynthesis	3.4.16.4	( b0632  or  b3182  or  b0839  or  b2010 )	"AMF
"	"DacA,B,C,D are all D-alanyl-D-alanine carboxypeptidases
DacB is also a DD-edopeptidase

neidhardt pg. 1032

A quadruple dacA dacB dacC dacD mutant was constructed and shown to grow as well as its isogenic wild-type strain, indicating that the loss of any known PBP-associated DD-carboxypeptidase activity is not deleterious for E. coli.
PMID: 8955390"	No energy	No energy	[p] : h2o[p] + murein5px4p[p] --> ala-D[p] + murein4px4p[p] 					
18799	MDDCP2pp	Yes	"murein D,D-carboxypeptidase (murein5px4px4p) (periplasm)"	[p] : h2o + murein5px4px4p --> ala-D + murein4px4px4p	Murein Biosynthesis	3.4.16.4	( b0632  or  b3182  or  b0839  or  b2010 )	"AMF
"	"DacA,B,C,D are all D-alanyl-D-alanine carboxypeptidases
DacB is also a DD-edopeptidase

neidhardt pg. 1032

A quadruple dacA dacB dacC dacD mutant was constructed and shown to grow as well as its isogenic wild-type strain, indicating that the loss of any known PBP-associated DD-carboxypeptidase activity is not deleterious for E. coli.
PMID: 8955390"	No energy	No energy	[p] : h2o[p] + murein5px4px4p[p] --> ala-D[p] + murein4px4px4p[p] 					
18800	MDDCP3pp	Yes	"murein D,D-carboxypeptidase (murein5p5p) (periplasm)"	[p] : h2o + murein5p5p --> ala-D + murein5p4p	Murein Biosynthesis	3.4.16.4	( b0632  or  b3182  or  b0839  or  b2010 )	"AMF
"	"DacA,B,C,D are all D-alanyl-D-alanine carboxypeptidases
DacB is also a DD-edopeptidase

neidhardt pg. 1032

A quadruple dacA dacB dacC dacD mutant was constructed and shown to grow as well as its isogenic wild-type strain, indicating that the loss of any known PBP-associated DD-carboxypeptidase activity is not deleterious for E. coli.
PMID: 8955390"	-3.36489	3.34628	[p] : h2o[p] + murein5p5p[p] --> ala-D[p] + murein5p4p[p] 					
18801	MDDCP4pp	Yes	"murein D,D-carboxypeptidase (murein5p4p) (periplasm)"	[p] : h2o + murein5p4p --> ala-D + murein4p4p	Murein Biosynthesis	3.4.16.4	( b0632  or  b3182  or  b0839  or  b2010 )	"AMF
"	"DacA,B,C,D are all D-alanyl-D-alanine carboxypeptidases
DacB is also a DD-edopeptidase

neidhardt pg. 1032

A quadruple dacA dacB dacC dacD mutant was constructed and shown to grow as well as its isogenic wild-type strain, indicating that the loss of any known PBP-associated DD-carboxypeptidase activity is not deleterious for E. coli.
PMID: 8955390"	-3.36489	3.34628	[p] : h2o[p] + murein5p4p[p] --> ala-D[p] + murein4p4p[p] 					
18802	MDDCP5pp	Yes	"murein D,D-carboxypeptidase (murein5p3p) (periplasm)"	[p] : h2o + murein5p3p --> ala-D + murein4p3p	Murein Biosynthesis	3.4.16.4	( b0632  or  b3182  or  b0839  or  b2010 )	"AMF
"	"DacA,B,C,D are all D-alanyl-D-alanine carboxypeptidases
DacB is also a DD-edopeptidase

neidhardt pg. 1032

A quadruple dacA dacB dacC dacD mutant was constructed and shown to grow as well as its isogenic wild-type strain, indicating that the loss of any known PBP-associated DD-carboxypeptidase activity is not deleterious for E. coli.
PMID: 8955390"	-3.36489	3.34628	[p] : h2o[p] + murein5p3p[p] --> ala-D[p] + murein4p3p[p] 					
18828	MDDEP1pp	Yes	"murein D,D-endopeptidase (murein4px4p) (periplasm)"	[p] : h2o + murein4px4p --> murein4p4p	Murein Recycling		( b3182  or  b2328  or  b2134 )	"AMF
"	"cleaves D,D- murein crosslinkings
AMF
PMID: 11454209

DacB also has an additional function
pbpG characterized in PMID: 7721700"	No energy	No energy	[p] : h2o[p] + murein4px4p[p] --> murein4p4p[p] 					
18851	MDDEP2pp	Yes	"murein D,D-endopeptidase (murein3px4p) (periplasm)"	[p] : h2o + murein3px4p --> murein4p3p	Murein Recycling		( b3182  or  b2328  or  b2134 )	"AMF
"	"cleaves D,D- murein crosslinkings
AMF
PMID: 11454209

DacB also has an additional function
pbpG characterized in PMID: 7721700"	No energy	No energy	[p] : h2o[p] + murein3px4p[p] --> murein4p3p[p] 					
18854	MDDEP3pp	Yes	"murein D,D-endopeptidase (murein5px4p) (periplasm)"	[p] : h2o + murein5px4p --> murein5p4p	Murein Recycling		( b3182  or  b2328  or  b2134 )	"AMF
"	"cleaves D,D- murein crosslinkings
AMF
PMID: 11454209

DacB also has an additional function
pbpG characterized in PMID: 7721700"	No energy	No energy	[p] : h2o[p] + murein5px4p[p] --> murein5p4p[p] 					
18855	MDDEP4pp	Yes	"murein D,D-endopeptidase (murein4px4px4p) (periplasm)"	[p] : h2o + murein4px4px4p --> murein4px4p4p	Murein Recycling		( b3182  or  b2328  or  b2134 )	"AMF
"	"cleaves D,D- murein crosslinkings
AMF
PMID: 11454209

DacB also has an additional function
pbpG characterized in PMID: 7721700"	No energy	No energy	[p] : h2o[p] + murein4px4px4p[p] --> murein4px4p4p[p] 					
541	MDH	No	malate dehydrogenase	[c] : mal-L + nad <==> h + nadh + oaa	Citric Acid Cycle	1.1.1.37	b3236			4.73639	4.5435	[c] : mal-L[c] + nad[c] <==> h[c] + nadh[c] + oaa[c] 					
2314	MDH2	No	Malate dehydrogenase (ubiquinone 8 as acceptor)	[c] : mal-L + q8 --> oaa + q8h2	Citric Acid Cycle	1.1.99.16	b2210	JLR		-18.6813	21.401	[c] : mal-L[c] + q8[c] --> oaa[c] + q8h2[c] 					
3204	MDH3	No	Malate dehydrogenase (menaquinone 8 as acceptor)	[c] : mal-L + mqn8 --> mql8 + oaa	Citric Acid Cycle	1.1.99.16	b2210	JLR	JLR- not positive if transfers to menaquinone	-17.2294	17.2464	[c] : mal-L[c] + mqn8[c] --> mql8[c] + oaa[c] 					
1630	MDRPD	No	5-Methylthio-5-deoxy-D-ribulose 1-phosphate dehydratase	[c] : 5mdru1p --> dkmpp + h2o	Arginine and Proline Metabolism			JLR- Based on reaction given for B. subtilis (Sekowska A and A. Danchin paper(2002) )	JLR- based on B. subtilis paper	-9.58412	3.68395	[c] : 5mdru1p[c] --> dkmpp[c] + h2o[c] 					
297	ME1	No	malic enzyme (NAD)	[c] : mal-L + nad --> co2 + nadh + pyr	Anaplerotic reactions	1.1.1.38	b1479			0.245034	4.7859	[c] : mal-L[c] + nad[c] --> co2[c] + nadh[c] + pyr[c] 					
2848	ME2	No	malic enzyme (NADP)	[c] : mal-L + nadp --> co2 + nadph + pyr	Anaplerotic reactions	1.1.1.40	b2463			0.245034	4.7859	[c] : mal-L[c] + nadp[c] --> co2[c] + nadph[c] + pyr[c] 					
3444	MECDPDH	No	"2C-methyl-D-erythritol 2,4 cyclodiphosphate dehydratase"	[c] : 2mecdp + h --> h2mb4p + h2o	Cofactor and Prosthetic Group Biosynthesis		b2515	"JLR- involved in ipdp and dmpp biosynthesis.  Not sure of enzyme name or H2O.  Had to add H to mass balance, charge doesn't balance
1.17.4.3  = 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase ??? IT
"	"JLR- these reactions are not biochemically verified, the cofactors required are unknown"	-29.2149	7.16217	[c] : 2mecdp[c] + (2) h[c] --> h2mb4p[c] + h2o[c] 					
237	MECDPS	No	"2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase"	[c] : 2p4c2me --> 2mecdp + cmp	Cofactor and Prosthetic Group Biosynthesis		b2746	EC 4.6.1.12		24.955	7.89633	[c] : 2p4c2me[c] --> 2mecdp[c] + cmp[c] 					
8891	MELIBt2pp	Yes	melibiose transport in via symport (periplasm)	h[p] + melib[p] --> h[c] + melib[c]	"Transport, Inner Membrane"		b4120	"NCD	"	"JLR- the enzyme can use H+, Na+, of Li+ gradient (prefers Na+)"	0	0	[c] : h[p] + melib[p] --> h[c] + melib[c] 					
13767	MELIBt3ipp	Yes	melibiose transport in via antiport (periplasm)	h[p] + melib[c] --> h[c] + melib[p]	"Transport, Inner Membrane"		b1528	AMF	"PMID: 10438792
charcetizes that SotB (ydeA) can export arabinose

PMID: 10671456 
states that SotB (ydea) xan export arabinose, but SotA exports arabinose

SetB, SetA functions are give in PMID: 10209755

AMF"	0	0	[c] : h[p] + melib[c] --> h[c] + melib[p] 					
9172	MELIBtex	Yes	melibiose transport via diffusion (extracellular to periplasm)	melib[e] <==> melib[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : melib[e] <==> melib[p] 					
2833	MEPCT	No	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	[c] : 2me4p + ctp + h --> 4c2me + ppi	Cofactor and Prosthetic Group Biosynthesis		b2747	EC 2.7.7.60		-1.92466	3.75933	[c] : 2me4p[c] + ctp[c] --> 4c2me[c] + ppi[c] 					
8892	METabcpp	Yes	L-methionine transport via ABC system (periplasm)	atp[c] + h2o[c] + met-L[p] --> adp[c] + h[c] + met-L[c] + pi[c]	"Transport, Inner Membrane"		( b0198  and  b0199  and  b0197 )		JLR- not sure about locus (two methionine systems metD and metP); genes for this reaction might include yaeE(metI) and abc(metN)	-7.01673	1.48181	[c] : atp[c] + h2o[c] + met-L[p] --> adp[c] + h[c] + met-L[c] + pi[c] 					
369	METAT	No	methionine adenosyltransferase	[c] : atp + h2o + met-L --> amet + pi + ppi	Methionine Metabolism	2.5.1.6	b2942			No energy	No energy	[c] : atp[c] + h2o[c] + met-L[c] --> amet[c] + pi[c] + ppi[c] 					
8893	METDabcpp	Yes	D-methionine transport via ABC system (periplasm)	atp[c] + h2o[c] + met-D[p] --> adp[c] + h[c] + met-D[c] + pi[c]	"Transport, Inner Membrane"		( b0198  and  b0199  and  b0197 )	JLR		-7.01673	1.48181	[c] : atp[c] + h2o[c] + met-D[p] --> adp[c] + h[c] + met-D[c] + pi[c] 					
9173	METDtex	Yes	D-methionine transport via diffusion (extracellular to periplasm)	met-D[e] <==> met-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : met-D[e] <==> met-D[p] 					
11298	METOX1s	Yes	methionine spontaneous oxidation	[c] : h2o2 + met-L --> h2o + metsox-S-L	Update			"MKA - reduction of exposed methionines may serve as a reactive oxygen sink
produces S and R enantiomers"	"spontaneous rxn - may be important reactive oxygen species sink.

met-L oxidized by other reactive oxygen species such as OH-(OH1), O2-, OCl-, NO3- (peroxynitrite)  "	No energy	No energy	[c] : h2o2[c] + met-L[c] --> h2o[c] + metsox-S-L[c] 					
11299	METOX2s	Yes	methionine spontaneous oxidation 2	[c] : h2o2 + met-L --> h2o + metsox-R-L	Update			"MKA - reduction of exposed methionines may serve as a reactive oxygen sink
produces S and R enantiomers"	"spontaneous rxn - may be important reactive oxygen species sink.

met-L oxidized by other reactive oxygen species such as OH-(OH1), O2-, OCl-, NO3- (peroxynitrite)  "	No energy	No energy	[c] : h2o2[c] + met-L[c] --> h2o[c] + metsox-R-L[c] 					
7846	METS	No	methionine synthase	[c] : 5mthf + hcys-L --> h + met-L + thf	Methionine Metabolism	2.1.1.13	( b4019  or  b3829 )			-2.57019	4.67683	[c] : 5mthf[c] + hcys-L[c] --> met-L[c] + thf[c] 					
11872	METSOX1abcpp	Yes	L-methionine S-oxide transport via ABC system (periplasm)	atp[c] + h2o[c] + metsox-S-L[p] --> adp[c] + h[c] + metsox-S-L[c] + pi[c]	Update			"MKA - transport assumed due to growth on met-s-ox-L, but mechanism (abc) unknown - guessed to be same as for met-L"	"MKA -

transport assumed due to growth on met-r-ox-L, but mechanism (abc) unknown - guessed to be same as for met-L  (but not confident enough to link to enzyme)

AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + metsox-S-L[p] --> adp[c] + h[c] + metsox-S-L[c] + pi[c] 					
11874	METSOX1tex	Yes	L-methionine S-oxide diffusion (extracellular)	metsox-S-L[e] <==> metsox-S-L[p]	Update			AMF	assumed diffusion through outer mem	0	0	[c] : metsox-S-L[e] <==> metsox-S-L[p] 					
11873	METSOX2abcpp	Yes	L-methionine R-oxide transport via ABC system (periplasm)	atp[c] + h2o[c] + metsox-R-L[p] --> adp[c] + h[c] + metsox-R-L[c] + pi[c]	Update			"MKA - transport assumed due to growth on met-r-ox-L, but mechanism (abc) unknown - guessed to be same as for met-L"	"MKA -

transport assumed due to growth on met-r-ox-L, but mechanism (abc) unknown - guessed to be same as for met-L  (but not confident enough to link to enzyme)

AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + metsox-R-L[p] --> adp[c] + h[c] + metsox-R-L[c] + pi[c] 					
11875	METSOX2tex	Yes	L-methionine R-oxide diffusion (extracellular)	metsox-R-L[e] <==> metsox-R-L[p]	"Transport, Outer Membrane"			AMF	assumed diffusion through outer mem	0	0	[c] : metsox-R-L[e] <==> metsox-R-L[p] 					
11876	METSOXR1	Yes	L-methionine-S-oxide reductase	[c] : metsox-S-L + trdrd --> h2o + met-L + trdox	Update	1.8.4.5	b4219	"different enzyme/reaction for met-r-ox reductase - Met-R-R
MKA"	"PMID: 11677230, 12504094, 11795868,

acts on Met-r-sulfoxide residues that are part of protiens (on surface) and free in cytosole

Met-sulfoxide residues spontaneous generated in cell by reactive oxygen and nitrogen species

MKA
"	No energy	No energy	[c] : metsox-S-L[c] + trdrd[c] --> h2o[c] + met-L[c] + trdox[c] 					
11877	METSOXR2	Yes	L-methionine-R-sulfoxide reductase	[c] : metsox-R-L + trdrd --> h2o + met-L + trdox	Update		b1778	"MKA
same reaction, different enzyme, for L-met-S-sulfoxide (METR1)"	"PMID: 11795868, 11677230, 12504094

required for cadmium (oxidative stress) resistance

may not primarily be accomplished by msrB - but there is small biochemical proof

acts on Met-r-sulfoxide residues that are part of protiens (on surface) and free in cytosol

MKA"	No energy	No energy	[c] : metsox-R-L[c] + trdrd[c] --> h2o[c] + met-L[c] + trdox[c] 					
9174	METtex	Yes	L-methionine transport via diffusion (extracellular to periplasm)	met-L[e] <==> met-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : met-L[e] <==> met-L[p] 					
1026	METTRS	Yes	Methionyl-tRNA synthetase	[c] : atp + met-L + trnamet --> amp + mettrna + ppi	Update	6.1.1.10	b2114		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + met-L[c] + trnamet[c] --> amp[c] + mettrna[c] + ppi[c] 					
13680	MG2tex	Yes	magnesium (Mg+2) transport via diffusion (extracellular to periplasm)	mg2[e] <==> mg2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : mg2[e] <==> mg2[p] 					
13663	MG2tpp	Yes	magnesium transport via diffusion	mg2[p] <==> mg2[c]	"Transport, Inner Membrane"		b3816		"The CorA permeases of S. typhimurium and E. coli mediate both influx and efflux of Mg2+. They transport Mg2+, Co2+ and Ni2+ but not Fe2+ (Papp and Maguire, 2004).

transport DB

http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=1.A.35

AMF"	0	0	[c] : mg2[p] <==> mg2[c] 					
13673	MG2uabcpp	Yes	"Magnesium (Mg+2) ABC transporter (ubtake, periplasm)"	atp[c] + h2o[c] + mg2[p] --> adp[c] + h[c] + mg2[c] + pi[c]	"Transport, Inner Membrane"		b4242	AMF	"from transportDB,
Mg2+/Ni2+-ATPase (uptake) MgtA
http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=3.A.3

also from PMID: 9622348

AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + mg2[p] --> adp[c] + h[c] + mg2[c] + pi[c] 					
269	MGSA	No	methylglyoxal synthase	[c] : dhap --> mthgxl + pi	Methylglyoxal Metabolism	4.2.3.3	b0963	"Previously EC 4.2.99.11
this rxn represents the enzymatic conversion or non-enzymatic fragmentation of dhap to mthgxl - NCD"		-13.0293	2.71948	[c] : dhap[c] --> h[c] + mthgxl[c] + pi[c] 					
2540	MI1PP	No	myo-inositol 1-phosphatase	[c] : h2o + mi1p-D --> inost + pi	Cell Envelope Biosynthesis	3.1.3.25	b2533	JLR		-3.54819	2.12947	[c] : h2o[c] + mi1p-D[c] --> h[c] + inost[c] + pi[c] 					
2661	MICITD	No	2-methylisocitrate dehydratase	[c] : 2mcacn + h2o --> micit	Alternate Carbon Metabolism	4.2.1.99	b0118	JLR	JLR- AcnB has been shown to have this activity.	-1.64172	4.4688	[c] : 2mcacn[c] + h2o[c] --> micit[c] 					
9175	MINOHPtex	Yes	myo-inositol phosphate transport via diffusion (extracellular to periplasm)	minohp[e] <==> minohp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : minohp[e] <==> minohp[p] 					
18811	MLDCP1App	Yes	"murein L,D-carboxypeptidase (murein5px4p) (periplasm)"	[p] : h2o + murein5px4p --> alaala + murein3px4p	Murein Biosynthesis	3.4.17.13		"AMF
"	"described activity in neid. pg. 1032
the periplasmic L,D-carboxypeptidase or L,D-dicarboxybpeptidase have not been identified
(LdcA is the cytoplasmic L,D-carboxypeptidase)
The presence of the ddp operon supports that periplasmic activity exists as well PMID: 10500118"	No energy	No energy	[p] : h2o[p] + murein5px4p[p] --> alaala[p] + murein3px4p[p] 					
18817	MLDCP1Bpp	Yes	"murein L,D-carboxypeptidase (murein4p4p) (periplasm)"	[p] : h2o + murein4p4p --> ala-D + murein4p3p	Murein Biosynthesis	3.4.17.13		"AMF
"	"described activity in neid. pg. 1032
the periplasmic L,D-carboxypeptidase or L,D-dicarboxybpeptidase have not been identified
(LdcA is the cytoplasmic L,D-carboxypeptidase)
The presence of the ddp operon supports that periplasmic activity exists as well PMID: 10500118"	-3.36489	3.34628	[p] : h2o[p] + murein4p4p[p] --> ala-D[p] + murein4p3p[p] 					
18815	MLDCP2App	Yes	"murein L,D-carboxypeptidase (murein5p5p) (periplasm)"	[p] : h2o + murein5p5p --> alaala + murein5p3p	Murein Biosynthesis	3.4.17.13		"AMF
"	"described activity in neid. pg. 1032
the periplasmic L,D-carboxypeptidase or L,D-dicarboxybpeptidase have not been identified
(LdcA is the cytoplasmic L,D-carboxypeptidase)
The presence of the ddp operon supports that periplasmic activity exists as well PMID: 10500118"	-3.36489	3.34628	[p] : h2o[p] + murein5p5p[p] --> alaala[p] + murein5p3p[p] 					
18818	MLDCP2Bpp	Yes	"murein L,D-carboxypeptidase (murein4p3p) (periplasm)"	[p] : h2o + murein4p3p --> ala-D + murein3p3p	Murein Biosynthesis	3.4.17.13		"AMF
"	"described activity in neid. pg. 1032
the periplasmic L,D-carboxypeptidase or L,D-dicarboxybpeptidase have not been identified
(LdcA is the cytoplasmic L,D-carboxypeptidase)
The presence of the ddp operon supports that periplasmic activity exists as well PMID: 10500118"	-3.36489	3.34628	[p] : h2o[p] + murein4p3p[p] --> ala-D[p] + murein3p3p[p] 					
18816	MLDCP3App	Yes	"murein L,D-carboxypeptidase (murein5px3p) (periplasm)"	[p] : h2o + murein5px3p --> alaala + murein3px3p	Murein Biosynthesis	3.4.17.13		"AMF
"	"described activity in neid. pg. 1032
the periplasmic L,D-carboxypeptidase or L,D-dicarboxybpeptidase have not been identified
(LdcA is the cytoplasmic L,D-carboxypeptidase)
The presence of the ddp operon supports that periplasmic activity exists as well PMID: 10500118"	No energy	No energy	[p] : h2o[p] + murein5px3p[p] --> alaala[p] + murein3px3p[p] 					
18852	MLDEP1pp	Yes	"murein L,D-endopeptidase (murein3px3p) (periplasm)"	[p] : h2o + murein3px3p --> murein3p3p	Murein Recycling			"AMF
"	"no specific L,D-endopeptidase has been characterized yet
AMF"	No energy	No energy	[p] : h2o[p] + murein3px3p[p] --> murein3p3p[p] 					
18853	MLDEP2pp	Yes	"murein L,D-endopeptidase (murein5px3p) (periplasm)"	[p] : h2o + murein5px3p --> murein5p3p	Murein Recycling			"AMF
"	"no specific L,D-endopeptidase has been characterized yet
AMF"	No energy	No energy	[p] : h2o[p] + murein5px3p[p] --> murein5p3p[p] 					
2513	MLTG1	No	Maltodextrin glucosidase (maltotriose)	[c] : h2o + malttr --> glc-D + malt	Alternate Carbon Metabolism		b0403	JLR		-3.32755	3.07096	[c] : h2o[c] + malttr[c] --> glc-D[c] + malt[c] 					
2512	MLTG2	No	Maltodextrin glucosidase (maltotetraose)	[c] : h2o + maltttr --> glc-D + malttr	Alternate Carbon Metabolism		b0403	JLR		-3.32755	3.07096	[c] : h2o[c] + maltttr[c] --> glc-D[c] + malttr[c] 					
2511	MLTG3	No	Maltodextrin glucosidase (maltopentaose)	[c] : h2o + maltpt --> glc-D + maltttr	Alternate Carbon Metabolism		b0403	JLR		-3.32755	3.07096	[c] : h2o[c] + maltpt[c] --> glc-D[c] + maltttr[c] 					
2510	MLTG4	No	Maltodextrin glucosidase (maltohexaose)	[c] : h2o + malthx --> glc-D + maltpt	Alternate Carbon Metabolism		b0403	JLR		-3.32755	3.07096	[c] : h2o[c] + malthx[c] --> glc-D[c] + maltpt[c] 					
3235	MLTG5	No	Maltodextrin glucosidase (maltoheptaose)	[c] : h2o + malthp --> glc-D + malthx	Alternate Carbon Metabolism		b0403	JLR		-3.32755	3.07096	[c] : h2o[c] + malthp[c] --> glc-D[c] + malthx[c] 					
18856	MLTGY1pp	Yes	murein lytic transglycosylase (murein4p4p) (periplasm)	[p] : murein4p4p --> (2) anhgm4p	Murein Recycling		( b4392  or  b2813  or  b2701  or  b1193  or  b2963 )	"AMF
this reaction assumes that there are two cleaving reactions freeing two GlcNac(anh)MurNac-tetrapeptides"	"MltA, MltB, Slt are well characterized for lytic transglycosylase activity on murein
PMID: 8405923
MltE, MltC also have been shown to have lytic transglycosylase activity, but specific cleavage is not definate
PMID: 9642199
MltD is predicted to perfrom this reaction as well

This reaction is the general endotransglycosylase for murein
AMF
"	-11.8087	4.3995	[p] : murein4p4p[p] --> (2) anhgm4p[p] 					
18857	MLTGY2pp	Yes	murein lytic transglycosylase (murein4p3p) (periplasm)	[p] : murein4p3p --> anhgm3p + anhgm4p	Murein Recycling		( b4392  or  b2813  or  b2701  or  b1193  or  b2963 )	"AMF
this reaction assumes that there are two cleaving reactions freeing two GlcNac(anh)MurNac-tetrapeptides"	"MltA, MltB, Slt are well characterized for lytic transglycosylase activity on murein
PMID: 8405923
MltE, MltC also have been shown to have lytic transglycosylase activity, but specific cleavage is not definate
PMID: 9642199
MltD is predicted to perfrom this reaction as well

This reaction is the general endotransglycosylase for murein
AMF
"	-11.8087	4.3995	[p] : murein4p3p[p] --> anhgm3p[p] + anhgm4p[p] 					
18858	MLTGY3pp	Yes	murein lytic transglycosylase (murein3p3p) (periplasm)	[p] : murein3p3p --> (2) anhgm3p	Murein Recycling		( b4392  or  b2813  or  b2701  or  b1193  or  b2963 )	"AMF
this reaction assumes that there are two cleaving reactions freeing two GlcNac(anh)MurNac-tetrapeptides"	"MltA, MltB, Slt are well characterized for lytic transglycosylase activity on murein
PMID: 8405923
MltE, MltC also have been shown to have lytic transglycosylase activity, but specific cleavage is not definate
PMID: 9642199
MltD is predicted to perfrom this reaction as well

This reaction is the general endotransglycosylase for murein
AMF
"	-11.8087	4.3995	[p] : murein3p3p[p] --> (2) anhgm3p[p] 					
18859	MLTGY4pp	Yes	murein lytic transglycosylase (murein4px4p4p) (periplasm)	[p] : murein4px4p4p --> anhgm4p + murein4px4p	Murein Recycling		( b4392  or  b2813  or  b2701  or  b1193  or  b2963 )	"AMF
this reaction assumes that there are two cleaving reactions freeing two GlcNac(anh)MurNac-tetrapeptides"	"MltA, MltB, Slt are well characterized for lytic transglycosylase activity on murein
PMID: 8405923
MltE, MltC also have been shown to have lytic transglycosylase activity, but specific cleavage is not definate
PMID: 9642199
MltD is predicted to perfrom this reaction as well

This reaction is the general endotransglycosylase for murein
AMF
"	No energy	No energy	[p] : murein4px4p4p[p] --> anhgm4p[p] + murein4px4p[p] 					
2519	MLTP1	No	Maltodextrin phosphorylase (maltopentaose)	[c] : maltpt + pi <==> g1p + maltttr	Alternate Carbon Metabolism		b3417	JLR		0.220639	2.79451	[c] : h[c] + maltpt[c] + pi[c] <==> g1p[c] + maltttr[c] 					
3238	MLTP2	No	Maltodextrin phosphorylase (maltohexaose)	[c] : malthx + pi <==> g1p + maltpt	Alternate Carbon Metabolism		b3417	JLR		0.220639	2.79451	[c] : h[c] + malthx[c] + pi[c] <==> g1p[c] + maltpt[c] 					
2517	MLTP3	No	Maltodextrin phosphorylase (maltoheptaose)	[c] : malthp + pi <==> g1p + malthx	Alternate Carbon Metabolism		b3417	JLR		0.220639	2.79451	[c] : h[c] + malthp[c] + pi[c] <==> g1p[c] + malthx[c] 					
3201	MMCD	No	Methylmalonyl-CoA decarboxylase	[c] : h + mmcoa-S --> co2 + ppcoa	Alternate Carbon Metabolism	4.1.1.41	b2919	JLR	Not sure about which form of mmcoa	-4.96805	1.79669	[c] : h[c] + mmcoa-S[c] --> co2[c] + ppcoa[c] 					
2876	MME	No	methylmalonyl-CoA epimerase	[c] : mmcoa-R <==> mmcoa-S	Alternate Carbon Metabolism	5.1.99.1			"added for modeling reasons, not sure if MMCD reaction uses S or R or if MM2 makes S or R."	0	0.5	[c] : mmcoa-R[c] <==> mmcoa-S[c] 					
13674	MMETt2pp	Yes	S-methylmethionine permease (periplasm)	h[p] + mmet[p] --> h[c] + mmet[c]	"Transport, Inner Membrane"		b0260	"NCD
AMF"	"PMID: 9882684
ecoli can grown on methyl-methionince, this gene is the putuative transporter
AMF

not sure of the method of transport
"	0	0	[c] : h[p] + mmet[p] --> h[c] + mmet[c] 		
13676	MMETtex	Yes	S-methyl-L-methionine transport via diffusion (extracellular to periplasm)	mmet[e] <==> mmet[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : mmet[e] <==> mmet[p] 		
2307	MMM2	No	Methylmalonyl-CoA mutase	[c] : succoa --> mmcoa-R	Alternate Carbon Metabolism	5.4.99.2	b2917	JLR	Not sure about which form of mmcoa	0.476686	2.05009	[c] : succoa[c] --> mmcoa-R[c] 		
13358	MN6PP	Yes	mannose 6-phosphate phosphatase	[c] : h2o + man6p --> man + pi	Update		b0822	AMF	"enzyme acts on a number of other sugar phosphates, these reactions were shown to be substrates and were in the model

(glyc3p was not tested, but high activity was shown ot glyc1p and glyc2p, so the reaction G3PT was assigned to this gene)

sbt-d - not in network yet, but could be a signalling molecule (not sure of the source for this statement), so added this reaction
PMID: 15657928
AMF"	-2.35942	1.9257	[c] : h2o[c] + man6p[c] --> h[c] + man[c] + pi[c] 		
8894	MNLptspp	Yes	mannitol transport via PEP:Pyr PTS (periplasm)	mnl[p] + pep[c] --> mnl1p[c] + pyr[c]	"Transport, Inner Membrane"		( b3599  and  b2415  and  b2416 )			-10.1729	3.20748	[c] : mnl[p] + pep[c] --> mnl1p[c] + pyr[c] 		
9176	MNLtex	Yes	mannitol transport via diffusion (extracellular to periplasm)	mnl[e] <==> mnl[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : mnl[e] <==> mnl[p] 		
488	MNNH	No	D-mannonate hydrolyase	[c] : mana --> 2ddglcn + h2o	Alternate Carbon Metabolism	4.2.1.8	b4322			-9.58412	3.68395	[c] : mana[c] --> 2ddglcn[c] + h2o[c] 		
14041	MNt2pp	Yes	manganese (Mn+2) transport in via proton symport (periplasm)	h[p] + mn2[p] --> h[c] + mn2[c]	"Transport, Inner Membrane"		b2392	AMF	"see PMID: 11466284
AMF"	0	0	[c] : h[p] + mn2[p] --> h[c] + mn2[c] 		
14043	MNtex	Yes	Manganese (Mn+2) transport via diffusion (extracellular to periplasm)	mn2[e] <==> mn2[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : mn2[e] <==> mn2[p] 		
1852	MOAT	No	3-deoxy-D-manno-octulosonic acid transferase	[c] : ckdo + lipidA --> cmp + h + kdolipid4	Lipopolysaccharide Biosynthesis / Recycling		b3633	JLR- NH page 1043	"Core LPS biosynthesis
see PMID: 12045108
for review

see PMID: 11054112
for WaaA, WaaC and WaaF reactions 

ADP-D-mannose can also serve as a surrogate substrate for WaaC"	1.81043	8.1998	[c] : ckdo[c] + lipidA[c] --> cmp[c] + kdolipid4[c] 		
4686	MOAT2	No	3-deoxy-D-manno-octulosonic acid transferase	[c] : ckdo + kdolipid4 --> cmp + h + kdo2lipid4	Lipopolysaccharide Biosynthesis / Recycling		b3633	JLR- NH page 1043	"Core LPS biosynthesis
see PMID: 12045108
for review

see PMID: 11054112
for WaaA, WaaC and WaaF reactions 

ADP-D-mannose can also serve as a surrogate substrate for WaaC
"	2.6136	8.17534	[c] : ckdo[c] + kdolipid4[c] --> cmp[c] + kdo2lipid4[c] 		
13497	MOAT3C	Yes	3-deoxy-D-manno-octulosonic acid transferase III (LPS core biosynthesis)	[c] : ckdo + phphhlipa --> cmp + h + kphphhlipa	Lipopolysaccharide Biosynthesis / Recycling		b3624	AMF	"see review for the function of WaaZ and WaaS

WaaS is speculative
PMID: 12045108
AMF"	0.803173	2.08341	[c] : ckdo[c] + phphhlipa[c] --> cmp[c] + kphphhlipa[c] 		
9247	MOBDabcpp	Yes	molybdate transport via ABC system (periplasm)	atp[c] + h2o[c] + mobd[p] --> adp[c] + h[c] + mobd[c] + pi[c]	"Transport, Inner Membrane"		( b0763  and  b0764  and  b0765  and  b0760 )		"Transported Specific to molybdate and tungstate
PMID: 9545596
PMID: 9325422"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + mobd[p] --> adp[c] + h[c] + mobd[c] + pi[c] 		
9248	MOBDtex	Yes	molybdate transport via diffusion (extracellular to periplasm)	mobd[e] <==> mobd[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : mobd[e] <==> mobd[p] 		
2786	MOHMT	No	3-methyl-2-oxobutanoate hydroxymethyltransferase	[c] : 3mob + h2o + mlthf --> 2dhp + thf	Cofactor and Prosthetic Group Biosynthesis	2.1.2.11	b0134			-0.243247	6.99624	[c] : 3mob[c] + h2o[c] + mlthf[c] --> 2dhp[c] + thf[c] 		
12604	MPTG	Yes	murein polymerizing transglycosylase	(2) uaagmda[c] --> (2) h[c] + murein5p5p[p] + (2) udcpdp[c]	Murein Biosynthesis		( b0149  or  b3396  or  b2519 )	"AMF
this is formation makes a murein unit with a leading ester bond already assumed, so this unit would be in the middle of a chain"	"MrcA and MrcB (best characeterized) are bifunctional transglycosylase and transpeptidase forming enzymes
PMID: 3906031
together they are lethal for a double deletion
PMID: 10542235

MrdA and FtsI are part of the cell cycle proteins and are predicted to be DD-transpeptidases
PMID: 10542235
Also, pbpC is thought to be a transglycolase only

The MPTG is a gneral reaction to make a two unit murein polymer
AMF"	-13.1605	6.7426	[c] : (2) uaagmda[c] --> murein5p5p[p] + (2) udcpdp[c] 		
18720	MPTG2	Yes	murein polymerizing transglycosylase 2 (three linked units)	murein5p5p[p] + uaagmda[c] --> h[c] + murein5p5p5p[p] + udcpdp[c]	Murein Biosynthesis		( b3396  or  b0149  or  b2519 )	"AMF
this is formation makes a murein unit with a leading ester bond already assumed, so this unit would be in the middle of a chain"	"MrcA and MrcB (best characeterized) are bifunctional transglycosylase and transpeptidase forming enzymes
PMID: 3906031
together they are lethal for a double deletion
PMID: 10542235

MrdA and FtsI are part of the cell cycle proteins and are predicted to be DD-transpeptidases
PMID: 10542235
Also, pbpC is thought to be a transglycolase only

The MPTG is a gneral reaction to make a two unit murein polymer
AMF"	64.6012	6.26414	[c] : (3) h[c] + murein5p5p[p] + uaagmda[c] --> murein5p5p5p[p] + udcpdp[c] 		
12346	MSO3abcpp	Yes	methanesulfonate transport via ABC system (periplasm)	atp[c] + h2o[c] + mso3[p] --> adp[c] + h[c] + mso3[c] + pi[c]	Update		( b0936  and  b0933  and  b0934 )		"only the ssu transport system will transport this and L-cysteate, amoung others

L-cysteate not included since the degradation products are dead ends

see PMID: 11750815
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + mso3[p] --> adp[c] + h[c] + mso3[c] + pi[c] 		
12347	MSO3tex	Yes	methanesulfonate transport via diffusion (extracellular to periplasm)	mso3[e] <==> mso3[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : mso3[e] <==> mso3[p] 		
307	MTAN	No	methylthioadenosine nucleosidase	[c] : 5mta + h2o --> 5mtr + ade	Arginine and Proline Metabolism	3.2.2.16	b0159			-2.26379	3.60328	[c] : 5mta[c] + h2o[c] --> 5mtr[c] + ade[c] 		
7850	MTHFC	No	methenyltetrahydrofolate cyclohydrolase	[c] : h2o + methf <==> 10fthf + h	Folate Metabolism	3.5.4.9	b0529			-0.372697	6.79725	[c] : h2o[c] + methf[c] <==> 10fthf[c] + h[c] 		
7853	MTHFD	No	methylenetetrahydrofolate dehydrogenase (NADP)	[c] : mlthf + nadp <==> methf + nadph	Folate Metabolism	1.5.1.5	b0529			1.83443	5.49245	[c] : mlthf[c] + nadp[c] <==> methf[c] + nadph[c] 		
7856	MTHFR2	No	"5,10-methylenetetrahydrofolate reductase (NADH)"	[c] : (2) h + mlthf + nadh --> 5mthf + nad	Folate Metabolism		b3941	tv		-2.47829	7.47022	[c] : h[c] + mlthf[c] + nadh[c] --> 5mthf[c] + nad[c] 		
301	MTRI	No	5-methylthioribose-1-phosphate isomerase	[c] : 5mdr1p <==> 5mdru1p	Arginine and Proline Metabolism	5.3.1.23			"JLR- no gene was assigned
"	-0.375177	7.48292	[c] : 5mdr1p[c] <==> 5mdru1p[c] 		
300	MTRK	No	5-methylthioribose kinase	[c] : 5mtr + atp --> 5mdr1p + adp + h	Arginine and Proline Metabolism	2.7.1.100			JLR- no gene was assigned	-3.46855	2.28701	[c] : 5mtr[c] + atp[c] --> 5mdr1p[c] + adp[c] 		
12477	MTRPOX	Yes	N-methyltryptophan oxidase	[c] : Nmtrp + h2o + o2 --> fald + h2o2 + trp-L	Update	1.5.3.2	b1059	"AMF
PMID: 11170472"	"PMID: 11170472
AMF
enzyme proven, but physiological function has yet to be determined

there are more N-methyl amino acids that are substrates"	-19.64	2.92555	[c] : h2o[c] + Nmtrp[c] + o2[c] --> fald[c] + h2o2[c] + trp-L[c] 		
13624	N2Otex	Yes	nitrious oxide transport via diffusion (extracellular to periplasm)	n2o[e] <==> n2o[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : n2o[e] <==> n2o[p] 		
13623	N2Otpp	Yes	nitrious oxide transport (diffusion)	n2o[p] <==> n2o[c]	"Transport, Inner Membrane"			AMF	"assumed diffusion throught the inner membrane
AMF"	0	0	[c] : n2o[p] <==> n2o[c] 		
3313	NACODA	No	N-acetylornithine deacetylase	[c] : acg5sa + h2o --> ac + glu5sa	Arginine and Proline Metabolism		b3957	JLR		-3.36489	3.34628	[c] : acg5sa[c] + h2o[c] --> ac[c] + glu5sa[c] 		
9178	NACtex	Yes	Nicotinic acid transport via diffusion (extracellular to periplasm)	nac[e] <==> nac[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : nac[e] <==> nac[p] 		
8995	NACtpp	Yes	Nicotinic acid uptake (periplasm)	nac[p] --> nac[c]	"Transport, Inner Membrane"			JLR		0	0	[c] : nac[p] --> nac[c] 		
145	NADDP	No	NAD diphosphatase	[c] : h2o + nad --> amp + (2) h + nmn	Cofactor and Prosthetic Group Biosynthesis	3.6.1.22	( b2411  or  b3996 )	See also EC 3.6.1.9	"Lig is a DNA repair gene, so it would be assumed to be in the cytoplasm
AMF

for the nudC gene
PMID: 7829480
confirms the assignement of the NADDP activity,
not sure about the periplasmic location of the enzyme - so both were assigned
AMF"	-6.6688	3.75933	[c] : h2o[c] + nad[c] --> amp[c] + nmn[c] 		
8968	NADDPpp	Yes	NAD diphosphatase (periplasm)	[p] : h2o + nad --> amp + (2) h + nmn	Cofactor and Prosthetic Group Biosynthesis	3.6.1.22	b3996	JLR	"PMID: 7829480
confirms the assignement of the NADDP activity,
not sure about the periplasmic location of the enzyme - so both were assigned
AMF"	-6.6688	3.75933	[p] : h2o[p] + nad[p] --> amp[p] + nmn[p] 		
1975	NADH10	No	NADH dehydrogenase (menaquinone-8 & 0 protons)	[c] : h + mqn8 + nadh --> mql8 + nad	Oxidative Phosphorylation	1.6.5.3	b1109	JLR		-21.9658	17.5891	[c] : h[c] + mqn8[c] + nadh[c] --> mql8[c] + nad[c] 		
2943	NADH5	No	NADH dehydrogenase (ubiquinone-8 )	[c] : h + nadh + q8 --> nad + q8h2	Oxidative Phosphorylation	1.6.5.3	b1109	"JLR- added quinone specific reaction, q8"		-23.4177	21.6781	[c] : h[c] + nadh[c] + q8[c] --> nad[c] + q8h2[c] 		
8996	NADH6pp	Yes	NADH dehydrogenase (ubiquinone-8 & 3.5 protons) (periplasm)	(4.5) h[c] + nadh[c] + q8[c] --> (3.5) h[p] + nad[c] + q8h2[c]	Oxidative Phosphorylation	1.6.5.3	( b2276  and  b2277  and  b2278  and  b2279  and  b2280  and  b2281  and  b2282  and  b2283  and  b2284  and  b2285  and  b2286  and  b2287  and  b2288 )	JLR		-23.4177	21.6781	[c] : (4.5) h[c] + nadh[c] + q8[c] --> (3.5) h[p] + nad[c] + q8h2[c] 		
8997	NADH7pp	Yes	NADH dehydrogenase (menaquinone-8 & 2 protons) (periplasm)	(3) h[c] + mqn8[c] + nadh[c] --> (2) h[p] + mql8[c] + nad[c]	Oxidative Phosphorylation	1.6.5.3	( b2276  and  b2277  and  b2278  and  b2279  and  b2280  and  b2281  and  b2282  and  b2283  and  b2284  and  b2285  and  b2286  and  b2287  and  b2288 )	JLR		-21.9658	17.5891	[c] : (3) h[c] + mqn8[c] + nadh[c] --> (2) h[p] + mql8[c] + nad[c] 		
8998	NADH8pp	Yes	NADH dehydrogenase (demethylmenaquinone-8 & 2.8 protons) (periplasm)	2dmmq8[c] + (3.8) h[c] + nadh[c] --> 2dmmql8[c] + (2.8) h[p] + nad[c]	Oxidative Phosphorylation	1.6.5.3	( b2276  and  b2277  and  b2278  and  b2279  and  b2280  and  b2281  and  b2282  and  b2283  and  b2284  and  b2285  and  b2286  and  b2287  and  b2288 )	JLR		-16.8994	15.3444	[c] : 2dmmq8[c] + (3.8) h[c] + nadh[c] --> 2dmmql8[c] + (2.8) h[p] + nad[c] 		
1974	NADH9	No	NADH dehydrogenase (demethylmenaquinone-8 & 0 protons)	[c] : 2dmmq8 + h + nadh --> 2dmmql8 + nad	Oxidative Phosphorylation	1.6.5.3	b1109	JLR		-16.8994	15.3444	[c] : 2dmmq8[c] + h[c] + nadh[c] --> 2dmmql8[c] + nad[c] 		
33	NADK	No	NAD kinase	[c] : atp + nad --> adp + h + nadp	Cofactor and Prosthetic Group Biosynthesis	2.7.1.23	b2615		JLR- Gene is reassigned to yfjB	-3.46855	2.28701	[c] : atp[c] + nad[c] --> adp[c] + nadp[c] 		
171	NADN	Yes	NAD nucleosidase	[c] : h2o + nad --> adprib + h + ncam	Update	3.2.2.5			"reaction needed to generate adprib (ADP-ribose)
adp-ribose is known to be a substrate of the NudE (b3397) gene
PMID: 12135348
AMF"	0.438808	3.53906	[c] : h2o[c] + nad[c] --> adprib[c] + h[c] + ncam[c] 		
13774	NADPHQR2	Yes	NADPH Quinone Reductase (Ubiquinone-8)	[c] : h + nadph + q8 --> nadp + q8h2	Update	1.6.99.6	b3028	"AMF
PMID: 8611590"	"characterized in PMID: 8611590
Im not entirely sure of this physiological function in E coli and the specificity of the enzyme
AMF"	-23.4177	21.6781	[c] : h[c] + nadph[c] + q8[c] --> nadp[c] + q8h2[c] 		
13775	NADPHQR3	Yes	NADPH Quinone Reductase (Menaquinone-8)	[c] : h + mqn8 + nadph --> mql8 + nadp	Update	1.6.99.6	b3028	"AMF
PMID: 8611590"	"characterized in PMID: 8611590
Im not entirely sure of this physiological function in E coli and the specificity of the enzyme
AMF"	-21.9658	17.5891	[c] : h[c] + mqn8[c] + nadph[c] --> mql8[c] + nadp[c] 		
13776	NADPHQR4	Yes	NADPH Quinone Reductase (2-Demethylmenaquinone-8)	[c] : 2dmmq8 + h + nadph --> 2dmmql8 + nadp	Update	1.6.99.6	b3028	"AMF
PMID: 8611590"	"characterized in PMID: 8611590
Im not entirely sure of this physiological function in E coli and the specificity of the enzyme
AMF"	-16.8994	15.3444	[c] : 2dmmq8[c] + h[c] + nadph[c] --> 2dmmql8[c] + nadp[c] 		
811	NADPPPS	No	NADP phosphatase	[c] : h2o + nadp --> nad + pi	Cofactor and Prosthetic Group Biosynthesis					-3.54819	2.12947	[c] : h2o[c] + nadp[c] --> h[c] + nad[c] + pi[c] 		
3546	NADS1	No	NAD synthase (nh3)	[c] : atp + dnad + nh4 --> amp + h + nad + ppi	Cofactor and Prosthetic Group Biosynthesis	6.3.1.5	b1740			-3.90043	3.80694	[c] : atp[c] + dnad[c] + nh4[c] --> amp[c] + nad[c] + ppi[c] 		
9179	NADtex	Yes	NAD transport via diffusion (extracellular to periplasm)	nad[e] <==> nad[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : nad[e] <==> nad[p] 		
2912	NADTRHD	Yes	NAD transhydrogenase	[c] : nad + nadph --> nadh + nadp	Oxidative Phosphorylation		( b3962  or  ( b1602  and  b1603 ) )	changed from TEST_NADTRHD		0	0.5	[c] : nad[c] + nadph[c] --> nadh[c] + nadp[c] 		
1793	NAMNPP	No	nicotinic acid mononucleotide pyrophosphorylase	[c] : atp + h2o + nac + prpp --> adp + nicrnt + pi + ppi	Cofactor and Prosthetic Group Biosynthesis	2.4.2.11	b0931	JLR	"reports of it being in the periplasm

PMID: 2211655
Nicotinic acid phosphoribosyltransferase has been reported to be localized in the periplasm of E. coli (59), and we have accumulated a substantial amount of unpublished data with nicotinic acid mononucleotide- and NAD-overproducing E. coli mutants which also suggest a periplasmic or cytoplasmic membrane localization of nicotinic acid phosphoribosyltransferase. If the enzyme is in fact located in the periplasm, it is apparently not processed as it is transferred across the cytoplasmic membrane.

The enzyme also uses ATP, which may not be in periplasm

"	-11.3917	4.42037	[c] : atp[c] + h2o[c] + nac[c] + prpp[c] --> adp[c] + nicrnt[c] + pi[c] + ppi[c] 					
8896	NAt3_1.5pp	Yes	sodium proton antiporter (H:NA is 1.5) (periplasm)	(3) h[p] + (2) na1[c] --> (3) h[c] + (2) na1[p]	"Transport, Inner Membrane"		b1186	JLR		0	0	[c] : (3) h[p] + (2) na1[c] --> (3) h[c] + (2) na1[p] 					
8895	NAt3_1pp	Yes	sodium proton antiporter (H:NA is 1:1) (periplasm)	h[p] + na1[c] <==> h[c] + na1[p]	"Transport, Inner Membrane"		b1216	JLR	JLR - not sure about how many protons	0	0	[c] : h[p] + na1[c] <==> h[c] + na1[p] 					
8897	NAt3_2pp	Yes	sodium proton antiporter (H:NA is 2) (periplasm)	(2) h[p] + na1[c] --> (2) h[c] + na1[p]	"Transport, Inner Membrane"		b0019	JLR		0	0	[c] : (2) h[p] + na1[c] --> (2) h[c] + na1[p] 					
9177	NAtex	Yes	sodium transport via diffusion (extracellular to periplasm)	na1[e] <==> na1[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : na1[e] <==> na1[p] 					
2816	NDPK1	No	nucleoside-diphosphate kinase (ATP:GDP)	[c] : atp + gdp <==> adp + gtp	Nucleotide Salvage Pathway	2.7.4.6	( b2518  or  b0474 )	"Many nucleoside diphosphates (eight described) can act as acceptors. 
While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions."	"Adk can substritute for Ndk activity 
PMID: 8650159
and PMID: 16297370
may be able to act on other nucleotides (XTP, ITP, but these were not specifically mentioned)
AMF"	0	0.5	[c] : atp[c] + gdp[c] <==> adp[c] + gtp[c] 					
190	NDPK2	No	nucleoside-diphosphate kinase (ATP:UDP)	[c] : atp + udp <==> adp + utp	Nucleotide Salvage Pathway	2.7.4.6	( b2518  or  b0474 )	"Many nucleoside diphosphates (eight described) can act as acceptors. 
While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions."	"Adk can substritute for Ndk activity 
PMID: 8650159
and PMID: 16297370
may be able to act on other nucleotides (XTP, ITP, but these were not specifically mentioned)
AMF"	0	0.5	[c] : atp[c] + udp[c] <==> adp[c] + utp[c] 					
191	NDPK3	No	nucleoside-diphosphate kinase (ATP:CDP)	[c] : atp + cdp <==> adp + ctp	Nucleotide Salvage Pathway	2.7.4.6	( b2518  or  b0474 )	"Many nucleoside diphosphates (eight described) can act as acceptors. 
While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions."	"Adk can substritute for Ndk activity 
PMID: 8650159
and PMID: 16297370
may be able to act on other nucleotides (XTP, ITP, but these were not specifically mentioned)
AMF"	0	0.5	[c] : atp[c] + cdp[c] <==> adp[c] + ctp[c] 					
192	NDPK4	No	nucleoside-diphosphate kinase (ATP:dTDP)	[c] : atp + dtdp <==> adp + dttp	Nucleotide Salvage Pathway	2.7.4.6	( b2518  or  b0474 )	"Many nucleoside diphosphates (eight described) can act as acceptors. 
While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions."	"Adk can substritute for Ndk activity 
PMID: 8650159
and PMID: 16297370
may be able to act on other nucleotides (XTP, ITP, but these were not specifically mentioned)
AMF"	0	0.5	[c] : atp[c] + dtdp[c] <==> adp[c] + dttp[c] 					
443	NDPK5	No	nucleoside-diphosphate kinase (ATP:dGDP)	[c] : atp + dgdp <==> adp + dgtp	Nucleotide Salvage Pathway	2.7.4.6	( b2518  or  b0474 )	"Many nucleoside diphosphates (eight described) can act as acceptors. 
While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions."	"Adk can substritute for Ndk activity 
PMID: 8650159
and PMID: 16297370
may be able to act on other nucleotides (XTP, ITP, but these were not specifically mentioned)
AMF"	0	0.5	[c] : atp[c] + dgdp[c] <==> adp[c] + dgtp[c] 					
132	NDPK6	No	nucleoside-diphosphate kinase (ATP:dUDP)	[c] : atp + dudp <==> adp + dutp	Nucleotide Salvage Pathway	2.7.4.6	( b2518  or  b0474 )	"Many nucleoside diphosphates (eight described) can act as acceptors. 
While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions."	"Adk can substritute for Ndk activity 
PMID: 8650159
and PMID: 16297370
may be able to act on other nucleotides (XTP, ITP, but these were not specifically mentioned)
AMF"	0	0.5	[c] : atp[c] + dudp[c] <==> adp[c] + dutp[c] 					
2801	NDPK7	No	nucleoside-diphosphate kinase (ATP:dCDP)	[c] : atp + dcdp <==> adp + dctp	Nucleotide Salvage Pathway	2.7.4.6	( b2518  or  b0474 )	"Many nucleoside diphosphates (eight described) can act as acceptors. 
While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions."	"Adk can substritute for Ndk activity 
PMID: 8650159
and PMID: 16297370
may be able to act on other nucleotides (XTP, ITP, but these were not specifically mentioned)
AMF"	0	0.5	[c] : atp[c] + dcdp[c] <==> adp[c] + dctp[c] 					
133	NDPK8	No	nucleoside-diphosphate kinase (ATP:dADP)	[c] : atp + dadp <==> adp + datp	Nucleotide Salvage Pathway	2.7.4.6	( b2518  or  b0474 )	"Many nucleoside diphosphates (eight described) can act as acceptors. 
While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions."	"Adk can substritute for Ndk activity 
PMID: 8650159
and PMID: 16297370
may be able to act on other nucleotides (XTP, ITP, but these were not specifically mentioned)
AMF"	0	0.5	[c] : atp[c] + dadp[c] <==> adp[c] + datp[c] 					
9180	NH4tex	Yes	ammonia transport via diffusion (extracellular to periplasm)	nh4[e] <==> nh4[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : nh4[e] <==> nh4[p] 					
8898	NH4tpp	Yes	ammonia reversible transport (periplasm)	nh4[p] <==> nh4[c]	"Transport, Inner Membrane"		b0451	NCD	"States that AmtB acts as a slowly conducting channel for NH3 that is neither dependent on the
membrane potential nor on ATP.

Also states that it has a binding site for nh4.

After reading, I think that it transfers nh4, but dosnt outright say it transports in the nh3 form.  there is an apparent equilibrim between nh3<=> nh4
PMID: 15876187
AMF"	0	0	[c] : nh4[p] <==> nh4[c] 					
13622	NHFRBO	Yes	NADH:flavorubredoxin oxidoreductase	[c] : h + nadh + (2) no --> h2o + n2o + nad	Update		( b2710  and  b2711 )	"AMF
not sure of reaction stoichiometry, some details are mentioned in PMID: 11751865"	"Not entirely sure of the reaction stoichiometry or the exact necessity of both genes

PMID: 11751865 gives probably products and reactants

PMID: 12529359 speaks more about the different NO defense mechanisms and regulation

AMF"	No energy	No energy	[c] : h[c] + nadh[c] + (2) no[c] --> h2o[c] + n2o[c] + nad[c] 					
13672	NI2abcpp	Yes	Nickle (Ni+2) ABC transporter (periplasm)	atp[c] + h2o[c] + ni2[c] --> adp[c] + h[c] + ni2[p] + pi[c]	"Transport, Inner Membrane"		b3469	AMF	"characterized in PMID: 10660539
ATP-dependent efflux
The activity was specific for Pb(II), Cd(II), Zn(II), and Hg(II), with the highest activity obtained when the metals were present as thiolate complexes of cysteine or glutathione.

from transportDB:
 Zn2+-, Cd2+-, Co2+-, Hg2+-, Ni2+-, Cu2+, Pb2+-ATPase (efflux) (Hou and Mitra, 2003) for ecoli

http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=3.A.3
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + ni2[c] --> adp[c] + h[c] + ni2[p] + pi[c] 		
9251	NI2tex	Yes	nickel transport via diffusion (extracellular to periplasm)	ni2[e] <==> ni2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ni2[e] <==> ni2[p] 		
13667	NI2tpp	Yes	nickel transport in/out via permease (no H+)	ni2[p] <==> ni2[c]	"Transport, Inner Membrane"		b3816		"The CorA permeases of S. typhimurium and E. coli mediate both influx and efflux of Mg2+. They transport Mg2+, Co2+ and Ni2+ but not Fe2+ (Papp and Maguire, 2004).

transport DB

http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=1.A.35

AMF"	0	0	[c] : ni2[p] <==> ni2[c] 		
9250	NI2uabcpp	Yes	"nickel transport via ABC system (uptake, periplasm)"	atp[c] + h2o[c] + ni2[p] --> adp[c] + h[c] + ni2[c] + pi[c]	"Transport, Inner Membrane"		( ( b3476  and  b3477  and  b3478  and  b3479  and  b3480 )  or  b4242 )		"PMID: 7867647
Other metals (cobalt, copper, iron) are bound at least 10-fold less tightly
Biosynthesis of NikA occurred only under anaerobic conditions and was dependent on the general anaerobic regulator FNR


from transportDB,
Mg2+/Ni2+-ATPase (uptake) MgtA
http://www.tcdb.org/tcdb/tcfamilybrowse.php?tcname=3.A.3

also from PMID: 9622348

AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + ni2[p] --> adp[c] + h[c] + ni2[c] + pi[c] 		
146	NMNAT	No	nicotinamide-nucleotide adenylyltransferase	[c] : atp + h + nmn --> nad + ppi	Cofactor and Prosthetic Group Biosynthesis	2.7.7.1	( b4390  or  b0639 )		nadD prefers nicrnt over nmn 20:1	-1.92466	3.75933	[c] : atp[c] + nmn[c] --> nad[c] + ppi[c] 		
3314	NMNDA	No	nicotinamide-nucleotide amidase	[c] : h2o + nmn --> nh4 + nicrnt	Cofactor and Prosthetic Group Biosynthesis	3.5.1.42				-4.69304	2.95123	[c] : h2o[c] + nmn[c] --> nh4[c] + nicrnt[c] 		
147	NMNN	No	NMN nucleosidase	[c] : h2o + nmn --> h + ncam + r5p	Cofactor and Prosthetic Group Biosynthesis	3.2.2.14				-1.55314	3.5987	[c] : h2o[c] + nmn[c] --> h[c] + ncam[c] + r5p[c] 		
8899	NMNPtpp	Yes	NMN permease (periplasm)	nmn[p] --> nmn[c]	"Transport, Inner Membrane"		b0751	JLR		0	0	[c] : nmn[p] --> nmn[c] 		
8999	NMNt7pp	Yes	NMN transport via NMN glycohydrolase (periplasm)	h2o[c] + nmn[p] --> h[c] + ncam[c] + r5p[c]	"Transport, Inner Membrane"	3.2.2.14		JLR	JLR- not sure if the glycohydrolase activity actually transports the ncam.	-1.55314	3.5987	[c] : h2o[c] + nmn[p] --> h[c] + ncam[c] + r5p[c] 		
9181	NMNtex	Yes	NMN transport via diffusion (extracellular to periplasm)	nmn[e] <==> nmn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : nmn[e] <==> nmn[p] 		
3315	NNAM	No	nicotinamidase	[c] : h2o + ncam --> nac + nh4	Cofactor and Prosthetic Group Biosynthesis	3.5.1.19	b1768			-4.69304	2.95123	[c] : h2o[c] + ncam[c] --> nac[c] + nh4[c] 		
6171	NNATr	Yes	nicotinate-nucleotide adenylyltransferase	[c] : atp + h + nicrnt <==> dnad + ppi	Update	2.7.7.18	b0639	JLR	nadD prefers nicrnt over nmn 20:1	-1.92466	3.75933	[c] : atp[c] + nicrnt[c] <==> dnad[c] + ppi[c] 		
2451	NNDMBRT	No	Nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase	[c] : dmbzid + nicrnt --> 5prdmbz + h + nac	Cofactor and Prosthetic Group Biosynthesis		b1991	JLR (Kegg R04148)	PMID: 7592411	0.710659	4.75459	[c] : dmbzid[c] + nicrnt[c] --> 5prdmbz[c] + h[c] + nac[c] 		
2769	NNDPR	No	nicotinate-nucleotide diphosphorylase (carboxylating)	[c] : (2) h + prpp + quln --> co2 + nicrnt + ppi	Cofactor and Prosthetic Group Biosynthesis	2.4.2.19	b0109			-10.6366	4.72926	[c] : (2) h[c] + prpp[c] + quln[c] --> co2[c] + nicrnt[c] + ppi[c] 		
8900	NO2t2rpp	Yes	"nitrite transport in via proton symport, reversible (periplasm)"	h[p] + no2[p] <==> h[c] + no2[c]	"Transport, Inner Membrane"		( b3367  or  b1223 )	JLR	"JLR- the actual reactions are not for narK,narU and nirC are not known."	0	0	[c] : h[p] + no2[p] <==> h[c] + no2[c] 		
9182	NO2tex	Yes	nitrite transport via diffusion (extracellular to periplasm)	no2[e] <==> no2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : no2[e] <==> no2[p] 		
9001	NO3R1bpp	Yes	Nitrate reductase (Ubiquinol-8)	no3[p] + q8h2[c] --> h2o[p] + no2[p] + q8[c]	Update	1.7.99.4	( ( b2203  and  b2206 )  and  b2202  and  b2205  and  b2204 )	JLR (assumed h2o is by-product)	Simon reference indicates that they don't believe the nitrate reductase generates a proton gradient (page 304)	No energy	No energy	[c] : no3[p] + q8h2[c] --> h2o[p] + no2[p] + q8[c] 					
9000	NO3R1pp	Yes	Nitrate reductase (Ubiquinol-8) (periplasm)	(2) h[c] + no3[c] + q8h2[c] --> (2) h[p] + h2o[c] + no2[c] + q8[c]	Oxidative Phosphorylation	1.7.99.4	( ( b1224  and  b1225  and  b1226  and  b1227 )  or  ( b1465  and  b1466  and  b1467  and  b1468 ) )	JLR (assumed h2o is by-product)	"characetrized in citation

NarZYWV was added as the same function as NarGHIJ"	No energy	No energy	[c] : (2) h[c] + no3[c] + q8h2[c] --> (2) h[p] + h2o[c] + no2[c] + q8[c] 					
9004	NO3R2bpp	Yes	Nitrate reductase (Menaquinol-8) (periplasm)	mql8[c] + no3[p] --> h2o[p] + mqn8[c] + no2[p]	Update	1.7.99.4	( ( b2203  and  b2206 )  and  b2202 )	JLR (assumed h2o is by-product)	Simon reference indicates that they don't believe the nitrate reductase generates a proton gradient (page 304)	No energy	No energy	[c] : mql8[c] + no3[p] --> h2o[p] + mqn8[c] + no2[p] 					
9002	NO3R2pp	Yes	Nitrate reductase (Menaquinol-8) (periplasm)	(2) h[c] + mql8[c] + no3[c] --> (2) h[p] + h2o[c] + mqn8[c] + no2[c]	Oxidative Phosphorylation		( ( b1224  and  b1225  and  b1226  and  b1227 )  or  ( b1465  and  b1466  and  b1467  and  b1468 ) )	JLR (assumed h2o is by-product)	"characetrized in citation

NarZYWV was added as the same function as NarGHIJ"	No energy	No energy	[c] : (2) h[c] + mql8[c] + no3[c] --> (2) h[p] + h2o[c] + mqn8[c] + no2[c] 					
8901	NO3t7pp	Yes	nitrate transport in via nitrite antiport (periplasm)	no2[c] + no3[p] --> no2[p] + no3[c]	"Transport, Inner Membrane"		( b1223  or  b1469 )	JLR	"JLR- the actual reactions are not for narK,narU and nirC are not known.

MKA - Cole paper:  NarKec primarily Nitrate/Nitrite antiporter"	0	0	[c] : no2[c] + no3[p] --> no2[p] + no3[c] 					
9183	NO3tex	Yes	nitrate transport via diffusion (extracellular to periplasm)	no3[e] <==> no3[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : no3[e] <==> no3[p] 					
13619	NODOx	Yes	nitric oxide dioxygenase	[c] : nadh + (2) no + (2) o2 --> h + nad + (2) no3	Update	1.14.12.17	b2552	AMF	"see PMID: 15667299
for review and formula for the reaction
AMF"	No energy	No energy	[c] : nadh[c] + (2) no[c] + (2) o2[c] --> h[c] + nad[c] + (2) no3[c] 					
13618	NODOy	Yes	nitric oxide dioxygenase	[c] : nadph + (2) no + (2) o2 --> h + nadp + (2) no3	Update	1.14.12.17	b2552	AMF	"see PMID: 15667299
for review and formula for the reaction
AMF"	No energy	No energy	[c] : nadph[c] + (2) no[c] + (2) o2[c] --> h[c] + nadp[c] + (2) no3[c] 					
13620	NOtex	Yes	nitric oxide transport via diffusion (extracellular to periplasm)	no[e] <==> no[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : no[e] <==> no[p] 					
13621	NOtpp	Yes	NO transport (diffusion)	no[p] <==> no[c]	"Transport, Inner Membrane"			AMF	"assumed diffusion, inner membrane"	0	0	[c] : no[p] <==> no[c] 					
41	NPHS	No	naphthoate synthase	[c] : sbzcoa --> coa + dhna	Cofactor and Prosthetic Group Biosynthesis	4.1.3.36	b2262			-13.677	11.5999	[c] : sbzcoa[c] --> coa[c] + dhna[c] 					
2697	NTD1	No	5'-nucleotidase (dUMP)	[c] : dump + h2o --> duri + pi	Nucleotide Salvage Pathway	3.1.3.5	( b2291  or  b4374  or  b2744 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : dump[c] + h2o[c] --> duri[c] + h[c] + pi[c] 					
175	NTD10	No	5'-nucleotidase (XMP)	[c] : h2o + xmp --> pi + xtsn	Update	3.1.3.5	b2744	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : h2o[c] + xmp[c] --> h[c] + pi[c] + xtsn[c] 					
12217	NTD10pp	Yes	5'-nucleotidase (XMP)	[p] : h2o + xmp --> pi + xtsn	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	reaction located in periplasm	-2.35942	1.9257	[p] : h2o[p] + xmp[p] --> h[p] + pi[p] + xtsn[p] 					
176	NTD11	No	5'-nucleotidase (IMP)	[c] : h2o + imp --> ins + pi	Update	3.1.3.5	b2744	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : h2o[c] + imp[c] --> h[c] + ins[c] + pi[c] 					
12218	NTD11pp	Yes	5'-nucleotidase (IMP)	[p] : h2o + imp --> ins + pi	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	reaction located in periplasm	-2.35942	1.9257	[p] : h2o[p] + imp[p] --> h[p] + ins[p] + pi[p] 					
10419	NTD12	Yes	5'-nucleotidase (dIMP)	[c] : dimp + h2o --> din + pi	Update	3.1.3.5	( b2291  or  b2744 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-6.941	6.52918	[c] : dimp[c] + h2o[c] --> din[c] + (2) h[c] + pi[c] 		
12354	NTD12pp	Yes	5'-nucleotidase (dIMP) (periplasm)	[p] : dimp + h2o --> din + pi	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	reaction located in periplasm	-6.941	6.52918	[p] : dimp[p] + h2o[p] --> din[p] + (2) h[p] + pi[p] 		
12219	NTD1pp	Yes	5'-nucleotidase (dUMP)	[p] : dump + h2o --> duri + pi	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31
"	reaction located in periplasm	-2.35942	1.9257	[p] : dump[p] + h2o[p] --> duri[p] + h[p] + pi[p] 		
448	NTD2	No	5'-nucleotidase (UMP)	[c] : h2o + ump --> pi + uri	Nucleotide Salvage Pathway	3.1.3.5	( b4374  or  b2744 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : h2o[c] + ump[c] --> h[c] + pi[c] + uri[c] 		
12220	NTD2pp	Yes	5'-nucleotidase (UMP)	[p] : h2o + ump --> pi + uri	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31
"	reaction located in periplasm	-2.35942	1.9257	[p] : h2o[p] + ump[p] --> h[p] + pi[p] + uri[p] 		
449	NTD3	No	5'-nucleotidase (dCMP)	[c] : dcmp + h2o --> dcyt + pi	Nucleotide Salvage Pathway	3.1.3.5	( b2291  or  b2744 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : dcmp[c] + h2o[c] --> dcyt[c] + h[c] + pi[c] 		
12221	NTD3pp	Yes	5'-nucleotidase (dCMP)	[p] : dcmp + h2o --> dcyt + pi	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31
"	reaction located in periplasm	-2.35942	1.9257	[p] : dcmp[p] + h2o[p] --> dcyt[p] + h[p] + pi[p] 		
450	NTD4	No	5'-nucleotidase (CMP)	[c] : cmp + h2o --> cytd + pi	Update	3.1.3.5	b2744	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : cmp[c] + h2o[c] --> cytd[c] + h[c] + pi[c] 		
12222	NTD4pp	Yes	5'-nucleotidase (CMP)	[p] : cmp + h2o --> cytd + pi	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31
"	reaction located in periplasm	-2.35942	1.9257	[p] : cmp[p] + h2o[p] --> cytd[p] + h[p] + pi[p] 		
451	NTD5	No	5'-nucleotidase (dTMP)	[c] : dtmp + h2o --> pi + thymd	Nucleotide Salvage Pathway	3.1.3.5	( b2291  or  b4374  or  b2744 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : dtmp[c] + h2o[c] --> h[c] + pi[c] + thymd[c] 		
12223	NTD5pp	Yes	5'-nucleotidase (dTMP)	[p] : dtmp + h2o --> pi + thymd	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	reaction located in periplasm	-2.35942	1.9257	[p] : dtmp[p] + h2o[p] --> h[p] + pi[p] + thymd[p] 		
452	NTD6	No	5'-nucleotidase (dAMP)	[c] : damp + h2o --> dad-2 + pi	Nucleotide Salvage Pathway	3.1.3.5	( b2291  or  b2744 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : damp[c] + h2o[c] --> dad-2[c] + h[c] + pi[c] 		
12224	NTD6pp	Yes	5'-nucleotidase (dAMP)	[p] : damp + h2o --> dad-2 + pi	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31
"	reaction located in periplasm	-2.35942	1.9257	[p] : damp[p] + h2o[p] --> dad-2[p] + h[p] + pi[p] 		
2698	NTD7	No	5'-nucleotidase (AMP)	[c] : amp + h2o --> adn + pi	Nucleotide Salvage Pathway	3.1.3.5	b2744	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : amp[c] + h2o[c] --> adn[c] + h[c] + pi[c] 		
12225	NTD7pp	Yes	5'-nucleotidase (AMP)	[p] : amp + h2o --> adn + pi	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	reaction located in periplasm	-2.35942	1.9257	[p] : amp[p] + h2o[p] --> adn[p] + h[p] + pi[p] 		
453	NTD8	No	5'-nucleotidase (dGMP)	[c] : dgmp + h2o --> dgsn + pi	Nucleotide Salvage Pathway	3.1.3.5	( b2291  or  b2744 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : dgmp[c] + h2o[c] --> dgsn[c] + h[c] + pi[c] 		
9815	NTD8pp	Yes	5'-nucleotidase (dGMP)	[p] : dgmp + h2o --> dgsn + pi	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31
KC"	reaction located in periplasm	-2.35942	1.9257	[p] : dgmp[p] + h2o[p] --> dgsn[p] + h[p] + pi[p] 		
174	NTD9	No	5'-nucleotidase (GMP)	[c] : gmp + h2o --> gsn + pi	Nucleotide Salvage Pathway	3.1.3.5	b2744	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	-2.35942	1.9257	[c] : gmp[c] + h2o[c] --> gsn[c] + h[c] + pi[c] 		
12226	NTD9pp	Yes	5'-nucleotidase (GMP)	[p] : gmp + h2o --> gsn + pi	Update	3.1.3.5	( b0480  or  b4055 )	"Wide specificity for 5'-nucleotides
Also see EC 3.1.3.31
"	reaction located in periplasm	-2.35942	1.9257	[p] : gmp[p] + h2o[p] --> gsn[p] + h[p] + pi[p] 		
745	NTP1	Yes	nucleoside-triphosphatase (ATP)	[c] : atp + h2o --> adp + h + pi	Update	3.6.1.15	( b0650  or  b4161 )		"PMID: 12183460
AMF

also,
from PMID: 12220175
YjeQ exhibits GTPase activity and also exhibits activity toward ATP, ITP, and CTP.

from PMID: 14973029
YjeQ is essential for growth and seems to interact with the ribosome

see also, PMID: 15466596
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] --> adp[c] + h[c] + pi[c] 		
14010	NTP10	Yes	nucleoside-triphosphatase (ITP)	[c] : h2o + itp --> h + idp + pi	Update	3.6.1.15	( b4161  or  b4394 )		"from PMID: 12220175
YjeQ exhibits GTPase activity and also exhibits activity toward ATP, ITP, and CTP.

from PMID: 14973029
YjeQ is essential for growth and seems to interact with the ribosome

see also, PMID: 15466596
AMF

YjjX association, see PMID: 16216582
acts on ITP, dITP, XTP
From personal communication with Author,  Zongchao Jia <jia@post.queensu.ca>: ""We know there is Pi generated but there are two possibilities - one is a single Pi cleaved; another is after first Pi is cleaved the second Pi gets cleaved as well. We simply don't know. But I guess some sort of HPLC/MS analysis of the products would clarify the situation.""
AMF
"	-7.01673	1.48181	[c] : h2o[c] + itp[c] --> h[c] + idp[c] + pi[c] 		
19556	NTP11	Yes	nucleoside-triphosphatase (dITP)	[c] : ditp + h2o --> didp + h + pi	Update	3.6.1.15	b4394		"YjjX association, see PMID: 16216582
acts on ITP, dITP, XTP
From personal communication with Author,  Zongchao Jia <jia@post.queensu.ca>: ""We know there is Pi generated but there are two possibilities - one is a single Pi cleaved; another is after first Pi is cleaved the second Pi gets cleaved as well. We simply don't know. But I guess some sort of HPLC/MS analysis of the products would clarify the situation.""
AMF"	-7.01673	1.48181	[c] : ditp[c] + h2o[c] --> didp[c] + h[c] + pi[c] 		
19555	NTP12	Yes	nucleoside-triphosphatase (XTP)	[c] : h2o + xtp --> h + pi + xdp	Update	3.6.1.15	b4394		"YjjX association, see PMID: 16216582
acts on ITP, dITP, XTP
From personal communication with Author,  Zongchao Jia <jia@post.queensu.ca>: ""We know there is Pi generated but there are two possibilities - one is a single Pi cleaved; another is after first Pi is cleaved the second Pi gets cleaved as well. We simply don't know. But I guess some sort of HPLC/MS analysis of the products would clarify the situation.""
AMF"	-7.01673	1.48181	[c] : h2o[c] + xtp[c] --> h[c] + pi[c] + xdp[c] 		
748	NTP3	Yes	nucleoside-triphosphatase (GTP)	[c] : gtp + h2o --> gdp + h + pi	Update	3.6.1.15	b4161		"from PMID: 12220175
YjeQ exhibits GTPase activity and also exhibits activity toward ATP, ITP, and CTP.

from PMID: 14973029
YjeQ is essential for growth and seems to interact with the ribosome

see also, PMID: 15466596
AMF"	-7.01673	1.48181	[c] : gtp[c] + h2o[c] --> gdp[c] + h[c] + pi[c] 		
9005	NTP3pp	Yes	nucleoside-triphosphatase (GTP) (periplasm)	[p] : gtp + h2o --> gdp + h + pi	Update	3.6.1.15	b0980		"Enzyme also acts on 2,3-bisphosphoglycerate. Periplasmic enzyme"	-7.01673	1.48181	[p] : gtp[p] + h2o[p] --> gdp[p] + h[p] + pi[p] 		
749	NTP5	Yes	nucleoside-triphosphatase (CTP)	[c] : ctp + h2o --> cdp + h + pi	Update	3.6.1.15	b4161		"from PMID: 12220175
YjeQ exhibits GTPase activity and also exhibits activity toward ATP, ITP, and CTP.

from PMID: 14973029
YjeQ is essential for growth and seems to interact with the ribosome

see also, PMID: 15466596
AMF"	-7.01673	1.48181	[c] : ctp[c] + h2o[c] --> cdp[c] + h[c] + pi[c] 		
1629	NTPP1	No	Nucleoside triphosphate pyrophosphorylase (dgtp)	[c] : dgtp + h2o --> dgmp + h + ppi	Nucleotide Salvage Pathway		( b2781  or  b0099 )	JLR	JLR-  (JSE model had it as removing 3 PI)	-8.59346	2.5066	[c] : dgtp[c] + h2o[c] --> dgmp[c] + ppi[c] 		
9745	NTPP10	Yes	Nucleoside triphosphate pyrophosphorylase (ditp)	[c] : ditp + h2o --> dimp + h + ppi	Update	3.6.1.19	b2954		"RdgB
enzyme acts on ipt, ditp, and xtp to remove them from the nuclueotide pools
PMID: 12297000
PMID: 12791149
AMF

this enxyme is not YhgN"	-4.01188	6.68618	[c] : ditp[c] + h[c] + h2o[c] --> dimp[c] + ppi[c] 		
9747	NTPP11	Yes	Nucleoside triphosphate pyrophosphorylase (xtp)	[c] : h2o + xtp --> h + ppi + xmp	Update	3.6.1.19	b2954	JLR; IT	"RdgB
enzyme acts on ipt, ditp, and xtp to remove them from the nuclueotide pools
PMID: 12297000
PMID: 12791149
AMF

this enxyme is not YhgN"	-8.59346	2.5066	[c] : h2o[c] + xtp[c] --> ppi[c] + xmp[c] 		
1632	NTPP2	No	Nucleoside triphosphate pyrophosphorylase (gtp)	[c] : gtp + h2o --> gmp + h + ppi	Nucleotide Salvage Pathway		( b2781  or  b0099 )	JLR	JLR-  (JSE model had it as removing 3 PI)	-8.59346	2.5066	[c] : gtp[c] + h2o[c] --> gmp[c] + ppi[c] 		
2411	NTPP3	No	Nucleoside triphosphate pyrophosphorylase (dctp)	[c] : dctp + h2o --> dcmp + h + ppi	Nucleotide Salvage Pathway		( b2781  or  b1759 )	JLR	"NudG has been characterized a number of times to act on altered CTP derivatives so that they are not incorporated into DNA
PMID: 12509230
PMID: 11676470
PMID: 11053429

AMF"	-8.59346	2.5066	[c] : dctp[c] + h2o[c] --> dcmp[c] + ppi[c] 		
2410	NTPP4	No	Nucleoside triphosphate pyrophosphorylase (ctp)	[c] : ctp + h2o --> cmp + h + ppi	Nucleotide Salvage Pathway		( b2781  or  b1759 )	JLR	"NudG has been characterized a number of times to act on altered CTP derivatives so that they are not incorporated into DNA
PMID: 12509230
PMID: 11676470
PMID: 11053429

AMF"	-8.59346	2.5066	[c] : ctp[c] + h2o[c] --> cmp[c] + ppi[c] 		
2409	NTPP5	No	Nucleoside triphosphate pyrophosphorylase (datp)	[c] : datp + h2o --> damp + h + ppi	Nucleotide Salvage Pathway		b2781	JLR		-8.59346	2.5066	[c] : datp[c] + h2o[c] --> damp[c] + ppi[c] 					
2412	NTPP6	No	Nucleoside triphosphate pyrophosphorylase (atp)	[c] : atp + h2o --> amp + h + ppi	Nucleotide Salvage Pathway		b2781	JLR		-8.59346	2.5066	[c] : atp[c] + h2o[c] --> amp[c] + ppi[c] 					
2413	NTPP7	No	Nucleoside triphosphate pyrophosphorylase (dttp)	[c] : dttp + h2o --> dtmp + h + ppi	Nucleotide Salvage Pathway		b2781	JLR		-8.59346	2.5066	[c] : dttp[c] + h2o[c] --> dtmp[c] + ppi[c] 					
2414	NTPP8	No	Nucleoside triphosphate pyrophosphorylase (utp)	[c] : h2o + utp --> h + ppi + ump	Nucleotide Salvage Pathway		b2781	JLR		-8.59346	2.5066	[c] : h2o[c] + utp[c] --> ppi[c] + ump[c] 					
9738	NTPP9	Yes	Nucleoside triphosphate pyrophosphorylase (itp)	[c] : h2o + itp --> h + imp + ppi	Update	3.6.1.19	b2954	JLR; IT	"RdgB
enzyme acts on ipt, ditp, and xtp to remove them from the nuclueotide pools
PMID: 12297000
PMID: 12791149
AMF

this enzyme is not YhgN"	-8.59346	2.5066	[c] : h2o[c] + itp[c] --> imp[c] + ppi[c] 					
1633	NTPTP1	No	Nucleoside triphosphate tripolyhydrolase	[c] : dgtp + h2o --> dgsn + pppi	Nucleotide Salvage Pathway	3.1.5.1	b0160	JLR	JLR- (JSE had 3 PI instead of PPPI)	No energy	No energy	[c] : dgtp[c] + h2o[c] --> dgsn[c] + h[c] + pppi[c] 					
1634	NTPTP2	No	Nucleoside triphosphate tripolyhydrolase	[c] : gtp + h2o --> gsn + pppi	Nucleotide Salvage Pathway	3.1.5.1	b0160	JLR	JLR- (JSE had 3 PI instead of PPPI)	No energy	No energy	[c] : gtp[c] + h2o[c] --> gsn[c] + h[c] + pppi[c] 					
3548	NTRIR2x	No	nitrite Reductase (NADH)	[c] : (5) h + (3) nadh + no2 --> (2) h2o + (3) nad + nh4	Oxidative Phosphorylation		( b3365  and  b3366 )	"JLR (assumed hydroxide anion and h come together to make water, EC 1.7.1.4)"		-91.9627	12.3333	[c] : (5) h[c] + (3) nadh[c] + no2[c] --> (2) h2o[c] + (3) nad[c] + nh4[c] 					
13756	NTRIR3pp	Yes	"nitrite Reductase (Ubiquinole-8, periplasm)"	(2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c]	Update		( b4070  and  b4071  and  b4072  and  b4073 )	AMF	"reaction taken from PMID:
low nitrate in the environment NrfA is made; with high nitrate NirB is made almost exclusively. PMID: 11004182
AMF"	-21.7095	63.9166	[c] : (2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c] 					
13757	NTRIR4pp	Yes	"nitrite Reductase (Menaquinole-8, periplasm)"	(2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p]	Update		( b4070  and  b4071  and  b4072  and  b4073 )	AMF	"reaction taken from PMID:
low nitrate in the environment NrfA is made; with high nitrate NirB is made almost exclusively. PMID: 11004182
AMF"	-26.0652	51.3836	[c] : (2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p] 					
13573	O16A4COLIPAtex	Yes	O16 antigen (x4) core oligosaccharide lipid A transport (periplasm to extracellular)	o16a4colipa[p] --> o16a4colipa[e]	Lipopolysaccharide Biosynthesis / Recycling			AMF	"this reaction is needed to have the LPS lipid A derivative presented to the outer membrane surface - both moved across the periplasm and flipped across the outer membrane

not sure on the method of transport

this paper talks about the possibility of the transport PMID: 15576375

AMF"	0	0	[c] : o16a4colipa[p] --> o16a4colipa[e] 					
13572	O16A4Lpp	Yes	O16 anitgen (x4) ligase (periplasm)	[p] : colipa + o16a4und --> h + o16a4colipa + udcpdp	Lipopolysaccharide Biosynthesis / Recycling		b3622	AMF	"PMID: 10574995
states that this is the only probable enzyme for the ligase reaction

length of 4 repeating units is arbritrary
AMF
"	No energy	No energy	[p] : colipa[p] + o16a4und[p] --> o16a4colipa[p] + udcpdp[p] 					
13569	O16AP1pp	Yes	O16 antigen polymerase (periplasm)	[p] : (2) o16aund --> h + o16a2und + udcpdp	Lipopolysaccharide Biosynthesis / Recycling		( b2035  and  b2027 )	AMF	"PMID: 10574995
states the action of the WzxB gene and diagrams and outlines many other probably function for genes assigned in this pathway

PMID: 7517391 gives functions again and talks about the functions of the genes thought to produce O16
says that O16GLCT2 could occur after transport (flipping to the cytoplasm)

Not sure about the order of reactions needed for O-acetylation and side chain D-glc

AMF"	-0.675884	3.38607	[p] : (2) o16aund[p] --> o16a2und[p] + udcpdp[p] 					
13570	O16AP2pp	Yes	O16 antigen polymerase (periplasm)	[p] : o16a2und + o16aund --> h + o16a3und + udcpdp	Lipopolysaccharide Biosynthesis / Recycling		( b2035  and  b2027 )	AMF	"PMID: 10574995
states the action of the WzxB gene and diagrams and outlines many other probably function for genes assigned in this pathway

PMID: 7517391 gives functions again and talks about the functions of the genes thought to produce O16
says that O16GLCT2 could occur after transport (flipping to the cytoplasm)

Not sure about the order of reactions needed for O-acetylation and side chain D-glc

AMF"	-0.675884	3.38607	[p] : o16a2und[p] + o16aund[p] --> o16a3und[p] + udcpdp[p] 					
13571	O16AP3pp	Yes	O16 antigen polymerase (periplasm)	[p] : o16a3und + o16aund --> h + o16a4und + udcpdp	Lipopolysaccharide Biosynthesis / Recycling		( b2035  and  b2027 )	AMF	"PMID: 10574995
states the action of the WzxB gene and diagrams and outlines many other probably function for genes assigned in this pathway

PMID: 7517391 gives functions again and talks about the functions of the genes thought to produce O16
says that O16GLCT2 could occur after transport (flipping to the cytoplasm)

Not sure about the order of reactions needed for O-acetylation and side chain D-glc

AMF"	-0.675884	3.38607	[p] : o16a3und[p] + o16aund[p] --> o16a4und[p] + udcpdp[p] 					
13564	O16AT	Yes	rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate O-acetyltransferase (LPS O16 antigen biosynthesis)	[c] : accoa + ragund --> aragund + coa	Lipopolysaccharide Biosynthesis / Recycling		b2033	AMF	"PMID: 10574995
states the action of the WzxB gene and diagrams and outlines many other probably function for genes assigned in this pathway

PMID: 7517391 gives functions again and talks about the functions of the genes thought to produce O16
says that O16GLCT2 could occur after transport (flipping to the cytoplasm)

Not sure about the order of reactions needed for O-acetylation and side chain D-glc

AMF"	-1.98374	4.73838	[c] : accoa[c] + ragund[c] --> aragund[c] + coa[c] 					
13568	O16AUNDtpp	Yes	"O16 antigen (flippase, cytoplasm to periplasm)"	o16aund[c] --> o16aund[p]	Lipopolysaccharide Biosynthesis / Recycling		b2037	AMF	"PMID: 10574995
states the action of the WzxB gene and diagrams and outlines many other probably function for genes assigned in this pathway

PMID: 7517391 gives functions again and talks about the functions of the genes thought to produce O16
says that O16GLCT2 could occur after transport (flipping to the cytoplasm)

Not sure about the order of reactions needed for O-acetylation and side chain D-glc

AMF"	0	0	[c] : o16aund[c] --> o16aund[p] 
13566	O16GALFT	Yes	galactofuranosyltransferase (LPS O16 antigen biosynthesis)	[c] : garagund + udpgalfur --> gfgaragund + h + udp	Lipopolysaccharide Biosynthesis / Recycling		b2034	AMF	"PMID: 10574995
states the action of the WzxB gene and diagrams and outlines many other probably function for genes assigned in this pathway

PMID: 7517391 gives functions again and talks about the functions of the genes thought to produce O16
says that O16GLCT2 could occur after transport (flipping to the cytoplasm)

Not sure about the order of reactions needed for O-acetylation and side chain D-glc

AMF"	-0.675884	3.38607	[c] : garagund[c] + udpgalfur[c] --> gfgaragund[c] + udp[c] 
13565	O16GLCT1	Yes	glucosyltransferase I (LPS O16 antigen biosynthesis)	[c] : aragund + udpg --> garagund + h + udp	Lipopolysaccharide Biosynthesis / Recycling		b2032	AMF	"PMID: 10574995
states the action of the WzxB gene and diagrams and outlines many other probably function for genes assigned in this pathway

PMID: 7517391 gives functions again and talks about the functions of the genes thought to produce O16
says that O16GLCT2 could occur after transport (flipping to the cytoplasm)

Not sure about the order of reactions needed for O-acetylation and side chain D-glc

AMF"	-0.675884	3.38607	[c] : aragund[c] + udpg[c] --> garagund[c] + udp[c] 
13567	O16GLCT2	Yes	glucosyltransferase II (LPS O16 antigen biosynthesis)	[c] : gfgaragund + udpg --> h + o16aund + udp	Lipopolysaccharide Biosynthesis / Recycling			AMF	"PMID: 10574995
states the action of the WzxB gene and diagrams and outlines many other probably function for genes assigned in this pathway

PMID: 7517391 gives functions again and talks about the functions of the genes thought to produce O16
says that O16GLCT2 could occur after transport (flipping to the cytoplasm)

Not sure about the order of reactions needed for O-acetylation and side chain D-glc

AMF"	-0.675884	3.38607	[c] : gfgaragund[c] + udpg[c] --> o16aund[c] + udp[c] 
13563	O16RHAT	Yes	rhamnosyltransferase (LPS O16 antigen biosynthesis)	[c] : dtdprmn + unaga --> dtdp + h + ragund	Lipopolysaccharide Biosynthesis / Recycling		( b2031  and  b4540 )	AMF	"This gene is a pseudogene interrupted by a IS, so it is possibly unfunctional

PMID: 10574995
states the action of the WzxB gene and diagrams and outlines many other probably function for genes assigned in this pathway

PMID: 7517391 gives functions again and talks about the functions of the genes thought to produce O16
says that O16GLCT2 could occur after transport (flipping to the cytoplasm)

Not sure about the order of reactions needed for O-acetylation and side chain D-glc

AMF"	-0.675884	3.38607	[c] : dtdprmn[c] + unaga[c] --> dtdp[c] + ragund[c] 
9184	O2tex	Yes	oxygen transport via diffusion (extracellular to periplasm)	o2[e] <==> o2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : o2[e] <==> o2[p] 
12315	O2-tex	Yes	superoxide anion transport via diffusion (extracellular to periplasm)	o2-[e] <==> o2-[p]	"Transport, Outer Membrane"				"assumed diffusion, this will probably react however
may not be used in modeling
AMF"	0	0	[c] : o2-[e] <==> o2-[p] 
9006	O2tpp	Yes	o2 transport via diffusion (periplasm)	o2[p] <==> o2[c]	"Transport, Inner Membrane"			"tv
renamed from O2TP to O2t to avoid confusion with transport reaction from cytosol to peroxisome
NCD"		0	0	[c] : o2[p] <==> o2[c] 
3203	OBTFL	No	2-Oxobutanoate formate lyase	[c] : 2obut + coa --> for + ppcoa	Alternate Carbon Metabolism		( b3114  or  ( b0902  and  b0903 ) )	JLR		-4.20818	4.17278	[c] : 2obut[c] + coa[c] --> for[c] + ppcoa[c] 
3549	OCBT	No	ornithine carbamoyltransferase	[c] : cbp + orn <==> citr-L + h + pi	Arginine and Proline Metabolism	2.1.3.3	( b4254  or  b0273 )			-10.9491	4.1903	[c] : cbp[c] + orn[c] <==> citr-L[c] + h[c] + pi[c] 
9243	OCDCAtexi	Yes	Octadecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)	ocdca[e] --> ocdca[p]	"Transport, Outer Membrane"		b2344		"Transport of C12 - C18 fatty acids are facilitated by the outer membrane FadL protein (PMID: 103228825), inner membrane transport and subsequently outer membrane can require FACOAL enzyme (PMID: 15067008)

smaller FA can also pass through, C6 - C11, but can also diffuse, so they weren't associated"	0	0	[c] : ocdca[e] --> ocdca[p] 
9244	OCDCEAtexi	Yes	Octadecenoate (n-C18:1) transport via facilitated irreversible diffusion (extracellular to periplasm)	ocdcea[e] --> ocdcea[p]	"Transport, Outer Membrane"		b2344		"Transport of C12 - C18 fatty acids are facilitated by the outer membrane FadL protein (PMID: 103228825), inner membrane transport and subsequently outer membrane can require FACOAL enzyme (PMID: 15067008)

smaller FA can also pass through, C6 - C11, but can also diffuse, so they weren't associated"	0	0	[c] : ocdcea[e] --> ocdcea[p] 
9187	OCTAtex	Yes	Octanoate transport via diffusion (extracellular to periplasm)	octa[e] <==> octa[p]	"Transport, Outer Membrane"				"assumed passive diffusion through the outer peptidoglycan layer

can also pass through FadL
"	0	0	[c] : octa[e] <==> octa[p] 
1149	OCTDPS	No	Octaprenyl pyrophosphate synthase	[c] : frdp + (5) ipdp --> octdp + (5) ppi	Cofactor and Prosthetic Group Biosynthesis		b3187	"tv
JLR- EC 2.5.1.-"		-72.0732	14.6301	[c] : frdp[c] + (5) ipdp[c] --> octdp[c] + (5) ppi[c] 
8148	ODECOAI	Yes	Octadecenoyl-coa cis-trans isomerization	[c] : odecoa --> od2coa	Membrane Lipid Metabolism	5.3.3.8	b3846	JLR	"Evidence in PMID: 12535077
From Ecocyc: A reaction in beta-oxidation of fatty acids, required to feed unsaturated fatty acids into the main pathway.  Not sure of reaction reversibility.
AMF
FadJ might also carry out this reaction.  No evidence found for it yet though.
JLR
"	0	0.5	[c] : odecoa[c] --> od2coa[c] 
1731	OHPBAT	No	O-Phospho-4-hydroxy-L-threonine:2-oxoglutarate aminotransferase	[c] : glu-L + ohpb <==> akg + phthr	Cofactor and Prosthetic Group Biosynthesis	2.6.1.52	b0907	NCD		0	0.5	[c] : glu-L[c] + ohpb[c] <==> akg[c] + phthr[c] 
1581	OHPHM	No	2-octaprenyl-6-hydroxyphenol methylase	[c] : 2ohph + amet --> 2omph + ahcys + h	Cofactor and Prosthetic Group Biosynthesis		b2232	"JLR- not sure about enzyme name (EC- 2.1.1.-)
"		No energy	No energy	[c] : 2ohph[c] + amet[c] --> 2omph[c] + ahcys[c] + h[c] 					
1346	OMBZLM	No	2-Octaprenyl-6-methoxy-benzoquinol methylase	[c] : 2ombzl + amet --> 2ommbl + ahcys + h	Cofactor and Prosthetic Group Biosynthesis		b3833	JLR		No energy	No energy	[c] : 2ombzl[c] + amet[c] --> 2ommbl[c] + ahcys[c] + h[c] 					
912	OMCDC	No	2-Oxo-4-methyl-3-carboxypentanoate decarboxylation	[c] : 3c4mop + h --> 4mop + co2	"Valine, Leucine, and Isoleucine Metabolism"		b0073	Continuation of EC 1.1.1.85 reaction	JLR- IPMD and OMCDC are in JSE as one reaction.  Included the two separate reactions in this model.	-4.96805	1.79669	[c] : 3c4mop[c] + h[c] --> 4mop[c] + co2[c] 					
1349	OMMBLHX	No	"2-Octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase"	[c] : 2ommbl + (0.5) o2 --> 2omhmbl	Cofactor and Prosthetic Group Biosynthesis		b0662	JLR- not sure about the reaction	JLR- not sure about any cofactors	-39.1491	5.09426	[c] : 2ommbl[c] + (0.5) o2[c] --> 2omhmbl[c] 					
446	OMPDC	No	orotidine-5'-phosphate decarboxylase	[c] : h + orot5p --> co2 + ump	Purine and Pyrimidine Biosynthesis	4.1.1.23	b1281			-6.26166	2.62936	[c] : h[c] + orot5p[c] --> co2[c] + ump[c] 					
1348	OMPHHX	No	2-octaprenyl-6-methoxyphenol hydroxylase	[c] : 2omph + (0.5) o2 --> 2ombzl	Cofactor and Prosthetic Group Biosynthesis		b2907	JLR- not sure about the reaction (EC 1.14.3.-)	JLR- not sure about any cofactors	-39.1491	5.09426	[c] : 2omph[c] + (0.5) o2[c] --> 2ombzl[c] 					
2366	OP4ENH	No	2-oxopent-4-enoate hydratase	[c] : h2o + op4en --> 4h2opntn	Alternate Carbon Metabolism	4.2.1.80	b0350	JLR		-8.45984	3.87293	[c] : h2o[c] + op4en[c] --> 4h2opntn[c] 					
1579	OPHBDC	No	Octaprenyl-hydroxybenzoate decarboxylase	[c] : 3ophb + h --> 2oph + co2	Cofactor and Prosthetic Group Biosynthesis		( b3843  or  b2311 )	JLR (EC - 4.1.1.-)		-1.19517	3.54202	[c] : 3ophb[c] + h[c] --> 2oph[c] + co2[c] 					
1580	OPHHX	No	2-Octaprenylphenol hydroxylase	[c] : 2oph + (0.5) o2 --> 2ohph	Cofactor and Prosthetic Group Biosynthesis		b3835	"JLR- not sure about this reaction (EC 1.13.14.-)
"	"JLR- not sure about reaction, EcoCyc gives this one. "	-39.1491	5.09426	[c] : 2oph[c] + (0.5) o2[c] --> 2ohph[c] 					
8902	ORNabcpp	Yes	ornithine transport via ABC system (periplasm)	atp[c] + h2o[c] + orn[p] --> adp[c] + h[c] + orn[c] + pi[c]	"Transport, Inner Membrane"		( b2310  and  b2307  and  b2306  and  b2308 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + orn[p] --> adp[c] + h[c] + orn[c] + pi[c] 					
1218	ORNDC	No	Ornithine Decarboxylase	[c] : h + orn --> co2 + ptrc	Arginine and Proline Metabolism	4.1.1.17	( b2965  or  b0693 )	JLR- added proton to balance		-4.96805	1.79669	[c] : h[c] + orn[c] --> co2[c] + ptrc[c] 					
9188	ORNtex	Yes	ornithine transport via diffusion (extracellular to periplasm)	orn[e] <==> orn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : orn[e] <==> orn[p] 					
447	ORPT	No	orotate phosphoribosyltransferase	[c] : orot5p + ppi <==> orot + prpp	Purine and Pyrimidine Biosynthesis	2.4.2.10	b3642			3.6643	3.87109	[c] : orot5p[c] + ppi[c] <==> orot[c] + prpp[c] 					
6182	OXAMTC	Yes	oxamate transcarbamoylase	[c] : oxur + pi --> cbp + oxam	Update	2.1.3.5		JLR	"Ref cites another reference that reported this activity in e.coli.  In addition deletion of allA, allantoin can still be used as a nitrogen source indicating that this reaction is needed"	-4.12638	3.94903	[c] : oxur[c] + pi[c] --> cbp[c] + oxam[c] 					
3443	OXGDC2	No	2-oxoglutarate decarboxylase	[c] : akg + h + thmpp --> co2 + ssaltpp	Cofactor and Prosthetic Group Biosynthesis	4.1.1.71	b2264	JLR		8.61951	3.497	[c] : akg[c] + h[c] + thmpp[c] --> co2[c] + ssaltpp[c] 					
3318	P5CD	No	1-pyrroline-5-carboxylate dehydrogenase	[c] : 1pyr5c + (2) h2o + nad --> glu-L + h + nadh	Arginine and Proline Metabolism	1.5.1.12	b1014	"Oxidizes other 1-pyrrolines, e.g. 3-hydroxy-1-pyrroline-5-carboxylate forms 4-hydroxyglutamate"	"JLR- before JSE had glu5sa going to glu-L, but glu5sa is spontaneously turned into 1pyr5c which can then be turned into glu-L.  So decoupled JSE reaction (similar to proC)."	2.30614	6.03723	[c] : 1pyr5c[c] + (2) h2o[c] + nad[c] --> glu-L[c] + h[c] + nadh[c] 					
3629	P5CR	No	pyrroline-5-carboxylate reductase	[c] : 1pyr5c + (2) h + nadph --> nadp + pro-L	Arginine and Proline Metabolism	1.5.1.2	b0386			No energy	No energy	[c] : 1pyr5c[c] + (2) h[c] + nadph[c] --> nadp[c] + pro-L[c] 					
19840	PA120abcpp	Yes	"phosphatidate transport via ABC system (n-C12:0, periplasm)"	atp[c] + h2o[c] + pa120[c] --> adp[c] + h[c] + pa120[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pa120[c] --> adp[c] + h[c] + pa120[p] + pi[c] 					
19841	PA140abcpp	Yes	"phosphatidate transport via ABC system (n-C14:0, periplasm)"	atp[c] + h2o[c] + pa140[c] --> adp[c] + h[c] + pa140[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pa140[c] --> adp[c] + h[c] + pa140[p] + pi[c] 					
19842	PA141abcpp	Yes	"phosphatidate transport via ABC system (n-C14:1, periplasm)"	atp[c] + h2o[c] + pa141[c] --> adp[c] + h[c] + pa141[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pa141[c] --> adp[c] + h[c] + pa141[p] + pi[c] 					
19843	PA160abcpp	Yes	"phosphatidate transport via ABC system (n-C16:0, periplasm)"	atp[c] + h2o[c] + pa160[c] --> adp[c] + h[c] + pa160[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pa160[c] --> adp[c] + h[c] + pa160[p] + pi[c] 					
19844	PA161abcpp	Yes	"phosphatidate transport via ABC system (n-C16:1, periplasm)"	atp[c] + h2o[c] + pa161[c] --> adp[c] + h[c] + pa161[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pa161[c] --> adp[c] + h[c] + pa161[p] + pi[c] 					
19845	PA180abcpp	Yes	"phosphatidate transport via ABC system (n-C18:0, periplasm)"	atp[c] + h2o[c] + pa180[c] --> adp[c] + h[c] + pa180[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pa180[c] --> adp[c] + h[c] + pa180[p] + pi[c] 					
19846	PA181abcpp	Yes	"phosphatidate transport via ABC system (n-C18:1, periplasm)"	atp[c] + h2o[c] + pa181[c] --> adp[c] + h[c] + pa181[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pa181[c] --> adp[c] + h[c] + pa181[p] + pi[c] 					
12237	PACALDt2rpp	Yes	phenylacetaldehyde reversible transport via proton symport (periplasm)	h[p] + pacald[p] <==> h[c] + pacald[c]	Update			"AMF
"	"pacald is created in the periplasm and can be used as a source for carbon and is utilized inside of the cell by FeaB, so there needs to be a transporter for it...  This is awefully similar to phe-L, so is could be transported by thje aromatic acid transporter --> AroP, PheP

AMF"	0	0	[c] : h[p] + pacald[p] <==> h[c] + pacald[c] 					
12240	PACALDtex	Yes	phenethylacetaldehyde transport via diffusion (extracellular to periplasm)	pacald[e] <==> pacald[p]	"Transport, Outer Membrane"			AMF	"PMID: 3309152 original paper source
PMID: 11729263 - review where it states that that tyroxdapp and 42a12booxpp are confirmed susbstrates and can be used in K-12 for nitrogen source only, not sure if they are transported inside the cell or not or if they can't be processed after transport"	0	0	[c] : pacald[e] <==> pacald[p] 					
3239	PACCOAL	No	phenylacetate-CoA ligase	[c] : atp + coa + pac --> amp + phaccoa + ppi	Alternate Carbon Metabolism	6.2.1.30	b1398	JLR	JLR studied in E.coli W strain	-2.74083	4.99608	[c] : atp[c] + coa[c] + h[c] + pac[c] --> amp[c] + phaccoa[c] + ppi[c] 					
3551	PANTS	No	pantothenate synthase	[c] : ala-B + atp + pant-R --> amp + h + pnto-R + ppi	Cofactor and Prosthetic Group Biosynthesis	6.3.2.1	b0133			-5.22858	4.12076	[c] : ala-B[c] + atp[c] + pant-R[c] --> amp[c] + pnto-R[c] + ppi[c] 					
19442	PAPA120	Yes	Phosphatidate phosphatase (n-C12:0)	[c] : h2o + pa120 --> 12dgr120 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pa120[c] --> 12dgr120[c] + h[c] + pi[c] 					
19833	PAPA120pp	Yes	"Phosphatidate phosphatase (periplasmic, n-C12:0)"	[p] : h2o + pa120 --> 12dgr120 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pa120[p] --> 12dgr120[p] + h[p] + pi[p] 					
19441	PAPA140	Yes	Phosphatidate phosphatase (n-C14:0)	[c] : h2o + pa140 --> 12dgr140 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pa140[c] --> 12dgr140[c] + h[c] + pi[c] 					
19834	PAPA140pp	Yes	"Phosphatidate phosphatase (periplasmic, n-C14:0)"	[p] : h2o + pa140 --> 12dgr140 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pa140[p] --> 12dgr140[p] + h[p] + pi[p] 					
19445	PAPA141	Yes	Phosphatidate phosphatase (n-C14:1)	[c] : h2o + pa141 --> 12dgr141 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pa141[c] --> 12dgr141[c] + h[c] + pi[c] 					
19835	PAPA141pp	Yes	"Phosphatidate phosphatase (periplasmic, n-C14:1)"	[p] : h2o + pa141 --> 12dgr141 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pa141[p] --> 12dgr141[p] + h[p] + pi[p] 					
19443	PAPA160	Yes	Phosphatidate phosphatase (n-C16:0)	[c] : h2o + pa160 --> 12dgr160 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pa160[c] --> 12dgr160[c] + h[c] + pi[c] 					
19836	PAPA160pp	Yes	"Phosphatidate phosphatase (periplasmic, n-C16:0)"	[p] : h2o + pa160 --> 12dgr160 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pa160[p] --> 12dgr160[p] + h[p] + pi[p] 					
19446	PAPA161	Yes	Phosphatidate phosphatase (n-C16:1)	[c] : h2o + pa161 --> 12dgr161 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pa161[c] --> 12dgr161[c] + h[c] + pi[c] 					
19837	PAPA161pp	Yes	"Phosphatidate phosphatase (periplasmic, n-C16:1)"	[p] : h2o + pa161 --> 12dgr161 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pa161[p] --> 12dgr161[p] + h[p] + pi[p] 					
19444	PAPA180	Yes	Phosphatidate phosphatase (n-C18:0)	[c] : h2o + pa180 --> 12dgr180 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pa180[c] --> 12dgr180[c] + h[c] + pi[c] 					
19838	PAPA180pp	Yes	"Phosphatidate phosphatase (periplasmic, n-C18:0)"	[p] : h2o + pa180 --> 12dgr180 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pa180[p] --> 12dgr180[p] + h[p] + pi[p] 					
19447	PAPA181	Yes	Phosphatidate phosphatase (n-C18:1)	[c] : h2o + pa181 --> 12dgr181 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pa181[c] --> 12dgr181[c] + h[c] + pi[c] 					
19839	PAPA181pp	Yes	"Phosphatidate phosphatase (periplasmic, n-C18:1)"	[p] : h2o + pa181 --> 12dgr181 + pi	Glycerophospholipid Metabolism	3.1.3.4	b1278	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pa181[p] --> 12dgr181[p] + h[p] + pi[p] 					
2700	PAPPT3	No	"phospho-N-acetylmuramoyl-pentapeptide-transferase (meso-2,6-diaminopimelate)"	[c] : udcpp + ugmda --> uagmda + ump	Cell Envelope Biosynthesis	2.7.8.13	b0087		JLR- used ugmda (KEGG indicates another compound but EcoCyc agrees with the way JSE has it)	0	0.5	[c] : udcpp[c] + ugmda[c] --> uagmda[c] + ump[c] 					
352	PAPSR	No	phosphoadenylyl-sulfate reductase (thioredoxin)	[c] : paps + trdrd --> (2) h + pap + so3 + trdox	Cysteine Metabolism	1.8.4.8	b2762	Previous EC 1.8.99.4. Now EC 1.8.4.8	"see PMID: 10075658
AMF"	No energy	No energy	[c] : paps[c] + trdrd[c] --> pap[c] + so3[c] + trdox[c] 					
13837	PAPSR2	Yes	phosphoadenylyl-sulfate reductase (glutaredoxin)	[c] : grxrd + paps --> grxox + (2) h + pap + so3	Update	1.8.4.8	b2762	Previous EC 1.8.99.4. Now EC 1.8.4.8	"see PMID: 10075658
AMF"	No energy	No energy	[c] : grxrd[c] + paps[c] --> grxox[c] + pap[c] + so3[c] 					
2655	PDE1	Yes	"3',5'-cyclic-nucleotide phosphodiesterase"	[c] : camp + h2o --> amp + h	Update	3.1.4.17	b1489	NCD	"chacterized in PMID: 11970957

the present study unequivocally indicates for the first time that Ec DOS exhibits PDE activity with cAMP and that this is regulated by the heme redox state

could also acto on other 3'5'-cyclic nucleosides according to ecocyc
AMF"	-9.69197	7.31295	[c] : camp[c] + h2o[c] --> amp[c] 					
865	PDH	No	pyruvate dehydrogenase	[c] : coa + nad + pyr --> accoa + co2 + nadh	Glycolysis/Gluconeogenesis		( b0114  and  b0115  and  b0116 )			-6.55393	5.78379	[c] : coa[c] + nad[c] + pyr[c] --> accoa[c] + co2[c] + nadh[c] 					
1729	PDX5PO	No	pyridoxine 5'-phosphate oxidase	[c] : o2 + pdx5p <==> h2o2 + pydx5p	Cofactor and Prosthetic Group Biosynthesis	1.4.3.5	b1638	NCD		-22.5124	1.7612	[c] : o2[c] + pdx5p[c] <==> h2o2[c] + pydx5p[c] 					
3552	PDX5PS	No	Pyridoxine 5'-phosphate synthase	[c] : dxyl5p + nad + phthr --> co2 + h + (2) h2o + nadh + pdx5p + pi	Cofactor and Prosthetic Group Biosynthesis		( b0052  and  b2564 )	JLR- two reactions combined (intermediate of the first is unknown)		-27.5931	10.9662	[c] : dxyl5p[c] + nad[c] + phthr[c] --> co2[c] + (2) h[c] + (2) h2o[c] + nadh[c] + pdx5p[c] + pi[c] 		
1821	PDXPP	No	Pyridoxine 5-phosphate phosphatase	[c] : h2o + pdx5p --> pi + pydxn	Cofactor and Prosthetic Group Biosynthesis			JLR		-2.35942	1.9257	[c] : h2o[c] + pdx5p[c] --> h[c] + pi[c] + pydxn[c] 		
19536	PE120abcpp	Yes	"phosphatidylethanolamine transport via ABC system (n-C12:0, periplasm)"	atp[c] + h2o[c] + pe120[c] --> adp[c] + h[c] + pe120[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pe120[c] --> adp[c] + h[c] + pe120[p] + pi[c] 		
19537	PE140abcpp	Yes	"phosphatidylethanolamine transport via ABC system (n-C14:0, periplasm)"	atp[c] + h2o[c] + pe140[c] --> adp[c] + h[c] + pe140[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pe140[c] --> adp[c] + h[c] + pe140[p] + pi[c] 		
19538	PE141abcpp	Yes	"phosphatidylethanolamine transport via ABC system (n-C14:1, periplasm)"	atp[c] + h2o[c] + pe141[c] --> adp[c] + h[c] + pe141[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pe141[c] --> adp[c] + h[c] + pe141[p] + pi[c] 		
19539	PE160abcpp	Yes	"phosphatidylethanolamine transport via ABC system (n-C16:0, periplasm)"	atp[c] + h2o[c] + pe160[c] --> adp[c] + h[c] + pe160[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pe160[c] --> adp[c] + h[c] + pe160[p] + pi[c] 		
19541	PE161abcpp	Yes	"phosphatidylethanolamine transport via ABC system (n-C16:1, periplasm)"	atp[c] + h2o[c] + pe161[c] --> adp[c] + h[c] + pe161[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pe161[c] --> adp[c] + h[c] + pe161[p] + pi[c] 		
19540	PE180abcpp	Yes	"phosphatidylethanolamine transport via ABC system (n-C18:0, periplasm)"	atp[c] + h2o[c] + pe180[c] --> adp[c] + h[c] + pe180[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pe180[c] --> adp[c] + h[c] + pe180[p] + pi[c] 		
19542	PE181abcpp	Yes	"phosphatidylethanolamine transport via ABC system (n-C18:1, periplasm)"	atp[c] + h2o[c] + pe181[c] --> adp[c] + h[c] + pe181[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pe181[c] --> adp[c] + h[c] + pe181[p] + pi[c] 		
12229	PEAMNOpp	Yes	Phenethylamine oxidase	[p] : h2o + o2 + peamn --> h2o2 + nh4 + pacald	Update	1.4.3.6	b1386	"JLR- Kegg reaction R02613
AMF
"	"phenylethylaminine can not be a sole substrate according to biolog data, which is contracting with PMID: 11729263 Growth of E. coli on PEA as the sole carbon and energy source induces

There would have to be a transport of the product into the cell if this reaction is in the cytoplasm. 

Downstream product processing is hypothesized in Ecocyc, but have not been worked out definatively.  This reaction was added to the periplasm, but is not utilized beyond that."	-18.53	2.13874	[p] : h2o[p] + o2[p] + peamn[p] --> h2o2[p] + nh4[p] + pacald[p] 		
12239	PEAMNtex	Yes	phenethylamine transport via diffusion (extracellular to periplasm)	peamn[e] <==> peamn[p]	"Transport, Outer Membrane"			AMF	"PMID: 3309152 original paper source
PMID: 11729263 - review where it states that that tyroxdapp and 42a12booxpp are confirmed susbstrates and can be used in K-12 for nitrogen source only, not sure if they are transported inside the cell or not or if they can't be processed after transport"	0	0	[c] : peamn[e] <==> peamn[p] 		
1721	PERD	No	Erythronate 4-phosphate (4per) dehydrogenase	[c] : 4per + nad <==> h + nadh + ohpb	Cofactor and Prosthetic Group Biosynthesis		b2320	JLR		4.73639	4.5435	[c] : 4per[c] + nad[c] <==> h[c] + nadh[c] + ohpb[c] 		
19456	PETNT161pp	Yes	phosphoethanolamine transferase (c-C16:1)	[p] : lipa + pe161 --> 12dgr161 + enlipa	Lipopolysaccharide Biosynthesis / Recycling		b3546	AMF	"eptB acts on lipidA (kdo2-lipid A) without any heptose attached (heptose deficient)

EptB is one of six putative pEtN transferases present in E. coli

Our studies show that EptB utilizes several different PE molecular species (Fig. 7) provided they contain at least one double bond...  Similarly, saturated PEs with shorter acyl chains (10:0/10:0, 12:0/12:0, and 14:0/14:0) were not substrates (data not shown).
PMID: 15795227
AMF"	1.99194	1.54996	[p] : lipa[p] + pe161[p] --> 12dgr161[p] + enlipa[p] 		
19457	PETNT181pp	Yes	phosphoethanolamine transferase (c-C16:1)	[p] : lipa + pe181 --> 12dgr181 + enlipa	Lipopolysaccharide Biosynthesis / Recycling		b3546	AMF	"eptB acts on lipidA (kdo2-lipid A) without any heptose attached (heptose deficient)

EptB is one of six putative pEtN transferases present in E. coli

Our studies show that EptB utilizes several different PE molecular species (Fig. 7) provided they contain at least one double bond...  Similarly, saturated PEs with shorter acyl chains (10:0/10:0, 12:0/12:0, and 14:0/14:0) were not substrates (data not shown).
PMID: 15795227
AMF"	1.99194	1.54996	[p] : lipa[p] + pe181[p] --> 12dgr181[p] + enlipa[p] 		
267	PFK	No	phosphofructokinase	[c] : atp + f6p --> adp + fdp + h	Glycolysis/Gluconeogenesis	2.7.1.11	( b3916  or  b1723 )	SMP		-4.65732	2.09859	[c] : atp[c] + f6p[c] --> adp[c] + fdp[c] 		
1208	PFK_2	No	Phosphofructokinase	[c] : atp + tag6p-D --> adp + h + tagdp-D	Alternate Carbon Metabolism	2.7.1.11	b3916	"Also EC 2.7.1.144
JLR"		-4.65732	2.09859	[c] : atp[c] + tag6p-D[c] --> adp[c] + tagdp-D[c] 		
1179	PFL	No	pyruvate formate lyase	[c] : coa + pyr --> accoa + for	Pyruvate Metabolism		( b3114  or  ( b0902  and  b0903 )  or  ( b3951  and  b3952 ) )	"JLR
E.C. - 2.3.1.54  MM

"		-4.20818	4.17278	[c] : coa[c] + pyr[c] --> accoa[c] + for[c] 
19819	PG120abcpp	Yes	"phosphatidylglycerol transport via ABC system (n-C12:0, periplasm)"	atp[c] + h2o[c] + pg120[c] --> adp[c] + h[c] + pg120[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pg120[c] --> adp[c] + h[c] + pg120[p] + pi[c] 
19820	PG140abcpp	Yes	"phosphatidylglycerol transport via ABC system (n-C14:0, periplasm)"	atp[c] + h2o[c] + pg140[c] --> adp[c] + h[c] + pg140[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pg140[c] --> adp[c] + h[c] + pg140[p] + pi[c] 
19821	PG141abcpp	Yes	"phosphatidylglycerol transport via ABC system (n-C14:1, periplasm)"	atp[c] + h2o[c] + pg141[c] --> adp[c] + h[c] + pg141[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pg141[c] --> adp[c] + h[c] + pg141[p] + pi[c] 
19822	PG160abcpp	Yes	"phosphatidylglycerol transport via ABC system (n-C16:0, periplasm)"	atp[c] + h2o[c] + pg160[c] --> adp[c] + h[c] + pg160[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pg160[c] --> adp[c] + h[c] + pg160[p] + pi[c] 
19823	PG161abcpp	Yes	"phosphatidylglycerol transport via ABC system (n-C16:1, periplasm)"	atp[c] + h2o[c] + pg161[c] --> adp[c] + h[c] + pg161[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pg161[c] --> adp[c] + h[c] + pg161[p] + pi[c] 
19824	PG180abcpp	Yes	"phosphatidylglycerol transport via ABC system (n-C18:0, periplasm)"	atp[c] + h2o[c] + pg180[c] --> adp[c] + h[c] + pg180[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pg180[c] --> adp[c] + h[c] + pg180[p] + pi[c] 
19825	PG181abcpp	Yes	"phosphatidylglycerol transport via ABC system (n-C18:1, periplasm)"	atp[c] + h2o[c] + pg181[c] --> adp[c] + h[c] + pg181[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pg181[c] --> adp[c] + h[c] + pg181[p] + pi[c] 
475	PGAMT	No	phosphoglucosamine mutase	[c] : gam1p <==> gam6p	Cell Envelope Biosynthesis	5.4.2.10	b3176	"involved in the pathway for bacterial cell-wall peptidoglycan and lipopolysaccharide biosyntheses, being an essential step in the pathway for UDP-N-acetylglucosamine biosynthesis. "		-1.18877	2.59673	[c] : gam1p[c] <==> gam6p[c] 
2865	PGCD	No	phosphoglycerate dehydrogenase	[c] : 3pg + nad --> 3php + h + nadh	Glycine and Serine Metabolism	1.1.1.95	b2913			4.73639	4.5435	[c] : 3pg[c] + nad[c] --> 3php[c] + h[c] + nadh[c] 
271	PGI	No	glucose-6-phosphate isomerase	[c] : g6p <==> f6p	Glycolysis/Gluconeogenesis	5.3.1.9	b4025			-0.246702	4.88847	[c] : g6p[c] <==> f6p[c] 
273	PGK	No	phosphoglycerate kinase	[c] : 3pg + atp <==> 13dpg + adp	Glycolysis/Gluconeogenesis	2.7.2.3	b2926	SMP		3.00718	2.24154	[c] : 3pg[c] + atp[c] + h[c] <==> 13dpg[c] + adp[c] 
278	PGL	No	6-phosphogluconolactonase	[c] : 6pgl + h2o --> 6pgc + h	Pentose Phosphate Pathway	3.1.1.31	b0767	"SMP 
Net reaction same as described in Lehringer 334"	"The pgl gene has not been identified, although the reaction is known to occur.  According to EcoCyc the reaction is also able to occur spontaneously.  Recent study found the gene is the ybhE.
JLR

Update, 3/2005 - gene located;  ybhE (now pgl)
MKA"	-6.75284	8.24739	[c] : 6pgl[c] + h2o[c] --> 6pgc[c] + h[c] 
2286	PGLYCP	No	Phosphoglycolate phosphatase	[c] : 2pglyc + h2o --> glyclt + pi	Alternate Carbon Metabolism	3.1.3.18	b3385	JLR	"This enzyme is normally used in CO2 fixation during photosynthesis, unknown why E. coli has this function"	-2.35942	1.9257	[c] : 2pglyc[c] + h2o[c] --> glyclt[c] + h[c] + pi[c] 
272	PGM	No	phosphoglycerate mutase	[c] : 2pg <==> 3pg	Glycolysis/Gluconeogenesis	5.4.2.1	( b3612  or  b4395  or  b0755 )	SMP		-1.18877	2.59673	[c] : 2pg[c] <==> 3pg[c] 
2819	PGMT	No	phosphoglucomutase	[c] : g1p <==> g6p	Alternate Carbon Metabolism	5.4.2.2	( b0688  or  b2690 )			-1.18877	2.59673	[c] : g1p[c] <==> g6p[c] 
19826	PGP120abcpp	Yes	"phosphatidylglycerophosphate transport via ABC system (n-C12:0, periplasm)"	atp[c] + h2o[c] + pgp120[c] --> adp[c] + h[c] + pgp120[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pgp120[c] --> adp[c] + h[c] + pgp120[p] + pi[c] 		
19827	PGP140abcpp	Yes	"phosphatidylglycerophosphate transport via ABC system (n-C14:0, periplasm)"	atp[c] + h2o[c] + pgp140[c] --> adp[c] + h[c] + pgp140[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pgp140[c] --> adp[c] + h[c] + pgp140[p] + pi[c] 		
19828	PGP141abcpp	Yes	"phosphatidylglycerophosphate transport via ABC system (n-C14:1, periplasm)"	atp[c] + h2o[c] + pgp141[c] --> adp[c] + h[c] + pgp141[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pgp141[c] --> adp[c] + h[c] + pgp141[p] + pi[c] 		
19829	PGP160abcpp	Yes	"phosphatidylglycerophosphate transport via ABC system (n-C16:0, periplasm)"	atp[c] + h2o[c] + pgp160[c] --> adp[c] + h[c] + pgp160[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pgp160[c] --> adp[c] + h[c] + pgp160[p] + pi[c] 		
19830	PGP161abcpp	Yes	"phosphatidylglycerophosphate transport via ABC system (n-C16:1, periplasm)"	atp[c] + h2o[c] + pgp161[c] --> adp[c] + h[c] + pgp161[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pgp161[c] --> adp[c] + h[c] + pgp161[p] + pi[c] 		
19831	PGP180abcpp	Yes	"phosphatidylglycerophosphate transport via ABC system (n-C18:0, periplasm)"	atp[c] + h2o[c] + pgp180[c] --> adp[c] + h[c] + pgp180[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pgp180[c] --> adp[c] + h[c] + pgp180[p] + pi[c] 		
19832	PGP181abcpp	Yes	"phosphatidylglycerophosphate transport via ABC system (n-C18:1, periplasm)"	atp[c] + h2o[c] + pgp181[c] --> adp[c] + h[c] + pgp181[p] + pi[c]	"Transport, Inner Membrane"		b0914	AMF	"PMID: 15304478 suggests that MsbA facilitates the rapid translocation of some lipids from the cytoplasmic to the periplasmic side of the inner membrane in living cells.
no specific mention of:
pa
pg
pgp
but PMID: 15890883 does mention that MsbA will transport:
pe

personal communication (Charles Rock, Jan. 7 06): 'MsbA is an interesting issue.  It certainly transports the lipid A molecule.  In msbA mutants, PE also accumulates inside the cell
suggesting that PE is also transported by MsbA.  However, some scientists think this may not be the case and the accumulation of PE inside the cell in msbA mutants arises from it sticking to the lipid A that is not moved out of the cell, so the phenotype is not due to a PE transport defect.  This implies the existence of another transporter that moves phospholipids, but it has not been identified. So we wait for more definitive experiments.'
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pgp181[c] --> adp[c] + h[c] + pgp181[p] + pi[c] 		
19329	PGPP120	Yes	phosphatidylglycerol phosphate phosphatase (n-C14:0)	[c] : h2o + pgp120 --> pg120 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pgp120[c] --> h[c] + pg120[c] + pi[c] 		
19852	PGPP120pp	Yes	"phosphatidylglycerol phosphate phosphatase (periplasm, n-C14:0)"	[p] : h2o + pgp120 --> pg120 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pgp120[p] --> h[p] + pg120[p] + pi[p] 		
19266	PGPP140	Yes	phosphatidylglycerol phosphate phosphatase (n-C14:0)	[c] : h2o + pgp140 --> pg140 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pgp140[c] --> h[c] + pg140[c] + pi[c] 		
19853	PGPP140pp	Yes	"phosphatidylglycerol phosphate phosphatase (periplasm, n-C14:0)"	[p] : h2o + pgp140 --> pg140 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pgp140[p] --> h[p] + pg140[p] + pi[p] 		
19269	PGPP141	Yes	phosphatidylglycerol phosphate phosphatase (n-C14:1)	[c] : h2o + pgp141 --> pg141 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pgp141[c] --> h[c] + pg141[c] + pi[c] 		
19854	PGPP141pp	Yes	"phosphatidylglycerol phosphate phosphatase (periplasm, n-C14:1)"	[p] : h2o + pgp141 --> pg141 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pgp141[p] --> h[p] + pg141[p] + pi[p] 		
19267	PGPP160	Yes	phosphatidylglycerol phosphate phosphatase (n-C16:0)	[c] : h2o + pgp160 --> pg160 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pgp160[c] --> h[c] + pg160[c] + pi[c] 		
19855	PGPP160pp	Yes	"phosphatidylglycerol phosphate phosphatase (periplasm, n-C16:0)"	[p] : h2o + pgp160 --> pg160 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pgp160[p] --> h[p] + pg160[p] + pi[p] 		
19270	PGPP161	Yes	phosphatidylglycerol phosphate phosphatase (n-C16:1)	[c] : h2o + pgp161 --> pg161 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pgp161[c] --> h[c] + pg161[c] + pi[c] 		
19856	PGPP161pp	Yes	"phosphatidylglycerol phosphate phosphatase (periplasm, n-C16:1)"	[p] : h2o + pgp161 --> pg161 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pgp161[p] --> h[p] + pg161[p] + pi[p] 
19268	PGPP180	Yes	phosphatidylglycerol phosphate phosphatase (n-C18:0)	[c] : h2o + pgp180 --> pg180 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pgp180[c] --> h[c] + pg180[c] + pi[c] 
19857	PGPP180pp	Yes	"phosphatidylglycerol phosphate phosphatase (periplasm, n-C18:0)"	[p] : h2o + pgp180 --> pg180 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pgp180[p] --> h[p] + pg180[p] + pi[p] 
19271	PGPP181	Yes	phosphatidylglycerol phosphate phosphatase (n-C18:1)	[c] : h2o + pgp181 --> pg181 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[c] : h2o[c] + pgp181[c] --> h[c] + pg181[c] + pi[c] 
19858	PGPP181pp	Yes	"phosphatidylglycerol phosphate phosphatase (periplasm, n-C18:1)"	[p] : h2o + pgp181 --> pg181 + pi	Glycerophospholipid Metabolism	3.1.3.27	( b0418  or  b1278 )	AMF	"from PMID: 2846511
PGPP activity is higher in the cytoplasmic membrane than the outer membrane, whereas PAPA activities are higher in the outer membrane.
It appears that PgpA activity is for PAPA where PgpB activity is for both PAPA and PGP.
PgpB is known to be located in both the inner and outer membrane, pgpA is acitve in the inner membrane.  However, it is not know which side of the membranes the active site for each of the enzymes is on.

removal of the phosphate moiety from PG-phosphate, is indeterminate because at least three different enzymes (PgpA, PgpB, and an unknown protein) are thought to catalyze this hydrolytic step.
PMID: 14527277

PMID: 9370315 states gene responsible is pgpB in E coli

reactions are set up to act on FA with two identical -acyl chain lengths

AMF"	-2.35942	1.9257	[p] : h2o[p] + pgp181[p] --> h[p] + pg181[p] + pi[p] 
19328	PGSA120	Yes	Phosphatidylglycerol synthase (n-C12:0)	[c] : cdpdddecg + glyc3p --> cmp + h + pgp120	Glycerophospholipid Metabolism	2.7.8.5	b1912	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : cdpdddecg[c] + glyc3p[c] --> cmp[c] + pgp120[c] 
19260	PGSA140	Yes	Phosphatidylglycerol synthase (n-C14:0)	[c] : cdpdtdecg + glyc3p --> cmp + h + pgp140	Glycerophospholipid Metabolism	2.7.8.5	b1912	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : cdpdtdecg[c] + glyc3p[c] --> cmp[c] + pgp140[c] 
19263	PGSA141	Yes	Phosphatidylglycerol synthase (n-C14:1)	[c] : cdpdtdec7eg + glyc3p --> cmp + h + pgp141	Glycerophospholipid Metabolism	2.7.8.5	b1912	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : cdpdtdec7eg[c] + glyc3p[c] --> cmp[c] + pgp141[c] 
19261	PGSA160	Yes	Phosphatidylglycerol synthase (n-C16:0)	[c] : cdpdhdecg + glyc3p --> cmp + h + pgp160	Glycerophospholipid Metabolism	2.7.8.5	b1912	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : cdpdhdecg[c] + glyc3p[c] --> cmp[c] + pgp160[c] 
19264	PGSA161	Yes	Phosphatidylglycerol synthase (n-C16:1)	[c] : cdpdhdec9eg + glyc3p --> cmp + h + pgp161	Glycerophospholipid Metabolism	2.7.8.5	b1912	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : cdpdhdec9eg[c] + glyc3p[c] --> cmp[c] + pgp161[c] 
19262	PGSA180	Yes	Phosphatidylglycerol synthase (n-C18:0)	[c] : cdpdodecg + glyc3p --> cmp + h + pgp180	Glycerophospholipid Metabolism	2.7.8.5	b1912	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : cdpdodecg[c] + glyc3p[c] --> cmp[c] + pgp180[c] 
19265	PGSA181	Yes	Phosphatidylglycerol synthase (n-C18:1)	[c] : cdpdodec11eg + glyc3p --> cmp + h + pgp181	Glycerophospholipid Metabolism	2.7.8.5	b1912	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-4.65732	2.09859	[c] : cdpdodec11eg[c] + glyc3p[c] --> cmp[c] + pgp181[c] 
11771	PHEMEabcpp	Yes	protoheme transport via ABC system (periplasm)	atp[c] + h2o[c] + pheme[c] --> adp[c] + h[c] + pheme[p] + pi[c]	Update		( b2201  and  b2200  and  b2199 )	AMF	"Analysis of a ccmA  deletion mutant has suggested that CcmAB is not essential for heme export [ Cook 00  ].

All subunits were assigned to the reaction anyway, needs further analysis."	-7.01673	1.48181	[c] : atp[c] + h2o[c] + pheme[c] --> adp[c] + h[c] + pheme[p] + pi[c] 
12331	PHEMEtiex	Yes	protoheme transport irreversible out via diffusion (periplasm to extracellular)	pheme[p] --> pheme[e]	"Transport, Outer Membrane"			"AMF
assumed diffusion
"	"Assumed that pheme can leave the periplasm without any energy requirement since it is exported by ccmABC
AMF"	0	0	[c] : pheme[p] --> pheme[e] 
8903	PHEt2rpp	Yes	L-phenylalanine reversible transport via proton symport (periplasm)	h[p] + phe-L[p] <==> h[c] + phe-L[c]	"Transport, Inner Membrane"		( b0112  or  b0576 )	NCD		0	0	[c] : h[p] + phe-L[p] <==> h[c] + phe-L[c] 
2860	PHETA1	No	phenylalanine transaminase	[c] : akg + phe-L <==> glu-L + phpyr	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	2.6.1.58	( b4054  or  b3770  or  b0928 )			0	0.5	[c] : akg[c] + phe-L[c] <==> glu-L[c] + phpyr[c] 
9189	PHEtex	Yes	L-phenylalanine transport via diffusion (extracellular to periplasm)	phe-L[e] <==> phe-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : phe-L[e] <==> phe-L[p] 		
1036	PHETRS	Yes	Phenylalanyl-tRNA synthetase	[c] : atp + phe-L + trnaphe --> amp + phetrna + ppi	Update	6.1.1.20	( b1713  and  b1714 )		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + phe-L[c] + trnaphe[c] --> amp[c] + phetrna[c] + ppi[c] 		
9009	PHYTSpp	Yes	Phytase (periplasm)	[p] : (6) h2o + minohp --> inost + (6) pi	Update		b0980	"JLR 
3.1.3.8 and 3.1.8.26"		-21.2891	12.7768	[p] : (6) h2o[p] + minohp[p] --> (6) h[p] + inost[p] + (6) pi[p] 		
8905	PIt2rpp	Yes	phosphate reversible transport via symport (periplasm)	h[p] + pi[p] <==> h[c] + pi[c]	"Transport, Inner Membrane"		( b2987  or  b3493 )	NCD		0	0	[c] : h[p] + pi[p] <==> h[c] + pi[c] 		
9190	PItex	Yes	phosphate transport via diffusion (extracellular to periplasm)	pi[e] <==> pi[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : pi[e] <==> pi[p] 		
8904	PIuabcpp	Yes	"phosphate transport via ABC system (uptake, periplasm)"	atp[c] + h2o[c] + pi[p] --> adp[c] + h[c] + (2) pi[c]	"Transport, Inner Membrane"		( b3726  and  b3725  and  b3727  and  b3728 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + pi[p] --> adp[c] + h[c] + (2) pi[c] 		
19892	PLIPA1A120pp	Yes	"Phospholipase A1 (phosphatidate, n-C12:0) (periplasm)"	[p] : h2o + pa120 --> 2ddecg3p + ddca + h	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa120[p] --> 2ddecg3p[p] + ddca[p] + h[p] 		
19893	PLIPA1A140pp	Yes	"Phospholipase A1 (phosphatidate, n-C14:0) (periplasm)"	[p] : h2o + pa140 --> 2tdecg3p + h + ttdca	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa140[p] --> 2tdecg3p[p] + h[p] + ttdca[p] 		
19896	PLIPA1A141pp	Yes	"Phospholipase A1 (phosphatidate, n-C14:1) (periplasm)"	[p] : h2o + pa141 --> 2tdec7eg3p + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-5.46248	3.50439	[p] : h2o[p] + pa141[p] --> 2tdec7eg3p[p] + h[p] + ttdcea[p] 		
19894	PLIPA1A160pp	Yes	"Phospholipase A1 (phosphatidate, n-C16:0) (periplasm)"	[p] : h2o + pa160 --> 2hdecg3p + h + hdca	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa160[p] --> 2hdecg3p[p] + h[p] + hdca[p] 		
19897	PLIPA1A161pp	Yes	"Phospholipase A1 (phosphatidate, n-C16:1) (periplasm)"	[p] : h2o + pa161 --> 2hdec9eg3p + h + hdcea	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa161[p] --> 2hdec9eg3p[p] + h[p] + hdcea[p] 		
19895	PLIPA1A180pp	Yes	"Phospholipase A1 (phosphatidate, n-C18:0) (periplasm)"	[p] : h2o + pa180 --> 2odecg3p + h + ocdca	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa180[p] --> 2odecg3p[p] + h[p] + ocdca[p] 		
19898	PLIPA1A181pp	Yes	"Phospholipase A1 (phosphatidate, n-C18:1) (periplasm)"	[p] : h2o + pa181 --> 2odec11eg3p + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa181[p] --> 2odec11eg3p[p] + h[p] + ocdcea[p] 		
19867	PLIPA1E120pp	Yes	"Phospholipase A1 (phosphatidylethanolamine, n-C12:0) (periplasm)"	[p] : h2o + pe120 --> 2agpe120 + ddca + h	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe120[p] --> 2agpe120[p] + ddca[p] + h[p] 		
19880	PLIPA1E140pp	Yes	"Phospholipase A1 (phosphatidylethanolamine, n-C14:0) (periplasm)"	[p] : h2o + pe140 --> 2agpe140 + h + ttdca	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe140[p] --> 2agpe140[p] + h[p] + ttdca[p] 		
19883	PLIPA1E141pp	Yes	"Phospholipase A1 (phosphatidylethanolamine, n-C14:1) (periplasm)"	[p] : h2o + pe141 --> 2agpe141 + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-5.46248	3.50439	[p] : h2o[p] + pe141[p] --> 2agpe141[p] + h[p] + ttdcea[p] 		
19881	PLIPA1E160pp	Yes	"Phospholipase A1 (phosphatidylethanolamine, n-C16:0) (periplasm)"	[p] : h2o + pe160 --> 2agpe160 + h + hdca	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe160[p] --> 2agpe160[p] + h[p] + hdca[p] 		
19884	PLIPA1E161pp	Yes	"Phospholipase A1 (phosphatidylethanolamine, n-C16:1) (periplasm)"	[p] : h2o + pe161 --> 2agpe161 + h + hdcea	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe161[p] --> 2agpe161[p] + h[p] + hdcea[p] 		
19882	PLIPA1E180pp	Yes	"Phospholipase A1 (phosphatidylethanolamine, n-C18:0) (periplasm)"	[p] : h2o + pe180 --> 2agpe180 + h + ocdca	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe180[p] --> 2agpe180[p] + h[p] + ocdca[p] 		
19885	PLIPA1E181pp	Yes	"Phospholipase A1 (phosphatidylethanolamine, n-C18:1) (periplasm)"	[p] : h2o + pe181 --> 2agpe181 + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe181[p] --> 2agpe181[p] + h[p] + ocdcea[p] 		
19878	PLIPA1G120pp	Yes	"Phospholipase A1 (phosphatidylglycerol, n-C12:0) (periplasm)"	[p] : h2o + pg120 --> 2agpg120 + ddca + h	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg120[p] --> 2agpg120[p] + ddca[p] + h[p] 		
19886	PLIPA1G140pp	Yes	"Phospholipase A1 (phosphatidylglycerol, n-C14:0) (periplasm)"	[p] : h2o + pg140 --> 2agpg140 + h + ttdca	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg140[p] --> 2agpg140[p] + h[p] + ttdca[p] 		
19889	PLIPA1G141pp	Yes	"Phospholipase A1 (phosphatidylglycerol, n-C14:1) (periplasm)"	[p] : h2o + pg141 --> 2agpg141 + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-5.46248	3.50439	[p] : h2o[p] + pg141[p] --> 2agpg141[p] + h[p] + ttdcea[p] 		
19887	PLIPA1G160pp	Yes	"Phospholipase A1 (phosphatidylglycerol, n-C16:0) (periplasm)"	[p] : h2o + pg160 --> 2agpg160 + h + hdca	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg160[p] --> 2agpg160[p] + h[p] + hdca[p] 		
19890	PLIPA1G161pp	Yes	"Phospholipase A1 (phosphatidylglycerol, n-C16:1) (periplasm)"	[p] : h2o + pg161 --> 2agpg161 + h + hdcea	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg161[p] --> 2agpg161[p] + h[p] + hdcea[p] 		
19888	PLIPA1G180pp	Yes	"Phospholipase A1 (phosphatidylglycerol, n-C18:0) (periplasm)"	[p] : h2o + pg180 --> 2agpg180 + h + ocdca	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg180[p] --> 2agpg180[p] + h[p] + ocdca[p] 		
19891	PLIPA1G181pp	Yes	"Phospholipase A1 (phosphatidylglycerol, n-C18:1) (periplasm)"	[p] : h2o + pg181 --> 2agpg181 + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.32	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg181[p] --> 2agpg181[p] + h[p] + ocdcea[p] 		
20071	PLIPA2A120pp	Yes	"Phospholipase A2 (phosphatidate, n-C12:0) (periplasm)"	[p] : h2o + pa120 --> 1ddecg3p + ddca + h	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa120[p] --> 1ddecg3p[p] + ddca[p] + h[p] 		
20072	PLIPA2A140pp	Yes	"Phospholipase A2 (phosphatidate, n-C14:0) (periplasm)"	[p] : h2o + pa140 --> 1tdecg3p + h + ttdca	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa140[p] --> 1tdecg3p[p] + h[p] + ttdca[p] 		
20073	PLIPA2A141pp	Yes	"Phospholipase A2 (phosphatidate, n-C14:1) (periplasm)"	[p] : h2o + pa141 --> 1tdec7eg3p + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-5.46248	3.50439	[p] : h2o[p] + pa141[p] --> 1tdec7eg3p[p] + h[p] + ttdcea[p] 		
20074	PLIPA2A160pp	Yes	"Phospholipase A2 (phosphatidate, n-C16:0) (periplasm)"	[p] : h2o + pa160 --> 1hdecg3p + h + hdca	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa160[p] --> 1hdecg3p[p] + h[p] + hdca[p] 		
20075	PLIPA2A161pp	Yes	"Phospholipase A2 (phosphatidate, n-C16:1) (periplasm)"	[p] : h2o + pa161 --> 1hdec9eg3p + h + hdcea	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa161[p] --> 1hdec9eg3p[p] + h[p] + hdcea[p] 		
20076	PLIPA2A180pp	Yes	"Phospholipase A2 (phosphatidate, n-C18:0) (periplasm)"	[p] : h2o + pa180 --> 1odecg3p + h + ocdca	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa180[p] --> 1odecg3p[p] + h[p] + ocdca[p] 		
20077	PLIPA2A181pp	Yes	"Phospholipase A2 (phosphatidate, n-C18:1) (periplasm)"	[p] : h2o + pa181 --> 1odec11eg3p + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pa181[p] --> 1odec11eg3p[p] + h[p] + ocdcea[p] 		
20078	PLIPA2E120pp	Yes	"Phospholipase A2 (phosphatidylethanolamine, n-C12:0) (periplasm)"	[p] : h2o + pe120 --> 1agpe120 + ddca + h	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe120[p] --> 1agpe120[p] + ddca[p] + h[p] 		
20079	PLIPA2E140pp	Yes	"Phospholipase A2 (phosphatidylethanolamine, n-C14:0) (periplasm)"	[p] : h2o + pe140 --> 1agpe140 + h + ttdca	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe140[p] --> 1agpe140[p] + h[p] + ttdca[p] 		
20080	PLIPA2E141pp	Yes	"Phospholipase A2 (phosphatidylethanolamine, n-C14:1) (periplasm)"	[p] : h2o + pe141 --> 1agpe141 + h + ttdcea	Glycerophospholipid Metabolism	3.1.14	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-7.05607	5.5862	[p] : h2o[p] + pe141[p] --> 1agpe141[p] + h[p] + ttdcea[p] 		
20081	PLIPA2E160pp	Yes	"Phospholipase A2 (phosphatidylethanolamine, n-C16:0) (periplasm)"	[p] : h2o + pe160 --> 1agpe160 + h + hdca	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe160[p] --> 1agpe160[p] + h[p] + hdca[p] 		
20082	PLIPA2E161pp	Yes	"Phospholipase A2 (phosphatidylethanolamine, n-C16:1) (periplasm)"	[p] : h2o + pe161 --> 1agpe161 + h + hdcea	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe161[p] --> 1agpe161[p] + h[p] + hdcea[p] 		
20083	PLIPA2E180pp	Yes	"Phospholipase A2 (phosphatidylethanolamine, n-C18:0) (periplasm)"	[p] : h2o + pe180 --> 1agpe180 + h + ocdca	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe180[p] --> 1agpe180[p] + h[p] + ocdca[p] 		
20084	PLIPA2E181pp	Yes	"Phospholipase A2 (phosphatidylethanolamine, n-C18:1) (periplasm)"	[p] : h2o + pe181 --> 1agpe181 + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pe181[p] --> 1agpe181[p] + h[p] + ocdcea[p] 		
20085	PLIPA2G120pp	Yes	"Phospholipase A2 (phosphatidylglycerol, n-C12:0) (periplasm)"	[p] : h2o + pg120 --> 1agpg120 + ddca + h	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg120[p] --> 1agpg120[p] + ddca[p] + h[p] 		
20086	PLIPA2G140pp	Yes	"Phospholipase A2 (phosphatidylglycerol, n-C14:0) (periplasm)"	[p] : h2o + pg140 --> 1agpg140 + h + ttdca	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg140[p] --> 1agpg140[p] + h[p] + ttdca[p] 		
20087	PLIPA2G141pp	Yes	"Phospholipase A2 (phosphatidylglycerol, n-C14:1) (periplasm)"	[p] : h2o + pg141 --> 1agpg141 + h + ttdcea	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-7.05607	5.5862	[p] : h2o[p] + pg141[p] --> 1agpg141[p] + h[p] + ttdcea[p] 		
20088	PLIPA2G160pp	Yes	"Phospholipase A2 (phosphatidylglycerol, n-C16:0) (periplasm)"	[p] : h2o + pg160 --> 1agpg160 + h + hdca	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg160[p] --> 1agpg160[p] + h[p] + hdca[p] 		
20089	PLIPA2G161pp	Yes	"Phospholipase A2 (phosphatidylglycerol, n-C16:1) (periplasm)"	[p] : h2o + pg161 --> 1agpg161 + h + hdcea	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg161[p] --> 1agpg161[p] + h[p] + hdcea[p] 		
20090	PLIPA2G180pp	Yes	"Phospholipase A2 (phosphatidylglycerol, n-C18:0) (periplasm)"	[p] : h2o + pg180 --> 1agpg180 + h + ocdca	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg180[p] --> 1agpg180[p] + h[p] + ocdca[p] 		
20091	PLIPA2G181pp	Yes	"Phospholipase A2 (phosphatidylglycerol, n-C18:1) (periplasm)"	[p] : h2o + pg181 --> 1agpg181 + h + ocdcea	Glycerophospholipid Metabolism	3.1.1.4	b3821	AMF	"PMID: 4946924 gives evidence for activity on pc, pe, pg, cardiolipin and this gene is hypothesized to be pldA by PMID: 14002
JLR

PMID: 2653433 characterizes pldA and states that although it can act as a phospholipase A1 or A2 or lysophospholipase L1 or L2 the enzyme will initially act as a phospholipase A1 in the Ecoli envelope where it is embeded in phopsholipids.  Also states a broad specificity.

From PMID: 11080680 _ Review on PldA
_The enzyme is strictly calcium dependent and displays a broad substrate specificity. Besides phospholipase A1 and A2 activity the enzyme also harbours lysophospholipase A1 and A2 activity, and mono- and diacylglyceride lipase activity. The minimal substrate requirements of the enzyme are a more or less polar head group esterified to an acyl chain of at least 14 carbon atoms._ _ enzyme assigned to act on n-C12 as well.

PldA was assigned to A2 activity as well (see TesA gene reaction)

Not sure which face of the membrane the active site of the enzyme lies.

AMF"	-3.8689	2.44385	[p] : h2o[p] + pg181[p] --> 1agpg181[p] + h[p] + ocdcea[p] 		
243	PMANM	No	phosphomannomutase	[c] : man1p <==> man6p	Alternate Carbon Metabolism	5.4.2.8	b2048			-1.18877	2.59673	[c] : man1p[c] <==> man6p[c] 					
808	PMDPHT	No	pyrimidine phosphatase	[c] : 5aprbu + h2o --> 4r5au + pi	Cofactor and Prosthetic Group Biosynthesis					-2.35942	1.9257	[c] : 5aprbu[c] + h2o[c] --> 4r5au[c] + h[c] + pi[c] 					
2781	PMPK	No	phosphomethylpyrimidine kinase	[c] : 4ampm + atp --> 2mahmp + adp	Cofactor and Prosthetic Group Biosynthesis	2.7.4.7	b2103		"see PMID: 15150256
AMF
"	0	0.5	[c] : 4ampm[c] + atp[c] --> 2mahmp[c] + adp[c] 					
2788	PNTK	No	pantothenate kinase	[c] : atp + pnto-R --> 4ppan + adp + h	Cofactor and Prosthetic Group Biosynthesis	2.7.1.33	b3974			-4.65732	2.09859	[c] : atp[c] + pnto-R[c] --> 4ppan[c] + adp[c] 					
8906	PNTOt4pp	Yes	Pantothenate sodium symporter (periplasm)	na1[p] + pnto-R[p] --> na1[c] + pnto-R[c]	"Transport, Inner Membrane"		b3258	JLR		0	0	[c] : na1[p] + pnto-R[p] --> na1[c] + pnto-R[c] 					
9191	PNTOtex	Yes	Pantothenate transport via diffusion (extracellular to periplasm)	pnto-R[e] <==> pnto-R[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : pnto-R[e] <==> pnto-R[p] 					
1187	POX	No	pyruvate oxidase	[c] : h2o + pyr + q8 --> ac + co2 + q8h2	Oxidative Phosphorylation	1.2.2.2	b0871	JLR		-35.8243	21.3463	[c] : h2o[c] + pyr[c] + q8[c] --> ac[c] + co2[c] + q8h2[c] 					
295	PPA	No	inorganic diphosphatase	[c] : h2o + ppi --> h + (2) pi	Anaplerotic reactions	3.6.1.1	( b4226  or  b2744  or  b2502 )			-5.44	1.58114	[c] : h2o[c] + ppi[c] --> (2) h[c] + (2) pi[c] 					
12355	PPA2	Yes	inorganic triphosphatase	[c] : h2o + pppi --> h + pi + ppi	Update	3.6.1.1	( b2744  or  b2502 )	"AMF
"	"SurE
PMID: 15489502
no 3'-nmp assigned since not in model
E. coli SurE showed significant activity toward nucleoside 5'-or3'-monophosphates (Fig. 3A). The protein hydrolyzed both purine and pyrimidine ribo- and deoxyribonucleotides effectively and had a neutral pH optimum (pH 7.0_7.2) (Fig. 3B). With all substrates, the protein showed saturation kinetics with high affinity to 3'-AMP, 5'-GMP, 5'-dGMP, 5'-AMP, and 3'-CMP.  The only non-nucleotide natural substrate hydrolyzed by the E. coli SurE was found to be polyphosphate.

YfbR is a Co2+-dependent 5'-nucleotidase with a strict specificity to deoxyribonucleotides. also, 4nphp

YjjG is an Mn2+-dependent 5'-nucleotidase specific to 5'-UMP, 5'-dUMP, and 5'-dTMP. also, 4nphp"	No energy	No energy	[c] : h2o[c] + pppi[c] --> pi[c] + ppi[c] 					
2253	PPAKr	No	Propionate kinase	[c] : adp + ppap <==> atp + ppa	Alternate Carbon Metabolism	2.7.2.1	b3115	JLR (R01353)		-3.00718	2.24154	[c] : adp[c] + ppap[c] <==> atp[c] + h[c] + ppa[c] 					
3553	PPBNGS	No	porphobilinogen synthase	[c] : (2) 5aop --> h + (2) h2o + ppbng	Cofactor and Prosthetic Group Biosynthesis	4.2.1.24	b0369			-15.1256	7.42284	[c] : (2) 5aop[c] --> h[c] + (2) h2o[c] + ppbng[c] 					
205	PPC	No	phosphoenolpyruvate carboxylase	[c] : co2 + h2o + pep --> h + oaa + pi	Anaplerotic reactions	4.1.1.31	b3956			-8.04098	3.65614	[c] : co2[c] + h2o[c] + pep[c] --> (2) h[c] + oaa[c] + pi[c] 					
87	PPCDC	No	phosphopantothenoylcysteine decarboxylase	[c] : 4ppcys + h --> co2 + pan4p	Cofactor and Prosthetic Group Biosynthesis	4.1.1.36	b3639		"PMID: 11278255
characterizes one of the functions and cites the work for the other characterization in the abstract
AMF"	-4.96805	1.79669	[c] : 4ppcys[c] + h[c] --> co2[c] + pan4p[c] 					
296	PPCK	No	phosphoenolpyruvate carboxykinase	[c] : atp + oaa --> adp + co2 + pep	Anaplerotic reactions	4.1.1.49	b3403			1.02425	3.68282	[c] : atp[c] + h[c] + oaa[c] --> adp[c] + co2[c] + pep[c] 					
2306	PPCSCT	No	Propanoyl-CoA: succinate CoA-transferase	[c] : ppcoa + succ --> ppa + succoa	Alternate Carbon Metabolism		b2920	JLR		0	0.5	[c] : ppcoa[c] + succ[c] --> ppa[c] + succoa[c] 					
13386	PPGPPDP	Yes	"guanosine-3',5'-bis(diphosphate) 3'-diphosphatase"	[c] : h2o + ppgpp --> gdp + ppi	Update	3.1.7.2	b3650	AMF	"4 reactions are involved in the ppGpp biosynthesis pathway
ppGpp is a signalling molecule

gppA : PMID: 8394006
RelA: PMID: 2844820
"	-5.92809	2.30864	[c] : h2o[c] + ppgpp[c] --> gdp[c] + ppi[c] 					
13882	PPK2r	Yes	polyphosphate kinase	[c] : atp + ppi <==> adp + pppi	Update	2.7.4.1	b2501	"ATP:polyphosphate phosphotransferase; KEGG R00196
SMP (11/21/2002)"	"from Ecocyc:
The reaction is readily reversible. PPK is most active with poly(Pi) substrates of chain lengths greater than 132 phosphoryl units.
AMF"	No energy	No energy	[c] : atp[c] + ppi[c] <==> adp[c] + h[c] + pppi[c] 					
4304	PPKr	Yes	polyphosphate kinase	[c] : atp + pi <==> adp + ppi	Update	2.7.4.1	b2501		"from Ecocyc:
The reaction is readily reversible. PPK is most active with poly(Pi) substrates of chain lengths greater than 132 phosphoryl units.
AMF"	-1.57673	1.48181	[c] : atp[c] + h[c] + pi[c] <==> adp[c] + ppi[c] 					
258	PPM	No	phosphopentomutase	[c] : r1p <==> r5p	Alternate Carbon Metabolism	5.4.2.7	( b4383  or  b3380 )			-1.18877	2.59673	[c] : r1p[c] <==> r5p[c] 					
4684	PPM2	No	phosphopentomutase 2 (deoxyribose)	[c] : 2dr1p <==> 2dr5p	Alternate Carbon Metabolism	5.4.2.7	b4383	"tv, JLR"		-1.18877	2.59673	[c] : 2dr1p[c] <==> 2dr5p[c] 					
3555	PPNCL2	No	phosphopantothenate-cysteine ligase	[c] : 4ppan + ctp + cys-L --> 4ppcys + cmp + h + ppi	Cofactor and Prosthetic Group Biosynthesis	6.3.2.5	b3639	JLR	"PMID: 11278255
characterizes one of the functions and cites the work for the other characterization in the abstract
AMF"	-5.22858	4.12076	[c] : 4ppan[c] + ctp[c] + cys-L[c] --> 4ppcys[c] + cmp[c] + ppi[c] 					
2861	PPND	No	prephenate dehydrogenase	[c] : nad + pphn --> 34hpp + co2 + nadh	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	1.3.1.12	b2600			-4.70358	12.5038	[c] : nad[c] + pphn[c] --> 34hpp[c] + co2[c] + nadh[c] 					
3849	PPNDH	No	prephenate dehydratase	[c] : h + pphn --> co2 + h2o + phpyr	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.2.1.51	b2599			-17.7087	10.1712	[c] : h[c] + pphn[c] --> co2[c] + h2o[c] + phpyr[c] 					
3646	PPPGO	No	protoporphyrinogen oxidase	[c] : (1.5) o2 + pppg9 --> (3) h2o + ppp9	Cofactor and Prosthetic Group Biosynthesis	1.3.3.4	b3850	change name from PPPGO2 to PPPGO -tv		No energy	No energy	[c] : (1.5) o2[c] + pppg9[c] --> (3) h2o[c] + ppp9[c] 					
3198	PPPNDO	No	Phenylpropanoate Dioxygenase	[c] : h + nadh + o2 + pppn --> cechddd + nad	Alternate Carbon Metabolism		( b2538  and  b2539  and  b2540  and  b2542 )	JLR- see PMID 9603882		-73.6331	11.2416	[c] : h[c] + nadh[c] + o2[c] + pppn[c] --> cechddd[c] + nad[c] 					
8907	PPPNt2rpp	Yes	"3-phenylpropionate transport via proton symport, reversible (periplasm)"	h[p] + pppn[p] <==> h[c] + pppn[c]	Putative Transporters		b2536	JLR		0	0	[c] : h[p] + pppn[p] <==> h[c] + pppn[c] 					
9192	PPPNtex	Yes	3-phenylpropionate transport via diffusion (extracellular to periplasm)	pppn[e] <==> pppn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : pppn[e] <==> pppn[p] 					
270	PPS	No	phosphoenolpyruvate synthase	[c] : atp + h2o + pyr --> amp + (2) h + pep + pi	Glycolysis/Gluconeogenesis	2.7.9.2	b1702	"SMP
Note: two protons generated"		-1.50112	4.21932	[c] : atp[c] + h2o[c] + pyr[c] --> amp[c] + h[c] + pep[c] + pi[c] 					
9010	PPTHpp	Yes	Phosphonate hydrogenase (periplasm)	[p] : h2o + ppt --> h2 + pi	Update		b0383	JLR	EcoCyc comments that it is a periplasmic enzyme	No energy	No energy	[p] : h2o[p] + ppt[p] --> h[p] + h2[p] + pi[p] 					
9193	PPTtex	Yes	Phosphonate transport via diffusion (extracellular to periplasm)	ppt[e] <==> ppt[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ppt[e] <==> ppt[p] 					
3556	PRAGSr	No	phosphoribosylglycinamide synthase	[c] : atp + gly + pram <==> adp + gar + h + pi	Purine and Pyrimidine Biosynthesis	6.3.4.13	b4005	"JLR- added reversible form of PRAGS
"		-3.65185	3.59073	[c] : atp[c] + gly[c] + pram[c] <==> adp[c] + gar[c] + h[c] + pi[c] 					
1051	PRAIi	No	phosphoribosylanthranilate isomerase (irreversible)	[c] : pran --> 2cpr5p	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	5.3.1.24	b1262	JLR- added irreversible form of PRAI	"irreversible, page 465 NH
JLR
AMF"	-1.17835	7.18704	[c] : pran[c] --> 2cpr5p[c] 					
3640	PRAIS	No	phosphoribosylaminoimidazole synthase	[c] : atp + fpram --> adp + air + (2) h + pi	Purine and Pyrimidine Biosynthesis	6.3.3.1	b2499			No energy	No energy	[c] : atp[c] + fpram[c] --> adp[c] + air[c] + h[c] + pi[c] 					
2864	PRAMPC	No	phosphoribosyl-AMP cyclohydrolase	[c] : h2o + prbamp --> prfp	Histidine Metabolism	3.5.4.19	b2026			3.97792	8.52022	[c] : h2o[c] + prbamp[c] --> h[c] + prfp[c] 					
3641	PRASCS	No	phosphoribosylaminoimidazolesuccinocarboxamide synthase	[c] : 5aizc + asp-L + atp <==> 25aics + adp + h + pi	Purine and Pyrimidine Biosynthesis	6.3.2.6	b2476			-9.6259	5.11124	[c] : 5aizc[c] + asp-L[c] + atp[c] <==> 25aics[c] + adp[c] + (2) h[c] + pi[c] 					
344	PRATPP	No	phosphoribosyl-ATP pyrophosphatase	[c] : h2o + prbatp --> h + ppi + prbamp	Histidine Metabolism	3.6.1.31	b2026			-8.59346	2.5066	[c] : h2o[c] + prbatp[c] --> ppi[c] + prbamp[c] 					
3558	PRFGS	No	phosphoribosylformylglycinamidine synthase	[c] : atp + fgam + gln-L + h2o --> adp + fpram + glu-L + h + pi	Purine and Pyrimidine Biosynthesis	6.3.5.3	b2557			-21.322	5.98696	[c] : atp[c] + fgam[c] + gln-L[c] + h2o[c] --> adp[c] + fpram[c] + glu-L[c] + (2) h[c] + pi[c] 					
345	PRMICI	Yes	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase	[c] : prfp <==> prlp	Histidine Metabolism	5.3.1.16	b2024		"assumed reversibility
AMF"	-1.17835	7.18704	[c] : prfp[c] <==> prlp[c] 					
8908	PROabcpp	Yes	L-proline transport via ABC system (periplasm)	atp[c] + h2o[c] + pro-L[p] --> adp[c] + h[c] + pi[c] + pro-L[c]	"Transport, Inner Membrane"		( b2677  and  b2678  and  b2679 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + pro-L[p] --> adp[c] + h[c] + pi[c] + pro-L[c] 					
3642	PROD2	No	Proline dehydrogenase	[c] : fad + pro-L --> 1pyr5c + fadh2 + h	Arginine and Proline Metabolism	1.5.99.8	b1014	JLR		No energy	No energy	[c] : fad[c] + pro-L[c] --> 1pyr5c[c] + fadh2[c] + h[c] 					
19732	PROGLYabcpp	Yes	L-Prolinylglycine (Pro-Gly) transport via ABC system (periplasm)	atp[c] + h2o[c] + progly[p] --> adp[c] + h[c] + pi[c] + progly[c]	"Transport, Inner Membrane"		( b3544  and  b3543  and  b3542  and  b3541  and  b3540 )	AMF	"PMID: 1702779 characterizes DppA as required for growth on Pro-gly
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + progly[p] --> adp[c] + h[c] + pi[c] + progly[c] 					
19733	PROGLYtex	Yes	L-Prolinylglycine transport via diffusion (extracellular to periplasm)	progly[e] <==> progly[p]	"Transport, Outer Membrane"			AMF	assumed diffusion through the outermembrane	0	0	[c] : progly[e] <==> progly[p] 					
8909	PROt2rpp	Yes	L-proline reversible transport via proton symport (periplasm)	h[p] + pro-L[p] <==> h[c] + pro-L[c]	"Transport, Inner Membrane"		b4111	NCD		0	0	[c] : h[p] + pro-L[p] <==> h[c] + pro-L[c] 					
8910	PROt4pp	Yes	Na+/Proline-L symporter (periplasm)	na1[p] + pro-L[p] --> na1[c] + pro-L[c]	"Transport, Inner Membrane"		b1015	JLR		0	0	[c] : na1[p] + pro-L[p] --> na1[c] + pro-L[c] 					
9194	PROtex	Yes	L-proline transport via diffusion (extracellular to periplasm)	pro-L[e] <==> pro-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : pro-L[e] <==> pro-L[p] 					
2917	PROTRS	Yes	Prolyl-tRNA synthetase	[c] : atp + pro-L + trnapro --> amp + ppi + protrna	Update	6.1.1.15	b0194		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + pro-L[c] + trnapro[c] --> amp[c] + ppi[c] + protrna[c] 					
343	PRPPS	No	phosphoribosylpyrophosphate synthetase	[c] : atp + r5p <==> amp + h + prpp	Histidine Metabolism	2.7.6.1	b1207			-2.66537	2.19769	[c] : atp[c] + r5p[c] <==> amp[c] + prpp[c] 					
328	PSCVT	No	3-phosphoshikimate 1-carboxyvinyltransferase	[c] : pep + skm5p <==> 3psme + pi	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	2.5.1.19	b0908			-1.02381	2.72189	[c] : pep[c] + skm5p[c] <==> 3psme[c] + h[c] + pi[c] 					
19332	PSD120	Yes	Phosphatidylserine decarboxylase (n-C12:0)	[c] : h + ps120 --> co2 + pe120	Glycerophospholipid Metabolism	4.1.1.65	b4160	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	3.82264	3.26832	[c] : (2) h[c] + ps120[c] --> co2[c] + pe120[c] 		
19285	PSD140	Yes	Phosphatidylserine decarboxylase (n-C14:0)	[c] : h + ps140 --> co2 + pe140	Glycerophospholipid Metabolism	4.1.1.65	b4160	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	3.82264	3.26832	[c] : (2) h[c] + ps140[c] --> co2[c] + pe140[c] 		
19288	PSD141	Yes	Phosphatidylserine decarboxylase (n-C14:1)	[c] : h + ps141 --> co2 + pe141	Glycerophospholipid Metabolism	4.1.1.65	b4160	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	3.82264	3.26832	[c] : (2) h[c] + ps141[c] --> co2[c] + pe141[c] 		
19289	PSD160	Yes	Phosphatidylserine decarboxylase (n-C16:0)	[c] : h + ps160 --> co2 + pe160	Glycerophospholipid Metabolism	4.1.1.65	b4160	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	3.82264	3.26832	[c] : (2) h[c] + ps160[c] --> co2[c] + pe160[c] 		
19290	PSD161	Yes	Phosphatidylserine decarboxylase (n-C16:1)	[c] : h + ps161 --> co2 + pe161	Glycerophospholipid Metabolism	4.1.1.65	b4160	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	3.82264	3.26832	[c] : (2) h[c] + ps161[c] --> co2[c] + pe161[c] 		
19291	PSD180	Yes	Phosphatidylserine decarboxylase (n-C18:0)	[c] : h + ps180 --> co2 + pe180	Glycerophospholipid Metabolism	4.1.1.65	b4160	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	3.82264	3.26832	[c] : (2) h[c] + ps180[c] --> co2[c] + pe180[c] 		
19292	PSD181	Yes	Phosphatidylserine decarboxylase (n-C18:1)	[c] : h + ps181 --> co2 + pe181	Glycerophospholipid Metabolism	4.1.1.65	b4160	AMF	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	3.82264	3.26832	[c] : (2) h[c] + ps181[c] --> co2[c] + pe181[c] 		
913	PSERT	No	phosphoserine transaminase	[c] : 3php + glu-L --> akg + pser-L	Glycine and Serine Metabolism	2.6.1.52	b0907			0	0.5	[c] : 3php[c] + glu-L[c] --> akg[c] + pser-L[c] 		
13828	PSERtex	Yes	phospho-L-serine transport via diffusion (extracellular to periplasm)	pser-L[e] <==> pser-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : pser-L[e] <==> pser-L[p] 		
4642	PSP_L	No	phosphoserine phosphatase (L-serine)	[c] : h2o + pser-L --> pi + ser-L	Glycine and Serine Metabolism	3.1.3.3	b4388			-2.35942	1.9257	[c] : h2o[c] + pser-L[c] --> h[c] + pi[c] + ser-L[c] 		
13822	PSP_Lpp	Yes	phospho-L-serine phosphatase (periplasmic)	[p] : h2o + pser-L --> pi + ser-L	Update		b4055	AMF	"from PMID: 9011040
AMF
very general phosphatase"	-2.35942	1.9257	[p] : h2o[p] + pser-L[p] --> h[p] + pi[p] + ser-L[p] 		
19331	PSSA120	Yes	Phosphatidylserine syntase (n-C12:0)	[c] : cdpdddecg + ser-L --> cmp + h + ps120	Glycerophospholipid Metabolism	2.7.8.8	b2585	AMF - not sure of reversibility	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-13.448	3.88795	[c] : cdpdddecg[c] + ser-L[c] --> cmp[c] + h[c] + ps120[c] 		
19278	PSSA140	Yes	Phosphatidylserine syntase (n-C14:0)	[c] : cdpdtdecg + ser-L --> cmp + h + ps140	Glycerophospholipid Metabolism	2.7.8.8	b2585	AMF - not sure of reversibility	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-13.448	3.88795	[c] : cdpdtdecg[c] + ser-L[c] --> cmp[c] + h[c] + ps140[c] 		
19283	PSSA141	Yes	Phosphatidylserine syntase (n-C14:1)	[c] : cdpdtdec7eg + ser-L --> cmp + h + ps141	Glycerophospholipid Metabolism	2.7.8.8	b2585	AMF - not sure of reversibility	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-13.448	3.88795	[c] : cdpdtdec7eg[c] + ser-L[c] --> cmp[c] + h[c] + ps141[c] 		
19279	PSSA160	Yes	Phosphatidylserine syntase (n-C16:0)	[c] : cdpdhdecg + ser-L --> cmp + h + ps160	Glycerophospholipid Metabolism	2.7.8.8	b2585	AMF - not sure of reversibility	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-13.448	3.88795	[c] : cdpdhdecg[c] + ser-L[c] --> cmp[c] + h[c] + ps160[c] 		
19282	PSSA161	Yes	Phosphatidylserine syntase (n-C16:1)	[c] : cdpdhdec9eg + ser-L --> cmp + h + ps161	Glycerophospholipid Metabolism	2.7.8.8	b2585	AMF - not sure of reversibility	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-13.448	3.88795	[c] : cdpdhdec9eg[c] + ser-L[c] --> cmp[c] + h[c] + ps161[c] 		
19280	PSSA180	Yes	Phosphatidylserine syntase (n-C18:0)	[c] : cdpdodecg + ser-L --> cmp + h + ps180	Glycerophospholipid Metabolism	2.7.8.8	b2585	AMF - not sure of reversibility	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-13.448	3.88795	[c] : cdpdodecg[c] + ser-L[c] --> cmp[c] + h[c] + ps180[c] 		
19281	PSSA181	Yes	Phosphatidylserine syntase (n-C18:1)	[c] : cdpdodec11eg + ser-L --> cmp + h + ps181	Glycerophospholipid Metabolism	2.7.8.8	b2585	AMF - not sure of reversibility	"reactions are set up to act on FA with two identical -acyl chain lengths
AMF"	-13.448	3.88795	[c] : cdpdodec11eg[c] + ser-L[c] --> cmp[c] + h[c] + ps181[c] 		
2313	PTA2	No	Phosphate acetyltransferase	[c] : pi + ppcoa --> coa + ppap	Alternate Carbon Metabolism		b2297	JLR (R00921)		4.17128	4.56164	[c] : h[c] + pi[c] + ppcoa[c] --> coa[c] + ppap[c] 		
1195	PTAr	No	phosphotransacetylase	[c] : accoa + pi <==> actp + coa	Pyruvate Metabolism	2.3.1.8	( b2297  or  b2458 )	"JLR- added reversible form of PTA reaction.  The reversible form already exists, but it is called PTA_do not use."		4.17128	4.56164	[c] : accoa[c] + h[c] + pi[c] <==> actp[c] + coa[c] 		
13823	PTHRpp	Yes	phospho-L-threonine phosphatase (periplasmic)	[p] : h2o + thrp --> pi + thr-L	Update		b4055	AMF	"from PMID: 9011040
AMF
very general phosphatase"	-3.54819	2.12947	[p] : h2o[p] + thrp[p] --> h[p] + pi[p] + thr-L[p] 		
1836	PTPATi	No	pantetheine-phosphate adenylyltransferase	[c] : atp + h + pan4p --> dpcoa + ppi	Cofactor and Prosthetic Group Biosynthesis	2.7.7.3	b3634	JLR- irreversible form of PTPAT		-1.92466	3.75933	[c] : atp[c] + pan4p[c] --> dpcoa[c] + ppi[c] 		
8911	PTRCabcpp	Yes	putrescine transport via ABC system (periplasm)	atp[c] + h2o[c] + ptrc[p] --> adp[c] + h[c] + pi[c] + ptrc[c]	"Transport, Inner Membrane"		( ( b1126  and  b1125  and  b1124  and  b1123 )  or  ( b0854  and  b0855  and  b0856  and  b0857 )  or  ( b1440  and  b1441  and  b1442  and  b1443 ) )		JLR- EcoCyc indicates taht ydcSTUV form an ABC transport system	-7.01673	1.48181	[c] : atp[c] + h2o[c] + ptrc[p] --> adp[c] + h[c] + pi[c] + ptrc[c] 		
8912	PTRCORNt7pp	Yes	putrescine/ornithine antiporter (periplasm)	orn[c] + ptrc[p] <==> orn[p] + ptrc[c]	"Transport, Inner Membrane"		b0692	AR		0	0	[c] : orn[c] + ptrc[p] <==> orn[p] + ptrc[c] 		
11865	PTRCt2pp	Yes	putrescine transport in via proton symport	h[p] + ptrc[p] --> h[c] + ptrc[c]	Update		b1296	AMF	"Added from PMID: 15590624 AMF

The work proves that this is a transporter, but does not give the method of transport.  Assumed irreversible symport.  Does not state about PotE trasnporter
"	0	0	[c] : h[p] + ptrc[p] --> h[c] + ptrc[c] 		
8913	PTRCt2rpp	Yes	"putrescine transport in via proton symport, reversible (periplasm)"	h[p] + ptrc[p] <==> h[c] + ptrc[c]	"Transport, Inner Membrane"		b0692	JLR		0	0	[c] : h[p] + ptrc[p] <==> h[c] + ptrc[c] 		
1266	PTRCTA	No	Putrescine Transaminase	[c] : akg + ptrc --> 4abutn + glu-L	Arginine and Proline Metabolism	2.6.1.29	b3073	JLR-	"JLR- could not find EC number, based on JSE model.  Assigned to pat gene, but location in genome is unknown (EcoCyc).
YgjG also acts on cadaverine (15dap)

"	2.42139	2.1337	[c] : akg[c] + ptrc[c] --> 4abutn[c] + glu-L[c] 		
9195	PTRCtex	Yes	putrescine transport via diffusion (extracellular to periplasm)	ptrc[e] <==> ptrc[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ptrc[e] <==> ptrc[p] 		
134	PUNP1	No	purine-nucleoside phosphorylase (Adenosine)	[c] : adn + pi <==> ade + r1p	Nucleotide Salvage Pathway	2.4.2.1	b4384	"Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase"	"the deoD gene, referred to below as E. coli PNP-I,
which cleaves adenosine (Ado) more effectively
than Ino and Guo. It was then found that incubation of E. coli in the presence of xanthosine (Xao, but no other base or nucleoside) led to the appearance of a second enzyme, coded for by the induced xapA gene, and capable of efficiently cleaving the 6-oxopurine nucleosides Xao, Guo and Ino (see Figure 1), but not Ado.
PMID: 15808857
AMF
"	1.28439	3.76698	[c] : adn[c] + h[c] + pi[c] <==> ade[c] + r1p[c] 		
135	PUNP2	No	purine-nucleoside phosphorylase (Deoxyadenosine)	[c] : dad-2 + pi <==> 2dr1p + ade	Nucleotide Salvage Pathway	2.4.2.1	b4384	"Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase"	"the deoD gene, referred to below as E. coli PNP-I,
which cleaves adenosine (Ado) more effectively
than Ino and Guo. It was then found that incubation of E. coli in the presence of xanthosine (Xao, but no other base or nucleoside) led to the appearance of a second enzyme, coded for by the induced xapA gene, and capable of efficiently cleaving the 6-oxopurine nucleosides Xao, Guo and Ino (see Figure 1), but not Ado.
PMID: 15808857
AMF"	1.28439	3.76698	[c] : dad-2[c] + h[c] + pi[c] <==> 2dr1p[c] + ade[c] 		
136	PUNP3	No	purine-nucleoside phosphorylase (Guanosine)	[c] : gsn + pi <==> gua + r1p	Nucleotide Salvage Pathway	2.4.2.1	( b2407  or  b4384 )	"Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase"	"the deoD gene, referred to below as E. coli PNP-I,
which cleaves adenosine (Ado) more effectively
than Ino and Guo. It was then found that incubation of E. coli in the presence of xanthosine (Xao, but no other base or nucleoside) led to the appearance of a second enzyme, coded for by the induced xapA gene, and capable of efficiently cleaving the 6-oxopurine nucleosides Xao, Guo and Ino (see Figure 1), but not Ado.
PMID: 15808857
AMF"	1.28439	3.76698	[c] : gsn[c] + h[c] + pi[c] <==> gua[c] + r1p[c] 		
137	PUNP4	No	purine-nucleoside phosphorylase (Deoxyguanosine)	[c] : dgsn + pi <==> 2dr1p + gua	Nucleotide Salvage Pathway	2.4.2.1	( b2407  or  b4384 )	"Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase"	"the deoD gene, referred to below as E. coli PNP-I,
which cleaves adenosine (Ado) more effectively
than Ino and Guo. It was then found that incubation of E. coli in the presence of xanthosine (Xao, but no other base or nucleoside) led to the appearance of a second enzyme, coded for by the induced xapA gene, and capable of efficiently cleaving the 6-oxopurine nucleosides Xao, Guo and Ino (see Figure 1), but not Ado.
PMID: 15808857
AMF"	1.28439	3.76698	[c] : dgsn[c] + h[c] + pi[c] <==> 2dr1p[c] + gua[c] 		
420	PUNP5	No	purine-nucleoside phosphorylase (Inosine)	[c] : ins + pi <==> hxan + r1p	Nucleotide Salvage Pathway	2.4.2.1	( b2407  or  b4384 )	"Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase"	"the deoD gene, referred to below as E. coli PNP-I,
which cleaves adenosine (Ado) more effectively
than Ino and Guo. It was then found that incubation of E. coli in the presence of xanthosine (Xao, but no other base or nucleoside) led to the appearance of a second enzyme, coded for by the induced xapA gene, and capable of efficiently cleaving the 6-oxopurine nucleosides Xao, Guo and Ino (see Figure 1), but not Ado.
PMID: 15808857
AMF"	1.28439	3.76698	[c] : h[c] + ins[c] + pi[c] <==> hxan[c] + r1p[c] 					
421	PUNP6	No	purine-nucleoside phosphorylase (Deoxyinosine)	[c] : din + pi <==> 2dr1p + hxan	Nucleotide Salvage Pathway	2.4.2.1	( b2407  or  b4384 )	"Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase"	"the deoD gene, referred to below as E. coli PNP-I,
which cleaves adenosine (Ado) more effectively
than Ino and Guo. It was then found that incubation of E. coli in the presence of xanthosine (Xao, but no other base or nucleoside) led to the appearance of a second enzyme, coded for by the induced xapA gene, and capable of efficiently cleaving the 6-oxopurine nucleosides Xao, Guo and Ino (see Figure 1), but not Ado.
PMID: 15808857
AMF"	1.28439	3.76698	[c] : din[c] + h[c] + pi[c] <==> 2dr1p[c] + hxan[c] 					
422	PUNP7	No	purine-nucleoside phosphorylase (Xanthosine)	[c] : pi + xtsn <==> r1p + xan	Nucleotide Salvage Pathway	2.4.2.1	b2407	"Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferasextsn	"	"the deoD gene, referred to below as E. coli PNP-I,
which cleaves adenosine (Ado) more effectively
than Ino and Guo. It was then found that incubation of E. coli in the presence of xanthosine (Xao, but no other base or nucleoside) led to the appearance of a second enzyme, coded for by the induced xapA gene, and capable of efficiently cleaving the 6-oxopurine nucleosides Xao, Guo and Ino (see Figure 1), but not Ado.
PMID: 15808857
AMF"	1.28439	3.76698	[c] : h[c] + pi[c] + xtsn[c] <==> r1p[c] + xan[c] 					
1728	PYAM5PO	No	pyridoxamine 5'-phosphate oxidase	[c] : h2o + o2 + pyam5p --> h2o2 + nh4 + pydx5p	Cofactor and Prosthetic Group Biosynthesis	1.4.3.5	b1638	NCD		-18.53	2.13874	[c] : h2o[c] + o2[c] + pyam5p[c] --> h2o2[c] + nh4[c] + pydx5p[c] 					
1727	PYDAMK	No	pyridoxamine kinase	[c] : atp + pydam --> adp + h + pyam5p	Cofactor and Prosthetic Group Biosynthesis	2.7.1.35	b2418	NCD		-4.65732	2.09859	[c] : atp[c] + pydam[c] --> adp[c] + pyam5p[c] 					
3019	PYDXK	No	pyridoxal kinase	[c] : atp + pydx --> adp + h + pydx5p	Cofactor and Prosthetic Group Biosynthesis	2.7.1.35	( b2418  or  b1636 )	NCD	"JLR- pdxY has high pyridoxal kinase activity, but low pyridoxine kinase activity. pdxK is the opposite but also other activities"	-4.65732	2.09859	[c] : atp[c] + pydx[c] --> adp[c] + pydx5p[c] 					
1726	PYDXNK	No	pyridoxine kinase	[c] : atp + pydxn --> adp + h + pdx5p	Cofactor and Prosthetic Group Biosynthesis	2.7.1.35	b2418	"NCD
JLR-Pyridoxine, pyridoxamine and various derivatives can also act as acceptors"		-4.65732	2.09859	[c] : atp[c] + pydxn[c] --> adp[c] + pdx5p[c] 					
1820	PYDXPP	No	Pyridoxal 5-phosphate phosphatase	[c] : h2o + pydx5p --> pi + pydx	Cofactor and Prosthetic Group Biosynthesis					-2.35942	1.9257	[c] : h2o[c] + pydx5p[c] --> h[c] + pi[c] + pydx[c] 					
265	PYK	No	pyruvate kinase	[c] : adp + h + pep --> atp + pyr	Glycolysis/Gluconeogenesis	2.7.1.40	( b1854  or  b1676 )	SMP		-5.51561	3.56586	[c] : adp[c] + pep[c] --> atp[c] + pyr[c] 					
1083	PYNP2r	No	pyrimidine-nucleoside phosphorylase (uracil)	[c] : pi + uri <==> r1p + ura	Nucleotide Salvage Pathway	2.4.2.2	b3831	JLR- added reversible form of PYNP2		1.28439	3.76698	[c] : h[c] + pi[c] + uri[c] <==> r1p[c] + ura[c] 					
9011	PYRt2rpp	Yes	pyruvate reversible transport via proton symport (periplasm)	h[p] + pyr[p] <==> h[c] + pyr[c]	"Transport, Inner Membrane"			JLR		0	0	[c] : h[p] + pyr[p] <==> h[c] + pyr[c] 					
9196	PYRtex	Yes	pyruvate transport via diffusion (extracellular to periplasm)	pyr[e] <==> pyr[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : pyr[e] <==> pyr[p] 					
20002	QMO2	Yes	quinol monooxygenase (Ubiquinol-8)	[c] : (2) o2 + q8h2 --> (2) h + (2) o2- + q8	Update		b3029	"AMF
PMID: 15613473"	"PMID: 15613473 
""Thus, the QuMo-MdaB cycle would also act as a quinone buffer, owing to the broad substrate specificity for these types of proteins"".  For this reason, the reaction was assigned to act on menaqinol and uqiquinol (demostrated to act on menadiol).
Not sure why the reaction is shown to generate superoxide ions.  Other monooxygenases use NAD(P)H.
the enzyme is NADH dependent.
AMF"	No energy	No energy	[c] : (2) o2[c] + q8h2[c] --> (2) h[c] + (2) o2-[c] + q8[c] 					
20004	QMO3	Yes	quinol monooxygenase (menaquinol 8)	[c] : mql8 + (2) o2 --> (2) h + mqn8 + (2) o2-	Update		b3029	"AMF
PMID: 15613473"	"PMID: 15613473 
""Thus, the QuMo-MdaB cycle would also act as a quinone buffer, owing to the broad substrate specificity for these types of proteins"".  For this reason, the reaction was assigned to act on menaqinol and uqiquinol (demostrated to act on menadiol).
Not sure why the reaction is shown to generate superoxide ions.  Other monooxygenases use NAD(P)H.
the enzyme is NADH dependent.
AMF"	No energy	No energy	[c] : mql8[c] + (2) o2[c] --> (2) h[c] + mqn8[c] + (2) o2-[c] 					
7869	QULNS	No	quinolinate synthase	[c] : dhap + iasp --> (2) h2o + pi + quln	Cofactor and Prosthetic Group Biosynthesis		b0750			-16.212	7.91369	[c] : dhap[c] + iasp[c] --> h[c] + (2) h2o[c] + pi[c] + quln[c] 					
9253	R15BPK	Yes	"ribose-1,5-bisphosphokinase"	[c] : atp + r15bp --> adp + prpp	Update		b4094	"AMF
same end product as phosphoribosylpyrophosphate synthetase"	PMID: 12700258 cloned and characterized	0.803173	2.08341	[c] : atp[c] + r15bp[c] --> adp[c] + prpp[c] 					
9256	R1PK	Yes	ribose 1-phosphokinase	[c] : atp + r1p --> adp + h + r15bp	Update			AMF	"No gene assignment, but PMID: 12700258 states that this is a definate intermediate in the pathway. Pg. 2799, bottom of left column."	-4.65732	2.09859	[c] : atp[c] + r1p[c] --> adp[c] + r15bp[c] 					
13218	R5PP	Yes	ribose 5-phosphate phosphatase	[c] : h2o + r5p --> pi + rib-D	Update		b0822	AMF	"enzyme acts on a number of other sugar phosphates, these reactions were shown to be substrates and were in the model

(glyc3p was not tested, but high activity was shown ot glyc1p and glyc2p, so the reaction G3PT was assigned to this gene)

sbt-d - not in network yet, but could be a signalling molecule (not sure of the source for this statement), so added this reaction
PMID: 15657928
AMF

"	-2.35942	1.9257	[c] : h2o[c] + r5p[c] --> h[c] + pi[c] + rib-D[c] 					
13819	R5PPpp	Yes	ribose 5-phosphate phosphatase	[p] : h2o + r5p --> pi + rib-D	Update		b4055	AMF	"from PMID: 9011040
AMF
very general phosphatase"	-2.35942	1.9257	[p] : h2o[p] + r5p[p] --> h[p] + pi[p] + rib-D[p] 					
13829	R5Ptex	Yes	Ribose 5-phosphate transport via diffusion (extracellular to periplasm)	r5p[e] <==> r5p[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : r5p[e] <==> r5p[p] 					
119	RBFK	No	riboflavin kinase	[c] : atp + ribflv --> adp + fmn + h	Cofactor and Prosthetic Group Biosynthesis	2.7.1.26	b0025			-4.65732	2.09859	[c] : atp[c] + ribflv[c] --> adp[c] + fmn[c] 					
1001	RBFSa	No	riboflavin synthase	[c] : 4r5au + db4p --> dmlz + (2) h2o + pi	Cofactor and Prosthetic Group Biosynthesis	2.5.1.9	b1662			-14.6837	9.11035	[c] : 4r5au[c] + db4p[c] --> dmlz[c] + h[c] + (2) h2o[c] + pi[c] 					
121	RBFSb	No	riboflavin synthase	[c] : (2) dmlz --> 4r5au + ribflv	Cofactor and Prosthetic Group Biosynthesis	2.5.1.9	b0415			-41.5093	12.6781	[c] : (2) dmlz[c] --> 4r5au[c] + ribflv[c] 					
255	RBK	No	ribokinase	[c] : atp + rib-D --> adp + h + r5p	Alternate Carbon Metabolism	2.7.1.15	b3752			-4.65732	2.09859	[c] : atp[c] + rib-D[c] --> adp[c] + r5p[c] 					
55	RBK_L1	No	L-ribulokinase (L-ribulose)	[c] : atp + rbl-L --> adp + h + ru5p-L	Alternate Carbon Metabolism	2.7.1.16	b0063	Ribitol and L-arabinitol can also act as acceptors. 	"PMID: 11747300

Paper states that AraB has 6 substrates with similar specificity and states what are not
abt - (arabitol) not included since no transporter could be found and the paper does not say explicitly that EC can grow on it)
rbl-D not included since it is not in the network and can not find data to support growth on it and can not grow on arabinose (FucI conversion)
AMF"	-4.04488	6.21545	[c] : atp[c] + rbl-L[c] --> adp[c] + ru5p-L[c] 					
2779	RBK_L2	Yes	L-ribulokinase (ribitol)	[c] : atp + rbt --> adp + h + rbt5p	Update	2.7.1.16	b0063		"PMID: 11747300

Paper states that AraB has 6 substrates with similar specificity and states what are not
abt - (arabitol) not included since no transporter could be found and the paper does not say explicitly that EC can grow on it)
rbl-D not included since it is not in the network and can not find data to support growth on it and can not grow on arabinose (FucI conversion)
AMF"	-4.65732	2.09859	[c] : atp[c] + rbt[c] --> adp[c] + rbt5p[c] 					
57	RBP4E	No	L-ribulose-phosphate 4-epimerase	[c] : ru5p-L <==> xu5p-D	Alternate Carbon Metabolism	5.1.3.4	( b0061  or  b4198  or  b3583 )			0	0.5	[c] : ru5p-L[c] <==> xu5p-D[c] 					
13498	RHAT1	Yes	rhamnosyltransferase I (LPS core biosynthesis)	[c] : dtdprmn + kphphhlipa --> dtdp + h + icolipa	Lipopolysaccharide Biosynthesis / Recycling		b3629	AMF	"see review for the function of WaaZ and WaaS
WaaS is speculative
PMID: 12045108

PMID: 11065359 talks about the enzyme in similar organism and sthe substrate


AMF"	No energy	No energy	[c] : dtdprmn[c] + kphphhlipa[c] --> dtdp[c] + (4) h[c] + icolipa[c] 					
2825	RHCCE	No	S-ribosylhomocysteine cleavage enzyme	[c] : rhcys --> dhptd + hcys-L	Methionine Metabolism		b2687	JLR		-9.97939	8.02486	[c] : rhcys[c] --> dhptd[c] + hcys-L[c] 					
8914	RIBabcpp	Yes	D-ribose transport via ABC system (periplasm)	atp[c] + h2o[c] + rib-D[p] --> adp[c] + h[c] + pi[c] + rib-D[c]	"Transport, Inner Membrane"		( ( b3749  and  b3751  and  b3750  and  b3748 )  or  ( b4087  and  b4088  and  b4086 )  or  ( b4231  and  b4227  and  b4485  and  b4230 ) )		"JLR-EcoCyc shows that the putative genes ytfQRST and yjfF form a  putative enzyme complex

AlsABC can transport allose and is a low affinity transporter for ribose."	-7.01673	1.48181	[c] : atp[c] + h2o[c] + rib-D[p] --> adp[c] + h[c] + pi[c] + rib-D[c] 					
9197	RIBtex	Yes	ribose transport via diffusion (extracellular to periplasm)	rib-D[e] <==> rib-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : rib-D[e] <==> rib-D[p] 					
252	RMI	No	L-rhamnose isomerase	[c] : rmn <==> rml	Alternate Carbon Metabolism	5.3.1.14	b3903			0.701765	9.00506	[c] : rmn[c] <==> rml[c] 					
253	RMK	No	rhamnulokinase	[c] : atp + rml --> adp + h + rml1p	Alternate Carbon Metabolism	2.7.1.5	b3904			-4.65732	2.09859	[c] : atp[c] + rml[c] --> adp[c] + rml1p[c] 					
9198	RMNtex	Yes	L-rhamnose transport via diffusion (extracellular to periplasm)	rmn[e] <==> rmn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : rmn[e] <==> rmn[p] 					
8915	RMNtpp	Yes	L-rhamnose transport via proton symport (periplasm)	h[p] + rmn[p] --> h[c] + rmn[c]	"Transport, Inner Membrane"		b3907	JLR		0	0	[c] : h[p] + rmn[p] --> h[c] + rmn[c] 					
1205	RMPA	No	Rhamnulose-1-phosphate aldolase	[c] : rml1p <==> dhap + lald-L	Alternate Carbon Metabolism	4.1.2.19	b3902	JLR	"PMID: 7016842
AMF"	4.43267	3.73524	[c] : rml1p[c] <==> dhap[c] + lald-L[c] 					
423	RNDR1	No	ribonucleoside-diphosphate reductase (ADP)	[c] : adp + trdrd --> dadp + h2o + trdox	Nucleotide Salvage Pathway	1.17.4.1	( b2234  and  b2235 )			-16.2581	8.92198	[c] : adp[c] + trdrd[c] --> dadp[c] + h2o[c] + trdox[c] 					
13841	RNDR1b	Yes	ribonucleoside-diphosphate reductase (ADP) (glutaredoxin)	[c] : adp + grxrd --> dadp + grxox + h2o	Update		( b2675  and  b2676 )	AMF	"reactions taken from Ecocyc, no difinative reference givene that characterizes the gene in E.coli
reaction seems very probable
AMF"	-16.2581	8.92198	[c] : adp[c] + grxrd[c] --> dadp[c] + grxox[c] + h2o[c] 					
424	RNDR2	No	ribonucleoside-diphosphate reductase (GDP)	[c] : gdp + trdrd --> dgdp + h2o + trdox	Nucleotide Salvage Pathway	1.17.4.1	( b2234  and  b2235 )			-16.2581	8.92198	[c] : gdp[c] + trdrd[c] --> dgdp[c] + h2o[c] + trdox[c] 					
13842	RNDR2b	Yes	ribonucleoside-diphosphate reductase (GDP) (glutaredoxin)	[c] : gdp + grxrd --> dgdp + grxox + h2o	Update		( b2675  and  b2676 )	AMF	"reactions taken from Ecocyc, no difinative reference givene that characterizes the gene in E.coli
reaction seems very probable
AMF"	-16.2581	8.92198	[c] : gdp[c] + grxrd[c] --> dgdp[c] + grxox[c] + h2o[c] 					
425	RNDR3	No	ribonucleoside-diphosphate reductase (CDP)	[c] : cdp + trdrd --> dcdp + h2o + trdox	Nucleotide Salvage Pathway	1.17.4.1	( b2234  and  b2235 )			-16.2581	8.92198	[c] : cdp[c] + trdrd[c] --> dcdp[c] + h2o[c] + trdox[c] 					
13843	RNDR3b	Yes	ribonucleoside-diphosphate reductase (CDP) (glutaredoxin)	[c] : cdp + grxrd --> dcdp + grxox + h2o	Update		( b2675  and  b2676 )	"AMF
"	"reactions taken from Ecocyc, no difinative reference givene that characterizes the gene in E.coli
reaction seems very probable
AMF"	-16.2581	8.92198	[c] : cdp[c] + grxrd[c] --> dcdp[c] + grxox[c] + h2o[c] 					
426	RNDR4	No	ribonucleoside-diphosphate reductase (UDP)	[c] : trdrd + udp --> dudp + h2o + trdox	Nucleotide Salvage Pathway	1.17.4.1	( b2234  and  b2235 )			-16.2581	8.92198	[c] : trdrd[c] + udp[c] --> dudp[c] + h2o[c] + trdox[c] 					
13844	RNDR4b	Yes	ribonucleoside-diphosphate reductase (UDP) (glutaredoxin)	[c] : grxrd + udp --> dudp + grxox + h2o	Update		( b2675  and  b2676 )	AMF	"reactions taken from Ecocyc, no difinative reference givene that characterizes the gene in E.coli
reaction seems very probable
AMF"	-16.2581	8.92198	[c] : grxrd[c] + udp[c] --> dudp[c] + grxox[c] + h2o[c] 					
13845	RNTR1c	Yes	ribonucleoside-triphosphate reductase (ATP) (flavodoxin)	[c] : atp + fldrd --> datp + fldox + h2o	Update		( b4238  or  ( b3924  and  b4238  and  b4237 ) )		"NrdD can catalyze RNTR reactions by itself un aerobic conditions

NrdD has to complex with NrdG and Fpr under aerobic conditions - NrdD and NrdG are known to be essential anaerobically

flavodoxin is assumed to be the donor in a similar organism and thus is used for E. coli
PMID: 10644700

outlined well in ecocyc
AMF"	No energy	No energy	[c] : atp[c] + fldrd[c] --> datp[c] + fldox[c] + h2o[c] 					
13847	RNTR2c	Yes	ribonucleoside-triphosphate reductase (GTP) (flavodoxin)	[c] : fldrd + gtp --> dgtp + fldox + h2o	Update		( b4238  or  ( b3924  and  b4238  and  b4237 ) )		"NrdD can catalyze RNTR reactions by itself un aerobic conditions

NrdD has to complex with NrdG and Fpr under aerobic conditions - NrdD and NrdG are known to be essential anaerobically

flavodoxin is assumed to be the donor in a similar organism and thus is used for E. coli
PMID: 10644700

outlined well in ecocyc
AMF"	No energy	No energy	[c] : fldrd[c] + gtp[c] --> dgtp[c] + fldox[c] + h2o[c] 					
13846	RNTR3c	Yes	ribonucleoside-triphosphate reductase (CTP) (flavodoxin)	[c] : ctp + fldrd --> dctp + fldox + h2o	Update		( b4238  or  ( b3924  and  b4238  and  b4237 ) )		"NrdD can catalyze RNTR reactions by itself un aerobic conditions

NrdD has to complex with NrdG and Fpr under aerobic conditions - NrdD and NrdG are known to be essential anaerobically

flavodoxin is assumed to be the donor in a similar organism and thus is used for E. coli
PMID: 10644700

outlined well in ecocyc
AMF"	No energy	No energy	[c] : ctp[c] + fldrd[c] --> dctp[c] + fldox[c] + h2o[c] 					
13848	RNTR4c	Yes	ribonucleoside-triphosphate reductase (UTP) (flavodoxin)	[c] : fldrd + utp --> dutp + fldox + h2o	Update		( b4238  or  ( b3924  and  b4238  and  b4237 ) )	AMF	"NrdD can catalyze RNTR reactions by itself un aerobic conditions

NrdD has to complex with NrdG and Fpr under aerobic conditions - NrdD and NrdG are known to be essential anaerobically

flavodoxin is assumed to be the donor in a similar organism and thus is used for E. coli
PMID: 10644700

outlined well in ecocyc
AMF"	No energy	No energy	[c] : fldrd[c] + utp[c] --> dutp[c] + fldox[c] + h2o[c] 					
281	RPE	No	ribulose 5-phosphate 3-epimerase	[c] : ru5p-D <==> xu5p-D	Pentose Phosphate Pathway	5.1.3.1	( b3386  or  b4301 )	SMP		0	0.5	[c] : ru5p-D[c] <==> xu5p-D[c] 					
280	RPI	No	ribose-5-phosphate isomerase	[c] : r5p <==> ru5p-D	Pentose Phosphate Pathway	5.3.1.6	( b2914  or  b4090 )	SMP		0.813593	7.35227	[c] : r5p[c] <==> ru5p-D[c] 					
2452	RZ5PP	No	alpha-ribazole 5-phosphate phosphatase	[c] : 5prdmbz + h2o --> pi + rdmbzi	Cofactor and Prosthetic Group Biosynthesis		b0638	JLR (Kegg Rxn R04594)		-2.35942	1.9257	[c] : 5prdmbz[c] + h2o[c] --> h[c] + pi[c] + rdmbzi[c] 					
2552	S7PI	No	sedoheptulose 7-phosphate isomerase	[c] : s7p --> gmhep7p	Cell Envelope Biosynthesis		b0222	JLR Kegg RXN R05645		-0.701765	9.00506	[c] : s7p[c] --> gmhep7p[c] 					
3303	SADH	No	Succinylarginine dihydrolase	[c] : (2) h + (2) h2o + sucarg --> co2 + (2) nh4 + sucorn	Arginine and Proline Metabolism	2.6.1.69	b1745	JLR- had to add h2o to balance (R04189)		-11.8327	4.95036	[c] : (2) h[c] + (2) h2o[c] + sucarg[c] --> co2[c] + (2) nh4[c] + sucorn[c] 					
1136	SADT2	No	Sulfate adenyltransferase	[c] : atp + gtp + h2o + so4 --> aps + gdp + pi + ppi	Cysteine Metabolism		( b2751  and  b2752 )	tv		6.99713	4.96716	[c] : atp[c] + gtp[c] + h2o[c] + so4[c] --> aps[c] + gdp[c] + pi[c] + ppi[c] 					
12479	SARCOX	Yes	sarcosine oxidase	[c] : h2o + o2 + sarcs --> fald + gly + h2o2	Update	1.5.3.1	b1059	"AMF
PMID: 11170472"	"PMID: 11170472
AMF
enzyme proven, but physiological function has yet to be determined

there are more N-methyl amino acids that are substrates"	-19.64	2.92555	[c] : h2o[c] + o2[c] + sarcs[c] --> fald[c] + gly[c] + h2o2[c] 					
13359	SBT6PP	Yes	sorbitol 6-phosphate phosphatase	[c] : h2o + sbt6p --> pi + sbt-D	Update		b0822	AMF	"enzyme acts on a number of other sugar phosphates, these reactions were shown to be substrates and were in the model

(glyc3p was not tested, but high activity was shown ot glyc1p and glyc2p, so the reaction G3PT was assigned to this gene)

sbt-d - not in network yet, but could be a signalling molecule (not sure of the source for this statement), so added this reaction
PMID: 15657928
AMF"	-2.35942	1.9257	[c] : h2o[c] + sbt6p[c] --> h[c] + pi[c] + sbt-D[c] 					
1207	SBTPD	No	sorbitol-6-phosphate dehydrogenase	[c] : nad + sbt6p <==> f6p + h + nadh	Alternate Carbon Metabolism	1.1.1.140	b2705	JLR	JLR- added reaction to the network.  Glucitol and sorbitol are equivalent according to EcoCyc.	3.78793	9.00908	[c] : nad[c] + sbt6p[c] <==> f6p[c] + h[c] + nadh[c] 					
8966	SBTptspp	Yes	D-sorbitol transport via PEP:Pyr PTS (periplasm)	pep[c] + sbt-D[p] --> pyr[c] + sbt6p[c]	"Transport, Inner Membrane"		( b2415  and  b2416  and  b2702  and  b2704  and  b2703 )		AMF- reaction is not in transportDB 11/15/04	-10.1729	3.20748	[c] : pep[c] + sbt-D[p] --> pyr[c] + sbt6p[c] 					
9199	SBTtex	Yes	D-sorbitol transport via diffusion (extracellular to periplasm)	sbt-D[e] <==> sbt-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : sbt-D[e] <==> sbt-D[p] 					
3462	SDPDS	No	succinyl-diaminopimelate desuccinylase	[c] : h2o + sl26da --> 26dap-LL + succ	Threonine and Lysine Metabolism	3.5.1.18	b2472			-3.36489	3.34628	[c] : h2o[c] + sl26da[c] --> 26dap-LL[c] + succ[c] 					
363	SDPTA	No	succinyldiaminopimelate transaminase	[c] : akg + sl26da <==> glu-L + sl2a6o	Threonine and Lysine Metabolism	2.6.1.17	b3359		"Ecocyc:
The gene has been independently cloned and sequenced as argD, encoding acetylornithine transaminase, by Heimberg et al [  Heimberg90  ] . In 1999 Ledwidge and Blanchard [ Ledwidge99  ] purified and sequenced the N-succinyldiaminopimelate-aminotransferase protein, showing that it is identical to the argD gene product.
PMID: 10074354

AMF"	0	0.5	[c] : akg[c] + sl26da[c] <==> glu-L[c] + sl2a6o[c] 					
2456	SELNPS	No	Selenophosphate synthase	[c] : atp + h2o + seln --> amp + pi + selnp	Unassigned	2.7.9.3	b1764	JLR		No energy	No energy	[c] : atp[c] + h2o[c] + seln[c] --> amp[c] + pi[c] + selnp[c] 					
3412	SERASr	No	(L-seryl)adenylate synthase	[c] : atp + h + ser-L <==> ppi + seramp	Cofactor and Prosthetic Group Biosynthesis		b0586	JLR	"may also participate in large complex w/ EntB,D and E
MKA

http://biocyc.org/ECOLI/new-image?type=PATHWAY&object=ENTBACSYN-PWY"	-6.2384	6.26117	[c] : atp[c] + (2) h[c] + ser-L[c] <==> ppi[c] + seramp[c] 					
349	SERAT	No	serine O-acetyltransferase	[c] : accoa + ser-L <==> acser + coa	Cysteine Metabolism	2.3.1.30	b3607			-3.97568	4.69324	[c] : accoa[c] + ser-L[c] <==> acser[c] + coa[c] 					
391	SERD_D	No	D-serine deaminase	[c] : ser-D --> nh4 + pyr	Glycine and Serine Metabolism		b2366	Previous EC 4.2.1.14. Now EC 4.3.1.18		-9.10889	2.74785	[c] : ser-D[c] --> nh4[c] + pyr[c] 					
390	SERD_L	No	L-serine deaminase	[c] : ser-L --> nh4 + pyr	Glycine and Serine Metabolism	4.3.1.17	( b4471  or  b1814  or  b2797  or  b3708 )	Previous EC 4.2.1.13. Now EC 4.3.1.17		-9.10889	2.74785	[c] : ser-L[c] --> nh4[c] + pyr[c] 					
8917	SERt2rpp	Yes	L-serine reversible transport via proton symport (periplasm)	h[p] + ser-L[p] <==> h[c] + ser-L[c]	"Transport, Inner Membrane"		( b2796  or  b3116 )	NCD		0	0	[c] : h[p] + ser-L[p] <==> h[c] + ser-L[c] 					
8918	SERt4pp	Yes	L-serine via sodium symport (periplasm)	na1[p] + ser-L[p] --> na1[c] + ser-L[c]	"Transport, Inner Membrane"		b3089	JLR		0	0	[c] : na1[p] + ser-L[p] --> na1[c] + ser-L[c] 					
9201	SERtex	Yes	L-serine transport via diffusion (extracellular to periplasm)	ser-L[e] <==> ser-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ser-L[e] <==> ser-L[p] 					
1031	SERTRS	Yes	Seryl-tRNA synthetase	[c] : atp + ser-L + trnaser --> amp + ppi + sertrna	Update	6.1.1.11	b0893		Added to incorporate tRNA peptides into model	-9.70121	4.06352	[c] : atp[c] + ser-L[c] + trnaser[c] --> amp[c] + ppi[c] + sertrna[c] 					
8755	SERTRS2	Yes	Seryl-tRNA synthetase (Selenocystein)	[c] : atp + ser-L + trnasecys --> amp + ppi + scsertrna	Update		b0893		"Added to incorporate tRNA peptides into model

used the annotation to make the second reaction"	29.5906	4.62958	[c] : atp[c] + ser-L[c] + trnasecys[c] --> amp[c] + ppi[c] + scsertrna[c] 					
2374	SFGTH	Yes	S-Formylglutathione hydralase	[c] : Sfglutth + h2o <==> for + gthrd + h	Update	3.1.2.12	b0355	NCD	"AMF
FrmA has been shown to generate this product which needs to be degraded,
PMID: 1731906

This gene next to that is a putuative gene
"	-21.7793	3.53002	[c] : h2o[c] + Sfglutth[c] <==> for[c] + gthrd[c] + h[c] 					
3304	SGDS	No	Succinylglutamate desuccinylase	[c] : h2o + sucglu --> glu-L + succ	Arginine and Proline Metabolism		b1744	JLR- (R00411)		-3.36489	3.34628	[c] : h2o[c] + sucglu[c] --> glu-L[c] + succ[c] 					
2310	SGSAD	No	Succinylglutamic semialdehyde dehydrogenase	[c] : h2o + nad + sucgsa --> (2) h + nadh + sucglu	Arginine and Proline Metabolism		b1746	JLR- had to add h2o to balance (R05049)		-9.85991	4.39284	[c] : h2o[c] + nad[c] + sucgsa[c] --> (2) h[c] + nadh[c] + sucglu[c] 					
3446	SHCHCS2	No	"2-succinyl-6-hydroxy-2,4-cyclohexadiene 1-carboxylate synthase"	[c] : ichor + ssaltpp --> 2shchc + pyr + thmpp	Cofactor and Prosthetic Group Biosynthesis		b2264	JLR		-34.6995	5.17064	[c] : ichor[c] + ssaltpp[c] --> 2shchc[c] + pyr[c] + thmpp[c] 					
1649	SHCHD2	No	sirohydrochlorin dehydrogenase (NAD)	[c] : dscl + nad --> h + nadh + scl	Cofactor and Prosthetic Group Biosynthesis		b3368	"JLR- uses nad rather than nadp (SHCHD)
EC 1.3.1.76"		No energy	No energy	[c] : dscl[c] + nad[c] --> h[c] + nadh[c] + scl[c] 					
3702	SHCHF	No	sirohydrochlorin ferrochetalase	[c] : fe2 + scl --> (3) h + sheme	Cofactor and Prosthetic Group Biosynthesis		b3368	EC  4.99.1.4	JLR- JSE model didn't have Fe2+	No energy	No energy	[c] : fe2[c] + scl[c] --> (3) h[c] + sheme[c] 					
1050	SHK3Dr	No	shikimate dehydrogenase	[c] : 3dhsk + h + nadph <==> nadp + skm	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	1.1.1.25	( b3281  or  b1692 )	"JLR- added reversible form of SHK3D
"		-1.77658	4.765	[c] : 3dhsk[c] + h[c] + nadph[c] <==> nadp[c] + skm[c] 					
336	SHKK	No	shikimate kinase	[c] : atp + skm --> adp + h + skm5p	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	2.7.1.71	( b3390  or  b0388 )			-3.46855	2.28701	[c] : atp[c] + skm[c] --> adp[c] + skm5p[c] 					
2871	SHSL1	No	O-succinylhomoserine lyase (L-cysteine)	[c] : cys-L + suchms --> cyst-L + h + succ	Methionine Metabolism	4.2.99.9	b3939	"new EC - EC 2.5.1.48
NJ"		-4.1753	3.85506	[c] : cys-L[c] + suchms[c] --> cyst-L[c] + h[c] + succ[c] 					
14040	SKMt2pp	Yes	shikimate transport in via proton symport (periplasm)	h[p] + skm[p] --> h[c] + skm[c]	"Transport, Inner Membrane"		b1981	AMF	see PMID: 9524262	0	0	[c] : h[p] + skm[p] --> h[c] + skm[c] 					
14039	SKMtex	Yes	shikimate transport via diffusion (extracellular to periplasm)	skm[e] <==> skm[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : skm[e] <==> skm[p] 					
13897	SO2tex	Yes	SO2 transport via diffusion (extracellular to periplasm)	so2[e] <==> so2[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : so2[e] <==> so2[p] 					
13898	SO2tpp	Yes	SO2 transport via diffusion (periplasm)	so2[p] <==> so2[c]	"Transport, Inner Membrane"				assumed diffusion	0	0	[c] : so2[p] <==> so2[c] 					
13731	SO3tex	Yes	sulfite transport via diffusion (extracellular to periplasm)	so3[e] <==> so3[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : so3[e] <==> so3[p] 					
9202	SO4tex	Yes	sulfate transport via diffusion (extracellular to periplasm)	so4[e] <==> so4[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : so4[e] <==> so4[p] 					
2309	SOTA	No	Succinylornithine transaminase	[c] : akg + sucorn --> glu-L + sucgsa	Arginine and Proline Metabolism		b1748	JLR (R04217)		2.42139	2.1337	[c] : akg[c] + sucorn[c] --> glu-L[c] + sucgsa[c] 					
8919	SPMDabcpp	Yes	spermidine transport via ABC system (periplasm)	atp[c] + h2o[c] + spmd[p] --> adp[c] + h[c] + pi[c] + spmd[c]	"Transport, Inner Membrane"		( ( b1126  and  b1125  and  b1124  and  b1123 )  or  ( b1440  and  b1441  and  b1442  and  b1443 ) )		JLR- EcoCyc indicates taht ydcSTUV form an ABC transport system	-7.01673	1.48181	[c] : atp[c] + h2o[c] + spmd[p] --> adp[c] + h[c] + pi[c] + spmd[c] 					
3320	SPMDAT1	No	Spermidine acetyltransferase	[c] : accoa + spmd --> N1aspmd + coa + h	Arginine and Proline Metabolism	2.3.1.57	b1584	"JLR
rxn DIAMT was redundant and has been deleted - NCD"		-2.48774	5.01459	[c] : accoa[c] + spmd[c] --> coa[c] + h[c] + N1aspmd[c] 					
3321	SPMDAT2	No	Spermidine acetyltransferase (N8)	[c] : accoa + spmd --> coa + h + n8aspmd	Arginine and Proline Metabolism	2.3.1.57	b1584	JLR		-2.48774	5.01459	[c] : accoa[c] + spmd[c] --> coa[c] + h[c] + n8aspmd[c] 					
9203	SPMDtex	Yes	spermidine transport via diffusion (extracellular to periplasm)	spmd[e] <==> spmd[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : spmd[e] <==> spmd[p] 					
312	SPMS	No	spermidine synthase	[c] : ametam + ptrc --> 5mta + h + spmd	Arginine and Proline Metabolism	2.5.1.16	b0121			No energy	No energy	[c] : ametam[c] + ptrc[c] --> 5mta[c] + h[c] + spmd[c] 					
2518	SPODM	No	superoxide dismutase	[c] : (2) h + (2) o2- --> h2o2 + o2	Unassigned	1.15.1.1	( b3908  or  b1656 )	JLR		No energy	No energy	[c] : (2) h[c] + (2) o2-[c] --> h2o2[c] + o2[c] 					
9801	SPODMpp	Yes	superoxide dismutase	[p] : (2) h + (2) o2- --> h2o2 + o2	Unassigned	1.15.1.1	b1646	"JLR
KC"	Periplasmic	No energy	No energy	[p] : (2) h[p] + (2) o2-[p] --> h2o2[p] + o2[p] 					
375	SSALx	No	succinate-semialdehyde dehydrogenase (NAD)	[c] : h2o + nad + sucsal --> (2) h + nadh + succ	Arginine and Proline Metabolism	1.2.1.16			"JLR- reaction assigned to sad, but no location yet in the genome (EcoCyc). Min 34 probably 55 KD protein. see PMID: 3276667"	-9.85991	4.39284	[c] : h2o[c] + nad[c] + sucsal[c] --> (2) h[c] + nadh[c] + succ[c] 					
2873	SSALy	No	succinate-semialdehyde dehydrogenase (NADP)	[c] : h2o + nadp + sucsal --> (2) h + nadph + succ	Arginine and Proline Metabolism	1.2.1.16	b2661			-9.85991	4.39284	[c] : h2o[c] + nadp[c] + sucsal[c] --> (2) h[c] + nadph[c] + succ[c] 					
2775	SUCBZL	No	o-succinylbenzoate-CoA ligase	[c] : atp + coa + sucbz --> amp + ppi + sbzcoa	Cofactor and Prosthetic Group Biosynthesis	6.2.1.26	b2260			-2.74083	4.99608	[c] : atp[c] + coa[c] + h[c] + sucbz[c] --> amp[c] + ppi[c] + sbzcoa[c] 					
40	SUCBZS	No	O-succinylbenzoate-CoA synthase	[c] : 2shchc --> h2o + sucbz	Cofactor and Prosthetic Group Biosynthesis		b2261			-20.1278	10.1015	[c] : 2shchc[c] --> h2o[c] + sucbz[c] 					
8921	SUCCt2_2pp	Yes	succinate transport via proton symport (2 H) (periplasm)	(2) h[p] + succ[p] --> (2) h[c] + succ[c]	"Transport, Inner Membrane"		b3528	JLR		0	0	[c] : (2) h[p] + succ[p] --> (2) h[c] + succ[c] 					
8922	SUCCt2_3pp	Yes	Succintate transport via proton symport (3 H) (periplasm)	(3) h[p] + succ[p] --> (3) h[c] + succ[c]	"Transport, Inner Membrane"		( b4138  or  b4123 )	JLR		0	0	[c] : (3) h[p] + succ[p] --> (3) h[c] + succ[c] 					
8923	SUCCt2bpp	Yes	Succinate efflux via proton symport (periplasm)	h[c] + succ[c] --> h[p] + succ[p]	"Transport, Inner Membrane"		b0621	JLR	JLR-  not sure about the number of H.	0	0	[c] : h[c] + succ[c] --> h[p] + succ[p] 					
9204	SUCCtex	Yes	succinate transport via diffusion (extracellular to periplasm)	succ[e] <==> succ[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : succ[e] <==> succ[p] 					
1178	SUCD1i	No	succinate dehydrogenase	[c] : fad + succ --> fadh2 + fum	Citric Acid Cycle	1.3.99.1	( b0721  and  b0722  and  b0723  and  b0724 )	JLR - made an irreversible version of the SUCD1 reaction		2.96898	7.05102	[c] : fad[c] + succ[c] --> fadh2[c] + fum[c] 					
2945	SUCD4	No	succinate dehyrdogenase	[c] : fadh2 + q8 <==> fad + q8h2	Oxidative Phosphorylation		( b0721  and  b0722  and  b0723  and  b0724 )	JLR		-11.7874	22.3153	[c] : fadh2[c] + q8[c] <==> fad[c] + q8h2[c] 					
8924	SUCFUMtpp	Yes	succinate:fumarate antiporter (periplasm)	fum[p] + succ[c] <==> fum[c] + succ[p]	"Transport, Inner Membrane"		( b4138  or  b4123  or  b0621 )	JLR		0	0	[c] : fum[p] + succ[c] <==> fum[c] + succ[p] 					
2845	SUCOAS	No	succinyl-CoA synthetase (ADP-forming)	[c] : atp + coa + succ <==> adp + pi + succoa	Citric Acid Cycle	6.2.1.5	( b0728  and  b0729 )			-1.1641	4.51371	[c] : atp[c] + coa[c] + succ[c] <==> adp[c] + pi[c] + succoa[c] 					
8925	SUCptspp	Yes	sucrose transport via PEP:Pyr  (periplasm)	pep[c] + sucr[p] --> pyr[c] + suc6p[c]	Putative Transporters		( b2417  and  b2429  and  b2415  and  b2416 )		"There is apparently a sucrose pts system (NH), the EIIBC gene isn't known.  YfeV is similar based on sequence, but has been shown to transport N-acetylmuramate."	-10.1729	3.20748	[c] : pep[c] + sucr[p] --> pyr[c] + suc6p[c] 					
9205	SUCRtex	Yes	sucrose transport transport via diffusion (extracellular to periplasm)	sucr[e] <==> sucr[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : sucr[e] <==> sucr[p] 					
8926	SULabcpp	Yes	sulfate transport via ABC system (periplasm)	atp[c] + h2o[c] + so4[p] --> adp[c] + h[c] + pi[c] + so4[c]	"Transport, Inner Membrane"		( ( b2422  and  b2425  and  b2424  and  b2423 )  or  ( b2422  and  b2424  and  b2423  and  b2413  and  b3917 ) )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + so4[p] --> adp[c] + h[c] + pi[c] + so4[c] 					
13611	SULFACabcpp	Yes	sulfoacetate transport via ABC system (periplasm)	atp[c] + h2o[c] + sulfac[p] --> adp[c] + h[c] + pi[c] + sulfac[c]	Update		( b0936  and  b0933  and  b0934 )		"only the ssu transport system will transport this and L-cysteate, amoung others

L-cysteate not included since the degradation products are dead ends

see PMID: 11750815
AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + sulfac[p] --> adp[c] + h[c] + pi[c] + sulfac[c] 					
13614	SULFACtex	Yes	sulfoaceate transport via diffusion (extracellular to periplasm)	sulfac[e] <==> sulfac[p]	"Transport, Outer Membrane"				assumed diffusion	0	0	[c] : sulfac[e] <==> sulfac[p] 					
730	SULR	No	sulfite reductase (NADPH2)	[c] : (3) h2o + h2s + (3) nadp <==> (5) h + (3) nadph + so3	Cysteine Metabolism	1.8.2.2	( b2763  and  b2764 )	"JLR- EC number is 1.8.1.2?
"		No energy	No energy	[c] : (3) h2o[c] + h2s[c] + (3) nadp[c] <==> (4) h[c] + (3) nadph[c] + so3[c] 					
19203	T2DECAI	Yes	trans-2-decenoyl-ACP isomerase	[c] : tdec2eACP <==> cdec3eACP	Cell Envelope Biosynthesis		b0954	"AMf
not sure of reversibility"	"Only FabA perfroms this reaction

FabA and FabZ exhibited broad, overlapping chain length specificities. The FabZ dehydratase efficiently catalyzed the dehydration of short chain beta -hydroxyacyl-ACPs and long chain saturated and unsaturated beta -hydroxyacyl-ACPs. FabA was most active on intermediate chain length beta -hydroxyacyl-ACPs and also possessed significant activity toward both short and long chain saturated beta -hydroxyacyl-ACPs. Significantly, FabA was virtually inactive in the dehydration of long chain unsaturated beta -hydroxyacyl-ACP. The introduction of the double bond at the 10-carbon stage of fatty acid synthesis by FabA was only detected in the presence of beta -ketoacyl-ACP synthase I (FabB).
PMID: 8910376
AMF"	0	0.5	[c] : tdec2eACP[c] <==> cdec3eACP[c] 					
2285	TAGURr	No	tagaturonate reductase	[c] : altrn + nad <==> h + nadh + tagur	Alternate Carbon Metabolism	1.1.1.58	b1521	JLR- reversible form of TAGUR		3.78793	9.00908	[c] : altrn[c] + nad[c] <==> h[c] + nadh[c] + tagur[c] 					
282	TALA	No	transaldolase	[c] : g3p + s7p <==> e4p + f6p	Pentose Phosphate Pathway	2.2.1.2	( b2464  or  b0008 )	SMP		-0.948467	7.22374	[c] : g3p[c] + s7p[c] <==> e4p[c] + f6p[c] 					
2290	TARTD	No	L(+)-tartrate dehydratase	[c] : tartr-L --> h2o + oaa	Alternate Carbon Metabolism	4.2.1.32	( b3061  and  b3062 )	JLR		-9.58412	3.68395	[c] : tartr-L[c] --> h2o[c] + oaa[c] 					
8928	TARTRt7pp	Yes	Tartrate/succinate antiporter (periplasm)	succ[c] + tartr-L[p] <==> succ[p] + tartr-L[c]	Putative Transporters		b3063	JLR		0	0	[c] : succ[c] + tartr-L[p] <==> succ[p] + tartr-L[c] 					
9206	TARTRtex	Yes	Tartrate transport via diffusion (extracellular to periplasm)	tartr-L[e] <==> tartr-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : tartr-L[e] <==> tartr-L[p] 					
3192	TAUDO	No	Taurine dioxygenase	[c] : akg + o2 + taur --> aacald + co2 + h + so3 + succ	Alternate Carbon Metabolism	1.14.11.17	b0368	JLR		No energy	No energy	[c] : akg[c] + o2[c] + taur[c] --> aacald[c] + co2[c] + so3[c] + succ[c] 					
8929	TAURabcpp	Yes	taurine transport via ABC system (periplasm)	atp[c] + h2o[c] + taur[p] --> adp[c] + h[c] + pi[c] + taur[c]	"Transport, Inner Membrane"		( b0365  and  b0366  and  b0367 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + taur[p] --> adp[c] + h[c] + pi[c] + taur[c] 					
9207	TAURtex	Yes	taurine transport via diffusion (extracellular to periplasm)	taur[e] <==> taur[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : taur[e] <==> taur[p] 					
13732	TCYNTtex	Yes	Thiocyanate transport via diffusion (extracellular to periplasm)	tcynt[e] <==> tcynt[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : tcynt[e] <==> tcynt[p] 					
19989	TDECOAI	Yes	tetradecenoyl-coa cis-trans isomerization	[c] : tdecoa --> td2coa	Membrane Lipid Metabolism	5.3.3.8	b3846	"JLR
AMF"	"Evidence in PMID: 12535077
From Ecocyc: A reaction in beta-oxidation of fatty acids, required to feed unsaturated fatty acids into the main pathway.  Not sure of reaction reversibility.
AMF
FadJ might also carry out this reaction.  No evidence found for it yet though.
JLR
"	0	0.5	[c] : tdecoa[c] --> td2coa[c] 					
3322	TDPADGAT	No	"dTDP-4-amino-4,6-dideoxy-D-glucose acetyltransferase"	[c] : accoa + dtdp4addg --> coa + dtdp4aaddg + h	Cell Envelope Biosynthesis		b3790	JLR	JLR- Riley has as putative	-2.48774	5.01459	[c] : accoa[c] + dtdp4addg[c] --> coa[c] + dtdp4aaddg[c] + h[c] 					
2494	TDPAGTA	No	"dTDP-4-amino-4,6-dideoxy-D-glucose transaminase"	[c] : dtdp4d6dg + glu-L --> akg + dtdp4addg	Cell Envelope Biosynthesis	2.6.1.33	b3791	JLR		2.95982	2.81783	[c] : dtdp4d6dg[c] + glu-L[c] --> akg[c] + dtdp4addg[c] 					
2492	TDPDRE	No	"dTDP-4-dehydrorhamnose 3,5-epimerase"	[c] : dtdp4d6dg --> dtdp4d6dm	Cell Envelope Biosynthesis	5.1.3.13	b2038	JLR		0	0.5	[c] : dtdp4d6dg[c] --> dtdp4d6dm[c] 					
2493	TDPDRR	No	dTDP-4-dehydrorhamnose reductase	[c] : dtdp4d6dm + h + nadph --> dtdprmn + nadp	Cell Envelope Biosynthesis	1.1.1.133	b2040	JLR		-1.77658	4.765	[c] : dtdp4d6dm[c] + h[c] + nadph[c] --> dtdprmn[c] + nadp[c] 					
2490	TDPGDH	No	"dTDPglucose 4,6-dehydratase"	[c] : dtdpglu --> dtdp4d6dg + h2o	Cell Envelope Biosynthesis	4.2.1.46	( b2041  or  b3788 )	JLR		-14.0592	3.01096	[c] : dtdpglu[c] --> dtdp4d6dg[c] + h2o[c] 					
1257	TDSK	No	Tetraacyldisaccharide 4'kinase	[c] : atp + lipidAds --> adp + h + lipidA	Cell Envelope Biosynthesis	2.7.1.130	b0915	tv		-4.65732	2.09859	[c] : atp[c] + lipidAds[c] --> adp[c] + lipidA[c] 					
19636	TDSR1	Yes	thiol:disulfide reductase (DsbC)	dsbcox[p] + dsbdrd[c] --> dsbcrd[p] + dsbdox[c]	Update		b4136	"see PMID: 16040611
AMF"	"Transfer of protons from cellular membrane protein DsbD to periplasmic DsbC/G protein(s) for protein modification.
see PMID: 16040611
AMF"	No energy	No energy	[c] : dsbcox[p] + dsbdrd[c] --> dsbcrd[p] + dsbdox[c] 					
19637	TDSR2	Yes	thiol:disulfide reductase (DsbG)	dsbdrd[c] + dsbgox[p] --> dsbdox[c] + dsbgrd[p]	Update		b4136	"see PMID: 16040611
AMF"	"Transfer of protons from cellular membrane protein DsbD to periplasmic DsbC/G protein(s) for protein modification.
see PMID: 16040611
AMF"	No energy	No energy	[c] : dsbdrd[c] + dsbgox[p] --> dsbdox[c] + dsbgrd[p] 					
1210	TGBPA	No	Tagatose-bisphosphate aldolase	[c] : tagdp-D <==> dhap + g3p	Alternate Carbon Metabolism	4.1.2.40	( ( b3132  and  b3137 )  or  ( b2095  and  b2096 ) )	JLR		5.38114	6.58758	[c] : tagdp-D[c] <==> dhap[c] + g3p[c] 					
9012	THD2pp	Yes	NAD(P) transhydrogenase (periplasm)	(2) h[p] + nadh[c] + nadp[c] --> (2) h[c] + nad[c] + nadph[c]	Oxidative Phosphorylation	1.6.1.1	( b1602  and  b1603 )	JLR - proton translocating form		0	0.5	[c] : (2) h[p] + nadh[c] + nadp[c] --> (2) h[c] + nad[c] + nadph[c] 					
2869	THDPS	No	tetrahydrodipicolinate succinylase	[c] : h2o + succoa + thdp --> coa + sl2a6o	Threonine and Lysine Metabolism	2.3.1.117	b0166			3.52349	7.8043	[c] : h2o[c] + succoa[c] + thdp[c] --> coa[c] + sl2a6o[c] 					
1855	THIORDX	Yes	hydrogen peroxide reductase (thioredoxin)	[c] : h2o2 + trdrd <==> (2) h2o + trdox	Update		b2480	NCD	"from PMID: 10644761
AMF"	-80.8959	8.65747	[c] : h2o2[c] + trdrd[c] <==> (2) h2o[c] + trdox[c] 					
8931	THMabcpp	Yes	thiamine transport via ABC system (periplasm)	atp[c] + h2o[c] + thm[p] --> adp[c] + h[c] + pi[c] + thm[c]	"Transport, Inner Membrane"		( b0068  and  b0067  and  b0066 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + thm[p] --> adp[c] + h[c] + pi[c] + thm[c] 					
8932	THMDt2pp	Yes	thymidine transport in via proton symport (periplasm)	h[p] + thymd[p] --> h[c] + thymd[c]	"Transport, Inner Membrane"		( b2393  or  b2964 )			0	0	[c] : h[p] + thymd[p] --> h[c] + thymd[c] 					
8933	THMDt2rpp	Yes	"thymidine transport in via proton symport, reversible (periplasm)"	h[p] + thymd[p] <==> h[c] + thymd[c]	"Transport, Inner Membrane"		b2406	JLR		0	0	[c] : h[p] + thymd[p] <==> h[c] + thymd[c] 					
9210	THMDtex	Yes	thymidine transport via diffusion (extracellular to periplasm)	thymd[e] <==> thymd[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : thymd[e] <==> thymd[p] 					
9208	THMtex	Yes	Thiamine transport via diffusion (extracellular to periplasm)	thm[e] <==> thm[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : thm[e] <==> thm[p] 					
8682	THRA2r	Yes	L-allo-Threonine Aldolase	[c] : athr-L <==> acald + gly	Update	4.1.2.5	b0870	AMF	"ltaA is the same as ltaE (ecocyc)

 The L-allo-threonine aldolase encoded by the ltaA gene is of the low-specificity type; it can act on both L-threonine and L-allo-threonine. The enzyme requires pyridoxal phosphate as a cofactor. L-allo-Threonine aldolase may serve in an alternative pathway for glycine biosynthesis when the major pathway is inert. [ Liu98  ]"	2.44073	2.95322	[c] : athr-L[c] <==> acald[c] + gly[c] 					
8934	THRabcpp	Yes	L-threonine transport via ABC system (periplasm)	atp[c] + h2o[c] + thr-L[p] --> adp[c] + h[c] + pi[c] + thr-L[c]	"Transport, Inner Membrane"		( b3454  and  b3455  and  b3457  and  b3460  and  b3456 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + thr-L[p] --> adp[c] + h[c] + pi[c] + thr-L[c] 					
2408	THRAr	No	Threonine Aldolase	[c] : thr-L <==> acald + gly	Threonine and Lysine Metabolism	4.1.2.5	( b0870  or  b2551 )	JLR	"ltaA is the same as ltaE (ecocyc)

 The L-allo-threonine aldolase encoded by the ltaA gene is of the low-specificity type; it can act on both L-threonine and L-allo-threonine. The enzyme requires pyridoxal phosphate as a cofactor. L-allo-Threonine aldolase may serve in an alternative pathway for glycine biosynthesis when the major pathway is inert. [ Liu98  ]"	2.44073	2.95322	[c] : thr-L[c] <==> acald[c] + gly[c] 					
392	THRD	No	L-threonine dehydrogenase	[c] : nad + thr-L --> 2aobut + h + nadh	Glycine and Serine Metabolism	1.1.1.103	b3616	"The product (L-2-amino-3-oxobutanoate) spontaneously deecarboxylates to amino acetone
See AOBUTDs"	"JLR- JSE has tdh and kbl both catalyzing the following: 
 thr-L + coa -> gly + accoa
This doesn't mass balance and doesn't agree with NH.  NH has THRD and GLYATi reactions."	4.73639	4.5435	[c] : nad[c] + thr-L[c] --> 2aobut[c] + h[c] + nadh[c] 					
324	THRD_L	No	L-threonine deaminase	[c] : thr-L --> 2obut + nh4	"Valine, Leucine, and Isoleucine Metabolism"		( b3772  or  b3117  or  b1814  or  b2797 )	Previous EC number: 4.2.1.16. New EC number 4.3.1.19. Can't enter this....		-7.59363	3.36006	[c] : thr-L[c] --> 2obut[c] + nh4[c] 					
13830	THRPtex	Yes	phospho-L-threonine transport via diffusion (extracellular to periplasm)	thrp[e] <==> thrp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : thrp[e] <==> thrp[p] 					
365	THRS	No	threonine synthase	[c] : h2o + phom --> pi + thr-L	Threonine and Lysine Metabolism	4.2.3.1	b0004			-3.87467	2.88737	[c] : h2o[c] + phom[c] --> h[c] + pi[c] + thr-L[c] 					
13874	THRt2pp	Yes	L-threonine efflux transport via proton antiport (periplasm)	h[p] + thr-L[c] --> h[c] + thr-L[p]	"Transport, Inner Membrane"		( b0813  or  b3823 )	AMF	"RhtA charcterized in PMID: 12648727
RhtA could also transport other AA, listed in ref

RhtC and RhtB characterized in PMID: 10386596
AMF"	0	0	[c] : h[p] + thr-L[c] --> h[c] + thr-L[p] 					
8935	THRt2rpp	Yes	L-threonine reversible transport via proton symport (periplasm)	h[p] + thr-L[p] <==> h[c] + thr-L[c]	"Transport, Inner Membrane"		b3116	NCD		0	0	[c] : h[p] + thr-L[p] <==> h[c] + thr-L[c] 					
8952	THRt4pp	Yes	L-threonine  via sodium symport (periplasm)	na1[p] + thr-L[p] --> na1[c] + thr-L[c]	"Transport, Inner Membrane"		b3089	JLR		0	0	[c] : na1[p] + thr-L[p] --> na1[c] + thr-L[c] 					
9209	THRtex	Yes	L-threonine transport via diffusion (extracellular to periplasm)	thr-L[e] <==> thr-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : thr-L[e] <==> thr-L[p] 					
1032	THRTRS	Yes	Threonyl-tRNA synthetase	[c] : atp + thr-L + trnathr --> amp + ppi + thrtrna	Update	6.1.1.3	b1719		Added to incorporate tRNA peptides into model	-9.70121	4.06352	[c] : atp[c] + thr-L[c] + trnathr[c] --> amp[c] + ppi[c] + thrtrna[c] 					
3644	THZPSN	No	thiazole phosphate synthesis	[c] : atp + cys-L + dxyl5p + tyr-L --> 4hba + 4mpetz + ala-L + amp + co2 + h + h2o + ppi	Cofactor and Prosthetic Group Biosynthesis		( b2530  and  b3992  and  ( b3990  and  b3991 )  and  b0423  and  b4407 )	JLR- added based on mechanisms proposed in Begley's review (Arch Microbiol (1999) 171:293-300). Not sure about ala by-product guessed based on incorporating sulfur into biotin.	"JLR- different than JSE. Still not confident about the reaction.
See new paper: PMID 14757766 (04/2004)"	-35.9844	7.86856	[c] : atp[c] + cys-L[c] + dxyl5p[c] + tyr-L[c] --> 4hba[c] + 4mpetz[c] + ala-L[c] + amp[c] + co2[c] + h2o[c] + ppi[c] 					
283	TKT1	No	transketolase	[c] : r5p + xu5p-D <==> g3p + s7p	Pentose Phosphate Pathway	2.2.1.1	( b2935  or  b2465 )	"SMP
Two reactions for transketolase: TKT1 and TKT2"		1.24304	7.61298	[c] : r5p[c] + xu5p-D[c] <==> g3p[c] + s7p[c] 					
4641	TKT2	No	transketolase	[c] : e4p + xu5p-D <==> f6p + g3p	Pentose Phosphate Pathway	2.2.1.1	( b2935  or  b2465 )	"SMP
Two reactions for transketolase: TKT1 and TKT2"		-0.948467	7.22374	[c] : e4p[c] + xu5p-D[c] <==> f6p[c] + g3p[c] 					
3323	TMAOR1	No	Trimethylamine N-oxide reductase (menaquinol 8)	[c] : h + mql8 + tmao --> h2o + mqn8 + tma	Oxidative Phosphorylation		( ( b0894  and  b0895  and  b0896 )  or  ( b1587  and  b1588  and  b1589  and  b1590 ) )	JLR	"Note that chimeric enzymes such as dmsA-ynfGH can also work (see ref for complete listing-- AGH,ABH,FGC)."	No energy	No energy	[c] : mql8[c] + tmao[c] --> h2o[c] + mqn8[c] + tma[c] 					
9013	TMAOR1pp	Yes	Trimethylamine N-oxide reductase (menaquinol 8) (periplasm)	h[p] + mql8[c] + tmao[p] --> h2o[p] + mqn8[c] + tma[p]	Oxidative Phosphorylation		( ( b0997  and  b0996 )  or  ( b1873  and  b1872 ) )	JLR	assumed torZ uses same quinones as torA	No energy	No energy	[c] : h[p] + mql8[c] + tmao[p] --> h[c] + h2o[p] + mqn8[c] + tma[p] 					
3326	TMAOR2	No	Trimethylamine N-oxide reductase (demethylmenaquinol 8)	[c] : 2dmmql8 + h + tmao --> 2dmmq8 + h2o + tma	Oxidative Phosphorylation		( b0894  and  b0895  and  b0896 )	JLR		No energy	No energy	[c] : 2dmmql8[c] + tmao[c] --> 2dmmq8[c] + h2o[c] + tma[c] 					
9014	TMAOR2pp	Yes	Trimethylamine N-oxide reductase (demethylmenaquinol 8) (periplasm)	2dmmql8[c] + h[p] + tmao[p] --> 2dmmq8[c] + h2o[p] + tma[p]	Oxidative Phosphorylation		( ( b0997  and  b0996 )  or  ( b1873  and  b1872 ) )	JLR	assumed torZ uses same quinones as torA	No energy	No energy	[c] : 2dmmql8[c] + h[p] + tmao[p] --> 2dmmq8[c] + h[c] + h2o[p] + tma[p] 					
9212	TMAOtex	Yes	Trimethylamine N-oxide transport via diffusion (extracellular to periplasm)	tmao[e] <==> tmao[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : tmao[e] <==> tmao[p] 					
9211	TMAtex	Yes	Trimethylamine transport via diffusion (extracellular to periplasm)	tma[e] <==> tma[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : tma[e] <==> tma[p] 		
432	TMDK1	No	thymidine kinase (ATP:thymidine)	[c] : atp + thymd --> adp + dtmp + h	Nucleotide Salvage Pathway	2.7.1.21	b1238			-4.65732	2.09859	[c] : atp[c] + thymd[c] --> adp[c] + dtmp[c] 		
435	TMDPP	No	thymidine phosphorylase	[c] : pi + thymd <==> 2dr1p + thym	Nucleotide Salvage Pathway	2.4.2.4	b4382			1.28439	3.76698	[c] : h[c] + pi[c] + thymd[c] <==> 2dr1p[c] + thym[c] 		
431	TMDS	No	thymidylate synthase	[c] : dump + mlthf --> dhf + dtmp	Nucleotide Salvage Pathway	2.1.1.45	b2827			-8.71968	7.52098	[c] : dump[c] + mlthf[c] --> dhf[c] + dtmp[c] 		
3627	TMK	Yes	thiamine kinase	[c] : atp + thm --> adp + h + thmmp	Cofactor and Prosthetic Group Biosynthesis	2.7.1.89	b1106		"see PMID: 15150256
AMF
"	-4.65732	2.09859	[c] : atp[c] + thm[c] --> adp[c] + thmmp[c] 		
7071	TMPK	Yes	thiamine-phosphate kinase	[c] : atp + thmmp --> adp + thmpp	Cofactor and Prosthetic Group Biosynthesis	2.7.4.16	b0417	cvcv	"see PMID: 15150256
AMF
"	0	0.5	[c] : atp[c] + thmmp[c] --> adp[c] + thmpp[c] 		
62	TMPPP	No	thiamine-phosphate diphosphorylase	[c] : 2mahmp + 4mpetz + h --> ppi + thmmp	Cofactor and Prosthetic Group Biosynthesis	2.5.1.3	b3993		"see PMID: 15150256
AMF
"	-4.37496	3.86683	[c] : 2mahmp[c] + 4mpetz[c] + h[c] --> ppi[c] + thmmp[c] 		
276	TPI	No	triose-phosphate isomerase	[c] : dhap <==> g3p	Glycolysis/Gluconeogenesis	5.3.1.1	b3919	SMP		0.429448	2.63724	[c] : dhap[c] <==> g3p[c] 		
13701	TPRDCOAS	Yes	triphosphoribosyl-dephospho-CoA synthase	[c] : atp + dpcoa --> 2tpr3dpcoa + ade	Update		b0613	This reaction makes the cofactor needed for citX enxyme	"Taken from PMID: 10924139
AMF

2tpr3dpcoa is needed to make and active CitDEF enzyme with the aid of CitX"	-2.57019	4.67683	[c] : atp[c] + dpcoa[c] --> 2tpr3dpcoa[c] + ade[c] 		
2817	TRDR	No	thioredoxin reductase (NADPH)	[c] : h + nadph + trdox --> nadp + trdrd	Oxidative Phosphorylation	1.8.1.9	b0888			4.26561	9.93439	[c] : h[c] + nadph[c] + trdox[c] --> nadp[c] + trdrd[c] 		
203	TRE6PH	No	trehalose-6-phosphate hydrolase	[c] : h2o + tre6p --> g6p + glc-D	Alternate Carbon Metabolism	3.2.1.93	b4239			-3.32755	3.07096	[c] : h2o[c] + tre6p[c] --> g6p[c] + glc-D[c] 		
2727	TRE6PP	No	trehalose-phosphatase	[c] : h2o + tre6p --> pi + tre	Alternate Carbon Metabolism	3.1.3.12	b1897	"TRE6PS is a part of TRE6PS/TRE6PP complex
IF"		-2.35942	1.9257	[c] : h2o[c] + tre6p[c] --> h[c] + pi[c] + tre[c] 		
692	TRE6PS	No	"alpha,alpha-trehalose-phosphate synthase (UDP-forming)"	[c] : g6p + udpg --> h + tre6p + udp	Alternate Carbon Metabolism	2.4.1.15	b1896	"TRE6PS is a part of TRE6PS/TRE6PP complex
IF"		-0.675884	3.38607	[c] : g6p[c] + udpg[c] --> tre6p[c] + udp[c] 		
695	TREH	No	"alpha,alpha-trehalase"	[c] : h2o + tre --> (2) glc-D	Alternate Carbon Metabolism	3.2.1.28	b3519	IF		-3.32755	3.07096	[c] : h2o[c] + tre[c] --> (2) glc-D[c] 		
8967	TREHpp	Yes	"alpha,alpha-trehalase (periplasm)"	[p] : h2o + tre --> (2) glc-D	Alternate Carbon Metabolism	3.2.1.28	b1197	JLR		-3.32755	3.07096	[p] : h2o[p] + tre[p] --> (2) glc-D[p] 		
8936	TREptspp	Yes	trehalose transport via PEP:Pyr PTS (periplasm)	pep[c] + tre[p] --> pyr[c] + tre6p[c]	"Transport, Inner Membrane"		( b2417  and  b2415  and  b2416  and  b4240 )			-10.1729	3.20748	[c] : pep[c] + tre[p] --> pyr[c] + tre6p[c] 		
9213	TREtex	Yes	trehalose transport via diffusion (extracellular to periplasm)	tre[e] <==> tre[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : tre[e] <==> tre[p] 		
1270	TRPAS2	No	Tryptophanase (L-tryptophan)	[c] : h2o + trp-L <==> indole + nh4 + pyr	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.1.99.1	b3708	JLR		1.1929	3.51808	[c] : h2o[c] + trp-L[c] <==> indole[c] + nh4[c] + pyr[c] 		
2862	TRPS1	No	tryptophan synthase (indoleglycerol phosphate)	[c] : 3ig3p + ser-L --> g3p + h2o + trp-L	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.2.1.20	( b1260  and  b1261 )			-9.15467	2.28774	[c] : 3ig3p[c] + ser-L[c] --> g3p[c] + h2o[c] + trp-L[c] 		
338	TRPS2	No	tryptophan synthase (indole)	[c] : indole + ser-L --> h2o + trp-L	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.2.1.20	( b1260  and  b1261 )	"A pyridoxal-phosphate protein.
 Also catalyses the conversion of serine and indole into tryptophan and water, and of indoleglycerol phosphate into indole and glyceraldehyde phosphate (the latter reaction was listed formerly as EC 4.1.2.8). "		-10.3018	2.60823	[c] : indole[c] + ser-L[c] --> h2o[c] + trp-L[c] 		
2553	TRPS3	No	tryptophan synthase (indoleglycerol phosphate)	[c] : 3ig3p --> g3p + indole	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	4.2.1.20	( b1260  and  b1261 )	JLR		1.14712	3.09192	[c] : 3ig3p[c] --> g3p[c] + indole[c] 		
8937	TRPt2rpp	Yes	L-tryptophan reversible transport via proton symport (periplasm)	h[p] + trp-L[p] <==> h[c] + trp-L[c]	"Transport, Inner Membrane"		( b0112  or  b3161  or  b3709 )	NCD		0	0	[c] : h[p] + trp-L[p] <==> h[c] + trp-L[c] 		
9214	TRPtex	Yes	L-tryptophan transport via diffusion (extracellular to periplasm)	trp-L[e] <==> trp-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : trp-L[e] <==> trp-L[p] 		
2916	TRPTRS	Yes	Tryptophanyl-tRNA synthetase	[c] : atp + trnatrp + trp-L --> amp + ppi + trptrna	Update	6.1.1.2	b3384		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + trnatrp[c] + trp-L[c] --> amp[c] + ppi[c] + trptrna[c] 		
7602	TRSARr	Yes	tartronate semialdehyde reductase	[c] : 2h3oppan + h + nadh <==> glyc-R + nad	Alternate Carbon Metabolism	1.1.1.60	( b0509  or  b3125 )	JLR		-5.16584	4.34649	[c] : 2h3oppan[c] + h[c] + nadh[c] <==> glyc-R[c] + nad[c] 		
8927	TSULabcpp	Yes	thiosulfate transport via ABC system (periplasm)	atp[c] + h2o[c] + tsul[p] --> adp[c] + h[c] + pi[c] + tsul[c]	"Transport, Inner Membrane"		( ( b2422  and  b2425  and  b2424  and  b2423 )  or  ( b2422  and  b2424  and  b2423  and  b3917 ) )	JLR		-7.01673	1.48181	[c] : atp[c] + h2o[c] + tsul[p] --> adp[c] + h[c] + pi[c] + tsul[c] 		
9215	TSULtex	Yes	thiosulfate transport via diffusion (extracellular to periplasm)	tsul[e] <==> tsul[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : tsul[e] <==> tsul[p] 		
9242	TTDCAtexi	Yes	Tetradecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)	ttdca[e] --> ttdca[p]	"Transport, Outer Membrane"		b2344		"Transport of C12 - C18 fatty acids are facilitated by the outer membrane FadL protein (PMID: 103228825), inner membrane transport and subsequently outer membrane can require FACOAL enzyme (PMID: 15067008)

smaller FA can also pass through, C6 - C11, but can also diffuse, so they weren't associated"	0	0	[c] : ttdca[e] --> ttdca[p] 		
19981	TTDCEAtexi	Yes	Tetradecenoate transport via facilitated irreversible diffusion (extracellular to periplasm)	ttdcea[e] --> ttdcea[p]	"Transport, Outer Membrane"		b2344		"Transport of C12 - C18 fatty acids are facilitated by the outer membrane FadL protein (PMID: 103228825), inner membrane transport and subsequently outer membrane can require FACOAL enzyme (PMID: 15067008)

smaller FA can also pass through, C6 - C11, but can also diffuse, so they weren't associated"	0	0	[c] : ttdcea[e] --> ttdcea[p] 		
9246	TUNGSabcpp	Yes	tungstate transport via ABC system (periplasm)	atp[c] + h2o[c] + tungs[p] --> adp[c] + h[c] + pi[c] + tungs[c]	"Transport, Inner Membrane"		( b0763  and  b0764  and  b0765  and  b0760 )		"Transported Specific to molybdate and tungstate
PMID: 9545596
PMID: 9325422"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + tungs[p] --> adp[c] + h[c] + pi[c] + tungs[c] 		
9249	TUNGStex	Yes	tungstate transport via diffusion (extracellular to periplasm)	tungs[p] <==> tungs[c]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : tungs[p] <==> tungs[c] 		
12241	TYMtex	Yes	tyramine transport via diffusion (extracellular to periplasm)	tym[e] <==> tym[p]	"Transport, Outer Membrane"			AMF	"PMID: 3309152 original paper source
PMID: 11729263 - review where it states that that tyroxdapp and 42a12booxpp are confirmed susbstrates and can be used in K-12 for nitrogen source only, not sure if they are transported inside the cell or not or if they can't be processed after transport"	0	0	[c] : tym[e] <==> tym[p] 		
12236	TYROXDApp	Yes	Tyramine:oxygen oxidoreductase(deaminating)(flavin-containing) (periplasm)	[p] : h2o + o2 + tym --> 4hoxpacd + h2o2 + nh4	Update	1.4.3.6	b1386	"SAB
also 1.4.3.4
AMF"	"PMID: 3309152 original paper source
PMID: 11729263 - review where it states that that tyroxdapp and 42a12booxpp are confirmed susbstrates and can be used in K-12 for nitrogen source only, not sure if they are transported inside the cell or not or if they can't be processed after transport"	-18.53	2.13874	[p] : h2o[p] + o2[p] + tym[p] --> 4hoxpacd[p] + h2o2[p] + nh4[p] 		
13824	TYRPpp	Yes	phospho-L-tyrosine phosphatase (periplasmic)	[p] : h2o + tyrp --> pi + tyr-L	Update		b4055	AMF	"from PMID: 9011040
AMF
very general phosphatase"	-1.89385	4.17277	[p] : h2o[p] + tyrp[p] --> h[p] + pi[p] + tyr-L[p] 		
13831	TYRPtex	Yes	phopho-L-tyrosine transport via diffusion (extracellular to periplasm)	tyrp[e] <==> tyrp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : tyrp[e] <==> tyrp[p] 		
8938	TYRt2rpp	Yes	L-tyrosine reversible transport via proton symport (periplasm)	h[p] + tyr-L[p] <==> h[c] + tyr-L[c]	"Transport, Inner Membrane"		( b0112  or  b0576  or  b1907 )	"NCD	"	JLR- PheP also transports tyrosine	0	0	[c] : h[p] + tyr-L[p] <==> h[c] + tyr-L[c] 		
331	TYRTA	No	tyrosine transaminase	[c] : akg + tyr-L <==> 34hpp + glu-L	"Tyrosine, Tryptophan, and Phenylalanine Metabolism"	2.6.1.5	( b4054  or  b0928 )			0	0.5	[c] : akg[c] + tyr-L[c] <==> 34hpp[c] + glu-L[c] 		
9217	TYRtex	Yes	L-tyrosine transport via diffusion (extracellular to periplasm)	tyr-L[e] <==> tyr-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : tyr-L[e] <==> tyr-L[p] 		
1689	TYRTRS	Yes	tyrosyl-tRNA synthetase	[c] : atp + trnatyr + tyr-L --> amp + ppi + tyrtrna	Update	6.1.1.1	b1637	NCD	Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + trnatyr[c] + tyr-L[c] --> amp[c] + ppi[c] + tyrtrna[c] 		
3328	U23GAAT	No	UDP-3-O-(3-hydroxymyristoyl)glucosamine acyltransferase	[c] : 3hmrsACP + u3hga --> ACP + h + u23ga	Cell Envelope Biosynthesis		b0179	JLR- NH page 1042		-2.48774	5.01459	[c] : 3hmrsACP[c] + u3hga[c] --> ACP[c] + h[c] + u23ga[c] 		
3329	UAAGDS	No	"UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase"	[c] : 26dap-M + atp + uamag --> adp + h + pi + ugmd	Cell Envelope Biosynthesis	6.3.2.13	b0085			-3.65185	3.59073	[c] : 26dap-M[c] + atp[c] + uamag[c] --> adp[c] + h[c] + pi[c] + ugmd[c] 		
13811	UACGALPpp	Yes	UDP-N-acetyl-D-galactosamine pyrophosphohydrolase (periplasm)	[p] : h2o + udpacgal --> acgal1p + (2) h + ump	Update	3.6.1.45	b0480	AMF	"see PMID: 3012467
AMF"	-7.47198	3.25471	[p] : h2o[p] + udpacgal[p] --> acgal1p[p] + ump[p] 		
13810	UACGAMPpp	Yes	UDP-N-acetyl-D-glucosamine pyrophosphohydrolase (periplasm)	[p] : h2o + uacgam --> acgam1p + (2) h + ump	Update	3.6.1.45	b0480	AMF	"see PMID: 3012467
AMF"	-7.47198	3.25471	[p] : h2o[p] + uacgam[p] --> acgam1p[p] + ump[p] 		
13801	UACGAMtex	Yes	UDP-N-acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)	uacgam[e] <==> uacgam[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : uacgam[e] <==> uacgam[p] 		
2497	UACMAMO	No	UDP-N-acetyl-D-mannosamine oxidoreductase	[c] : h2o + (2) nad + uacmam --> (3) h + (2) nadh + uacmamu	Cell Envelope Biosynthesis		b3787	JLR (Kegg rxn R03317)		-4.69406	8.30383	[c] : h2o[c] + (2) nad[c] + uacmam[c] --> (3) h[c] + (2) nadh[c] + uacmamu[c] 		
479	UAG2E	Yes	UDP-N-acetylglucosamine 2-epimerase	[c] : uacgam <==> uacmam	Cell Envelope Biosynthesis	5.1.3.14	b3786		"assumed reversible
AMF"	0	0.5	[c] : uacgam[c] <==> uacmam[c] 		
3447	UAGAAT	No	UDP-N-acetylglucosamine acyltransferase	[c] : 3hmrsACP + uacgam <==> ACP + u3aga	Cell Envelope Biosynthesis	2.3.1.129	b0181	JLR- NH page 1041		-1.98374	4.73838	[c] : 3hmrsACP[c] + uacgam[c] <==> ACP[c] + u3aga[c] 		
477	UAGCVT	No	UDP-N-acetylglucosamine 1-carboxyvinyltransferase	[c] : pep + uacgam --> pi + uaccg	Cell Envelope Biosynthesis	2.5.1.7	b3189			-1.02381	2.72189	[c] : pep[c] + uacgam[c] --> h[c] + pi[c] + uaccg[c] 		
476	UAGDP	No	UDP-N-acetylglucosamine diphosphorylase	[c] : acgam1p + h + utp --> ppi + uacgam	Cell Envelope Biosynthesis	2.7.7.23	b3730			-1.12149	3.25471	[c] : acgam1p[c] + utp[c] --> ppi[c] + uacgam[c] 		
2701	UAGPT3	No	UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase	[c] : uacgam + uagmda --> h + uaagmda + udp	Cell Envelope Biosynthesis		b0090	"No exact EC number yet: EC 2.4.1.- catalyzed by murG gene in Bacillus subtilis
Also found in H. pylori.  Ref: Mendz pg 161 (tv)"		-0.675884	3.38607	[c] : uacgam[c] + uagmda[c] --> uaagmda[c] + udp[c] 		
3331	UAMAGS	No	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase	[c] : atp + glu-D + uama --> adp + h + pi + uamag	Cell Envelope Biosynthesis	6.3.2.9	b0088			-3.65185	3.59073	[c] : atp[c] + glu-D[c] + uama[c] --> adp[c] + h[c] + pi[c] + uamag[c] 		
3330	UAMAS	No	UDP-N-acetylmuramoyl-L-alanine synthetase	[c] : ala-L + atp + uamr --> adp + h + pi + uama	Cell Envelope Biosynthesis	6.3.2.8	b0091			-3.65185	3.59073	[c] : ala-L[c] + atp[c] + uamr[c] --> adp[c] + h[c] + pi[c] + uama[c] 		
2703	UAPGR	No	UDP-N-acetylenolpyruvoylglucosamine reductase	[c] : h + nadph + uaccg --> nadp + uamr	Cell Envelope Biosynthesis	1.1.1.158	b3972			-12.9174	5.04951	[c] : h[c] + nadph[c] + uaccg[c] --> nadp[c] + uamr[c] 		
694	UDCPDP	No	undecaprenyl-diphosphatase	[c] : h2o + udcpdp --> h + pi + udcpp	Cell Envelope Biosynthesis	3.6.1.27	( b3057  or  b0841  or  b1278 )		"Other enzymes are present that carry out this reaction if bacA (UppP) is deleted - these are YbjG and PgpB

Whether the dephosphorylation of C55-PP occurs on both membrane sides or only on one side remains to be elucidated.

tripple deletion of YbjG, UppP, PgpB did not perform this action
PMID: 15138271
AMF"	-7.01673	1.48181	[c] : h2o[c] + udcpdp[c] --> h[c] + pi[c] + udcpp[c] 		
13553	UDCPDPpp	Yes	undecaprenyl-diphosphatase (periplasm)	[p] : h2o + udcpdp --> h + pi + udcpp	Cell Envelope Biosynthesis	3.6.1.27	( b3057  or  b0841  or  b1278 )	AMF	"Other enzymes are present that carry out this reaction if bacA (UppP) is deleted - these are YbjG and PgpB

Whether the dephosphorylation of C55-PP occurs on both membrane sides or only on one side remains to be elucidated.

tripple deletion of YbjG, UppP, PgpB did not perform this action
PMID: 15138271
AMF"	-7.01673	1.48181	[p] : h2o[p] + udcpdp[p] --> h[p] + pi[p] + udcpp[p] 		
1254	UDCPDPS	No	Undecaprenyl diphosphate synthase	[c] : frdp + (8) ipdp --> (8) ppi + udcpdp	Cofactor and Prosthetic Group Biosynthesis		b0174	tv		-115.317	23.4082	[c] : frdp[c] + (8) ipdp[c] --> (8) ppi[c] + udcpdp[c] 		
13474	UDCPPtppi	Yes	undecaprenyl phosphate transport (cytoplasm to periplasm)	udcpp[p] --> udcpp[c]	Lipopolysaccharide Biosynthesis / Recycling			"AMF
assumed flipping"	"latest article with an update for all these reactions is given in figure and text of PMID: 15695810

The UPLA4FNF reaction is said to be catalyzed by arnD gene, but hasn't been identified yet

transport for undeaprenyl chains is unknown
AMF"	0	0	[c] : udcpp[p] --> udcpp[c] 		
13804	UDPACGALtex	Yes	UDP-N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)	udpacgal[e] <==> udpacgal[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : udpacgal[e] <==> udpacgal[p] 		
200	UDPG4E	No	UDPglucose 4-epimerase	[c] : udpg <==> udpgal	Alternate Carbon Metabolism	5.1.3.2	b0759			0	0.5	[c] : udpg[c] <==> udpgal[c] 		
2491	UDPGALM	No	UDPgalactopyranose mutase	[c] : udpgal --> udpgalfur	Cell Envelope Biosynthesis	5.4.99.9	b2036	JLR		-0.111829	1.90698	[c] : udpgal[c] --> udpgalfur[c] 		
13809	UDPGALPpp	Yes	UDPgalactose pyrophosphohydrolase	[p] : h2o + udpgal --> gal1p + (2) h + ump	Update	3.6.1.45	b0480	AMF	"see PMID: 3012467
AMF"	-7.47198	3.25471	[p] : h2o[p] + udpgal[p] --> gal1p[p] + ump[p] 		
13799	UDPGALtex	Yes	UDPgalactose transport via diffusion (extracellular to periplasm)	udpgal[e] <==> udpgal[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : udpgal[e] <==> udpgal[p] 		
3196	UDPGD	No	UDPglucose 6-dehydrogenase	[c] : h2o + (2) nad + udpg --> (3) h + (2) nadh + udpglcur	Cell Envelope Biosynthesis	1.1.1.22	b2028	JLR		-4.69406	8.30383	[c] : h2o[c] + (2) nad[c] + udpg[c] --> (3) h[c] + (2) nadh[c] + udpglcur[c] 		
13467	UDPGDC	Yes	UDP-glucuronate C-4'' decarboxylase	[c] : nad + udpglcur --> co2 + nadh + udpLa4o	Lipopolysaccharide Biosynthesis / Recycling		b2255	AMF	"latest article with an update for all these reactions is given in figure and text of PMID: 15695810

The UPLA4FNF reaction is said to be catalyzed by arnD gene, but hasn't been identified yet

transport for undeaprenyl chains is unknown
AMF"	-0.863487	6.05959	[c] : nad[c] + udpglcur[c] --> co2[c] + nadh[c] + udpLa4o[c] 		
13807	UDPGLCURtex	Yes	UDP-D-glucuronate transport via diffusion (extracellular to periplasm)	udpglcur[e] <==> udpglcur[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : udpglcur[e] <==> udpglcur[p] 		
13808	UDPGPpp	Yes	UDPglucose pyrophosphohydrolase	[p] : h2o + udpg --> g1p + (2) h + ump	Update	3.6.1.45	b0480	AMF	"see PMID: 3012467
AMF"	-7.47198	3.25471	[p] : h2o[p] + udpg[p] --> g1p[p] + ump[p] 		
13798	UDPGtex	Yes	UDPglucose transport via diffusion (extracellular to periplasm)	udpg[e] <==> udpg[p]	"Transport, Outer Membrane"			AMF	assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : udpg[e] <==> udpg[p] 		
13468	UDPKAAT	Yes	UDP-4''-ketopentose:UDP-4-amino-4-deoxy-L-arabinose aminotransferase	[c] : glu-L + udpLa4o <==> akg + udpLa4n	Lipopolysaccharide Biosynthesis / Recycling		b2253	AMF	"latest article with an update for all these reactions is given in figure and text of PMID: 15695810

The UPLA4FNF reaction is said to be catalyzed by arnD gene, but hasn't been identified yet

transport for undeaprenyl chains is unknown
AMF"	2.95982	2.81783	[c] : glu-L[c] + udpLa4o[c] <==> akg[c] + udpLa4n[c] 		
13812	UGLCURPpp	Yes	UDP-D-glucuronate pyrophosphohydrolase (periplasm)	[p] : h2o + udpglcur --> glcur1p + (2) h + ump	Update	3.6.1.45	b0480	AMF	"see PMID: 3012467
AMF"	-7.47198	3.25471	[p] : h2o[p] + udpglcur[p] --> glcur1p[p] + ump[p] 		
1171	UGLT	No	UDPglucose--hexose-1-phosphate uridylyltransferase	[c] : gal1p + udpg <==> g1p + udpgal	Alternate Carbon Metabolism	2.7.7.12	b0758	NCD		0	0.5	[c] : gal1p[c] + udpg[c] <==> g1p[c] + udpgal[c] 		
3332	UGLYCH	No	Ureidoglycolate hydrolase	[c] : (2) h + h2o + urdglyc --> co2 + glx + (2) nh4	Nitrogen Metabolism	3.5.3.19	b0505	JLR	"JLR- kegg and ecocyc have different byproducts then the paper, went with the databases"	-6.04263	5.10652	[c] : (2) h[c] + h2o[c] + urdglyc[c] --> co2[c] + glx[c] + (2) nh4[c] 		
3437	UGMDDS	No	"UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine synthetase"	[c] : alaala + atp + ugmd --> adp + h + pi + ugmda	Cell Envelope Biosynthesis	6.3.2.15	b0086			-3.65185	3.59073	[c] : alaala[c] + atp[c] + ugmd[c] --> adp[c] + h[c] + pi[c] + ugmda[c] 		
3438	UHGADA	No	UDP-3-O-acetylglucosamine deacetylase	[c] : h2o + u3aga --> ac + u3hga	Cell Envelope Biosynthesis		b0096	tc		-3.36489	3.34628	[c] : h2o[c] + u3aga[c] --> ac[c] + u3hga[c] 		
13469	ULA4NFT	Yes	UDP-L-Ara4N formyltransferase	[c] : 10fthf + udpLa4n --> h + thf + udpLa4fn	Lipopolysaccharide Biosynthesis / Recycling		b2255	AMF	"latest article with an update for all these reactions is given in figure and text of PMID: 15695810

The UPLA4FNF reaction is said to be catalyzed by arnD gene, but hasn't been identified yet

transport for undeaprenyl chains is unknown
AMF"	2.87372	4.66034	[c] : 10fthf[c] + udpLa4n[c] --> thf[c] + udpLa4fn[c] 		
13473	ULA4Ntppi	Yes	transport (cytoplasm to periplasm)	uLa4n[c] --> uLa4n[p]	Lipopolysaccharide Biosynthesis / Recycling			"AMF
assumed flipping"	"latest article with an update for all these reactions is given in figure and text of PMID: 15695810

The UPLA4FNF reaction is said to be catalyzed by arnD gene, but hasn't been identified yet

transport for undeaprenyl chains is unknown
AMF"	0	0	[c] : uLa4n[c] --> uLa4n[p] 		
12642	UM3PL	Yes	UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelat e ligase	[c] : LalaDgluMdap + uamr --> h2o + ugmd	Murein Recycling		b4233	"AMF
PMID: 8808921"	"added action on both tri- and tetra- peptide
AMF
PMID: 8808921
"	3.36489	3.34628	[c] : LalaDgluMdap[c] + uamr[c] --> h2o[c] + ugmd[c] 		
12644	UM4PCP	Yes	"UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine L,D-carboxypeptidase"	[c] : h2o + um4p --> ala-D + ugmd	Murein Recycling		b1192	AMF	"LdcA is a cytoplasmic LD-carboxypeptidase
four different similar susbstrates
PMID: 10428950"	-3.36489	3.34628	[c] : h2o[c] + um4p[c] --> ala-D[c] + ugmd[c] 		
12643	UM4PL	Yes	UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate-D-alanine ligase	[c] : LalaDgluMdapDala + uamr --> h2o + um4p	Murein Recycling		b4233	"AMF
PMID: 8808921"	"added action on both tri- and tetra- peptide
AMF
PMID: 8808921"	3.36489	3.34628	[c] : LalaDgluMdapDala[c] + uamr[c] --> h2o[c] + um4p[c] 		
2813	UMPK	No	UMP kinase	[c] : atp + ump <==> adp + udp	Nucleotide Salvage Pathway	2.7.4.14	( b0910  or  b0171 )			0	0.5	[c] : atp[c] + ump[c] <==> adp[c] + udp[c] 		
12311	UMPtex	Yes	UMP transport via diffusion (extracellular to periplasm)	ump[e] <==> ump[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ump[e] <==> ump[p] 		
13554	UNAGAtpp	Yes	"undecaprenyl diphospho N-acetyl-glucosamine transferase (flippase, cytoplasm to periplasm)"	unaga[c] --> unaga[p]	Lipopolysaccharide Biosynthesis / Recycling		b3792	AMF	"characterization of WzxE gene, also talks about WzzE and WzyE function

paper states that only WzyE can transport UNAGA, others state differently
PMID: 12621029

review is excellent with diagram of core LPS oligosaccharide and pointing to specific papers
see PMID: 12045108"	0	0	[c] : unaga[c] --> unaga[p] 					
3645	UNK3	No	2-keto-4-methylthiobutyrate transamination	[c] : 2kmb + glu-L --> akg + met-L	Arginine and Proline Metabolism					0	0.5	[c] : 2kmb[c] + glu-L[c] --> akg[c] + met-L[c] 					
13471	UPLA4FNF	Yes	undecaprenyl phosphate-L-Ara4FN formylase	[c] : h2o + uLa4fn --> for + uLa4n	Lipopolysaccharide Biosynthesis / Recycling			AMF	"latest article with an update for all these reactions is given in figure and text of PMID: 15695810

The UPLA4FNF reaction is said to be catalyzed by arnD gene, but hasn't been identified yet

transport for undeaprenyl chains is unknown
AMF"	-10.1616	2.96763	[c] : h2o[c] + uLa4fn[c] --> for[c] + h[c] + uLa4n[c] 					
13470	UPLA4FNT	Yes	undecaprenyl phosphate-L-Ara4FN transferase	[c] : udcpp + udpLa4fn --> uLa4fn + udp	Lipopolysaccharide Biosynthesis / Recycling		b2254	AMF	"latest article with an update for all these reactions is given in figure and text of PMID: 15695810

The UPLA4FNF reaction is said to be catalyzed by arnD gene, but hasn't been identified yet

transport for undeaprenyl chains is unknown
AMF"	0	0.5	[c] : udcpp[c] + udpLa4fn[c] --> udp[c] + uLa4fn[c] 					
3701	UPP3MT	No	uroporphyrinogen methyltransferase	[c] : (2) amet + uppg3 --> (2) ahcys + dscl + h	Cofactor and Prosthetic Group Biosynthesis	2.1.1.107	( b3803  or  b3368 )	See also SHCHD and SHCHF	JLR- JSE reaction had only one amet not two	No energy	No energy	[c] : (2) amet[c] + uppg3[c] --> (2) ahcys[c] + dscl[c] + h[c] 					
5	UPP3S	No	uroporphyrinogen-III synthase	[c] : hmbil --> h2o + uppg3	Cofactor and Prosthetic Group Biosynthesis	4.2.1.75	b3804			No energy	No energy	[c] : hmbil[c] --> h2o[c] + uppg3[c] 					
6	UPPDC1	No	uroporphyrinogen decarboxylase (uroporphyrinogen III)	[c] : (4) h + uppg3 --> (4) co2 + cpppg3	Cofactor and Prosthetic Group Biosynthesis	4.1.1.37	b3997	Acts on a number of porphyrinogens		No energy	No energy	[c] : (4) h[c] + uppg3[c] --> (4) co2[c] + cpppg3[c] 					
2692	UPPRT	No	uracil phosphoribosyltransferase	[c] : prpp + ura --> ppi + ump	Nucleotide Salvage Pathway	2.4.2.9	b2498			-3.6643	3.87109	[c] : prpp[c] + ura[c] --> ppi[c] + ump[c] 					
8939	URAt2pp	Yes	uracil transport in via proton symport (periplasm)	h[p] + ura[p] --> h[c] + ura[c]	"Transport, Inner Membrane"		b2497			0	0	[c] : h[p] + ura[p] --> h[c] + ura[c] 					
8940	URAt2rpp	Yes	"uracil transport in via proton symport, reversible (periplasm)"	h[p] + ura[p] <==> h[c] + ura[c]	Putative Transporters		b1006	JLR		0	0	[c] : h[p] + ura[p] <==> h[c] + ura[c] 					
9218	URAtex	Yes	uracil transport via diffusion (extracellular to periplasm)	ura[e] <==> ura[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : ura[e] <==> ura[p] 					
6181	URDGLYCD	Yes	ureidoglycolate dehydrogenase	[c] : nad + urdglyc --> h + nadh + oxur	Update	1.1.1.154	b0517	JLR		4.73639	4.5435	[c] : nad[c] + urdglyc[c] --> h[c] + nadh[c] + oxur[c] 					
9219	UREAtex	Yes	Urea transport via diffusion (extracellular to periplasm)	urea[e] <==> urea[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : urea[e] <==> urea[p] 					
8941	UREAtpp	Yes	Urea transport via facilitate diffusion (periplasm)	urea[p] <==> urea[c]	"Transport, Inner Membrane"		b3927	JLR	"JLR  (JSE had reaction using 2 Hext)
"	0	0	[c] : urea[p] <==> urea[c] 					
166	URIC	Yes	uricase	[c] : (2) h2o + o2 + urate --> alltn + co2 + h2o2	Update	1.7.3.3		"A copper protein. The initial products decompose to form allantoin. The intermediate products unknown. 
Exact stoichiometry unclear.
"	"reaction added to complete the pathway of Purine Catabolism
no gene assoiciation, pathway in PMID: 10986234
AMF"	-26.7423	8.22697	[c] : (2) h2o[c] + o2[c] + urate[c] --> alltn[c] + co2[c] + h2o2[c] 					
1567	URIDK2r	No	uridylate kinase (dUMP)	[c] : atp + dump <==> adp + dudp	Nucleotide Salvage Pathway		b0171	JLR- reversible form of URIDK2		0	0.5	[c] : atp[c] + dump[c] <==> adp[c] + dudp[c] 					
6175	URIH	Yes	Uridine hydrolase	[c] : h2o + uri --> rib-D + ura	Update	3.2.2.8	( b2162  or  b0651  or  b0030 )	JLR		-2.26379	3.60328	[c] : h2o[c] + uri[c] --> rib-D[c] + ura[c] 
437	URIK2	No	uridine kinase (GTP:Uridine)	[c] : gtp + uri --> gdp + h + ump	Nucleotide Salvage Pathway	2.7.1.48	b2066			-4.65732	2.09859	[c] : gtp[c] + uri[c] --> gdp[c] + ump[c] 
8942	URIt2pp	Yes	uridine transport in via proton symport (periplasm)	h[p] + uri[p] --> h[c] + uri[c]	"Transport, Inner Membrane"		( b2393  or  b2964 )			0	0	[c] : h[p] + uri[p] --> h[c] + uri[c] 
8943	URIt2rpp	Yes	"uridine transport in via proton symport, reversible (periplasm)"	h[p] + uri[p] <==> h[c] + uri[c]	"Transport, Inner Membrane"		b2406	JLR		0	0	[c] : h[p] + uri[p] <==> h[c] + uri[c] 
9220	URItex	Yes	uridine transport via diffusion (extracellular to periplasm)	uri[e] <==> uri[p]	"Transport, Outer Membrane"		b0411		"assumed passive diffusion through the outer peptidoglycan layer

Tsx is responsible for the permeation of ribo- and deoxy-nucleosides, across the outer membrane of E. coli"	0	0	[c] : uri[e] <==> uri[p] 
1255	USHD	No	UDP-sugar hydrolase	[c] : h2o + u23ga --> (2) h + lipidX + ump	Cell Envelope Biosynthesis		b0524	"tv
JLR- EC 3.6.1.45"	Previously assigned to ushA in iJE660a and iJR904.	-7.47198	3.25471	[c] : h2o[c] + u23ga[c] --> lipidX[c] + ump[c] 
8944	VALabcpp	Yes	L-valine transport via ABC system (periplasm)	atp[c] + h2o[c] + val-L[p] --> adp[c] + h[c] + pi[c] + val-L[c]	"Transport, Inner Membrane"		( b3454  and  b3455  and  b3457  and  b3460  and  b3456 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + val-L[p] --> adp[c] + h[c] + pi[c] + val-L[c] 
8945	VALt2rpp	Yes	L-valine reversible transport via proton symport (periplasm)	h[p] + val-L[p] <==> h[c] + val-L[c]	"Transport, Inner Membrane"		b0401	NCD	"JLR- h/na symporter not known, Lactobacillus has a proton symport rxn."	0	0	[c] : h[p] + val-L[p] <==> h[c] + val-L[c] 
320	VALTA	No	valine transaminase	[c] : akg + val-L <==> 3mob + glu-L	"Valine, Leucine, and Isoleucine Metabolism"	2.6.1.42	b3770			0	0.5	[c] : akg[c] + val-L[c] <==> 3mob[c] + glu-L[c] 
9221	VALtex	Yes	L-valine transport via diffusion (extracellular to periplasm)	val-L[e] <==> val-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : val-L[e] <==> val-L[p] 
1027	VALTRS	Yes	Valyl-tRNA synthetase	[c] : atp + trnaval + val-L --> amp + ppi + valtrna	Update	6.1.1.9	b4258		Added to incorporate tRNA peptides into model	-4.72457	3.42862	[c] : atp[c] + h[c] + trnaval[c] + val-L[c] --> amp[c] + ppi[c] + valtrna[c] 
1216	VPAMT	No	Valine-pyruvate aminotransferase	[c] : 3mob + ala-L --> pyr + val-L	Alanine and Aspartate Metabolism	2.6.1.66	b3572	JLR	NH indicates that this reaction is reversible	0	0.5	[c] : 3mob[c] + ala-L[c] --> pyr[c] + val-L[c] 
2504	X5PL3E	No	L-xylulose 5-phosphate 3-epimerase	[c] : xu5p-L --> ru5p-L	Alternate Carbon Metabolism		b4197	JLR		0	0.5	[c] : xu5p-L[c] --> ru5p-L[c] 
165	XAND	Yes	xanthine dehydrogenase	[c] : h2o + nad + xan --> h + nadh + urate	Update	1.1.1.204	( b2866  and  b2867  and  b2868 )	Acts on a variety of purines and aldehydes. The animal enzyme can be interconverted to EC 1.1.3.22 xanthine oxidase (the oxidase form). 	"pathway in PMID: 10986234
does not mention an electron acceptor (NAD) in the paper, so further charcterization is needed, but reaction is outlined
AMF"	-7.13927	6.82464	[c] : h2o[c] + nad[c] + xan[c] --> h[c] + nadh[c] + urate[c] 
8946	XANt2pp	Yes	xanthine transport in via proton symport (periplasm)	h[p] + xan[p] --> h[c] + xan[c]	Putative Transporters		b3654			0	0	[c] : h[p] + xan[p] --> h[c] + xan[c] 
9222	XANtex	Yes	xanthine transport via diffusion (extracellular to periplasm)	xan[e] <==> xan[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : xan[e] <==> xan[p] 
9015	XANtpp	Yes	xanthine reversible transport (periplasm)	xan[p] <==> xan[c]	"Transport, Inner Membrane"			NCD	JLR- not sure about the reaction 	0	0	[c] : xan[p] <==> xan[c] 
12312	XMPtex	Yes	XMP transport via diffusion (extracellular to periplasm)	xmp[e] <==> xmp[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : xmp[e] <==> xmp[p] 
440	XPPT	No	xanthine phosphoribosyltransferase	[c] : prpp + xan --> ppi + xmp	Nucleotide Salvage Pathway	2.4.2.22	b0238			-3.6643	3.87109	[c] : prpp[c] + xan[c] --> ppi[c] + xmp[c] 
6178	XTSNH	Yes	Xanthosine hydrolase	[c] : h2o + xtsn --> rib-D + xan	Update	3.2.2.8	b0030	JLR		-2.26379	3.60328	[c] : h2o[c] + xtsn[c] --> rib-D[c] + xan[c] 
8948	XTSNt2rpp	Yes	Xanthosine transport via proton symport (periplasm)	h[p] + xtsn[p] <==> h[c] + xtsn[c]	"Transport, Inner Membrane"		b2406	JLR		0	0	[c] : h[p] + xtsn[p] <==> h[c] + xtsn[c] 
9223	XTSNtex	Yes	xanthosine transport via diffusion (extracellular to periplasm)	xtsn[e] <==> xtsn[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : xtsn[e] <==> xtsn[p] 
8949	XYLabcpp	Yes	D-xylose transport via ABC system (periplasm)	atp[c] + h2o[c] + xyl-D[p] --> adp[c] + h[c] + pi[c] + xyl-D[c]	"Transport, Inner Membrane"		( b3566  and  b3567  and  b3568 )			-7.01673	1.48181	[c] : atp[c] + h2o[c] + xyl-D[p] --> adp[c] + h[c] + pi[c] + xyl-D[c] 
204	XYLI1	No	xylose isomerase	[c] : xyl-D <==> xylu-D	Alternate Carbon Metabolism	5.3.1.5	b3565	Some enzymes also convert D-glucose to D-fructose		-0.246702	4.88847	[c] : xyl-D[c] <==> xylu-D[c] 
242	XYLI2	Yes	xylose isomerase	[c] : glc-D <==> fru	Update	5.3.1.5	b3565	Special case of xylose isomerase	"Under appropriate conditions, the isomerase also efficiently catalyzed the conversion of D-glucose to D-fructose.

PMID: 6344793

AMF

not entirely sure of reversibility, but this seems like the logical choice"	-0.246702	4.88847	[c] : glc-D[c] <==> fru[c] 
254	XYLK	No	xylulokinase	[c] : atp + xylu-D --> adp + h + xu5p-D	Alternate Carbon Metabolism	2.7.1.17	( b3564  or  b0063 )		"PMID: 11747300

Paper states that AraB has 6 substrates with similar specificity and states what are not
abt - (arabitol) not included since no transporter could be found and the paper does not say explicitly that EC can grow on it)
rbl-D not included since it is not in the network and can not find data to support growth on it and can not grow on arabinose (FucI conversion)
AMF

No notes on XylB"	-4.04488	6.21545	[c] : atp[c] + xylu-D[c] --> adp[c] + xu5p-D[c] 
10567	XYLK2	Yes	Xylulose kinase	[c] : atp + xylu-L --> adp + h + xu5p-D	Update	2.7.1.17	b0063	"kb 11/23/02

MKA - 3/11/05"	"PMID: 11747300

Paper states that AraB has 6 substrates with similar specificity and states what are not
abt - (arabitol) not included since no transporter could be found and the paper does not say explicitly that EC can grow on it)
rbl-D not included since it is not in the network and can not find data to support growth on it and can not grow on arabinose (FucI conversion)
AMF"	-4.04488	6.21545	[c] : atp[c] + xylu-L[c] --> adp[c] + xu5p-D[c] 
3125	XYLKr2	Yes	Xylulose kinase	[c] : atp + xylu-D <==> adp + h + xu5p-D	Update	2.7.1.17	b3580	kb 11/23/02	"LyxK is deemed cryptic because the promoter is cryptic, so the function of LyxK is assigned
AMF

promoter region interupted by insert in wt"	-4.04488	6.21545	[c] : atp[c] + xylu-D[c] <==> adp[c] + xu5p-D[c] 
8955	XYLt2pp	Yes	D-xylose transport in via proton symport (periplasm)	h[p] + xyl-D[p] --> h[c] + xyl-D[c]	"Transport, Inner Membrane"		b4031			0	0	[c] : h[p] + xyl-D[p] --> h[c] + xyl-D[c] 
9224	XYLtex	Yes	D-xylose transport via diffusion (extracellular to periplasm)	xyl-D[e] <==> xyl-D[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : xyl-D[e] <==> xyl-D[p] 
8950	XYLUt2pp	Yes	L-xylulose transport in via proton symport (periplasm)	h[p] + xylu-L[p] --> h[c] + xylu-L[c]	Update		( b3577  and  b3578  and  b3579 )	JLR		0	0	[c] : h[p] + xylu-L[p] --> h[c] + xylu-L[c] 
9225	XYLUtex	Yes	L-xylulose transport via diffusion (extracellular to periplasm)	xylu-L[e] <==> xylu-L[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : xylu-L[e] <==> xylu-L[p] 
13652	ZN2abcpp	Yes	Zinc (Zn+2) ABC transporter (periplasm)	atp[c] + h2o[c] + zn2[c] --> adp[c] + h[c] + pi[c] + zn2[p]	"Transport, Inner Membrane"		b3469	AMF	"characterized in PMID: 10660539
ATP-dependent efflux
The activity was specific for Pb(II), Cd(II), Zn(II), and Hg(II), with the highest activity obtained when the metals were present as thiolate complexes of cysteine or glutathione.

AMF"	-7.01673	1.48181	[c] : atp[c] + h2o[c] + zn2[c] --> adp[c] + h[c] + pi[c] + zn2[p] 
13682	Zn2tex	Yes	zinc (Zn+2) transport via diffusion (extracellular to periplasm)	zn2[e] <==> zn2[p]	"Transport, Outer Membrane"				assumed passive diffusion through the outer peptidoglycan layer	0	0	[c] : zn2[e] <==> zn2[p] 
14038	ZNabcpp	Yes	zinc (Zn+2) transport via ABC system (periplasm)	atp[c] + h2o[c] + zn2[p] --> adp[c] + h[c] + pi[c] + zn2[c]	"Transport, Inner Membrane"		( b1857  and  b1859  and  b1858 )	AMF	see PMID: 9680209 	-7.01673	1.48181	[c] : atp[c] + h2o[c] + zn2[p] --> adp[c] + h[c] + pi[c] + zn2[c] 
14034	ZNt3pp	Yes	zinc (Zn+2) transport out via proton antiport (periplasm)	h[p] + zn2[c] --> h[c] + zn2[p]	"Tranpsort, Inner Membrane"		b0752	AMF	"these results indicate that ZitB is an antiporter catalyzing the obligatory exchange of Zn2+ or Cd2+ for H+. The exchange stoichiometry of metal ion for proton is likely to be 1:1
PMID: 14715669 
AMF"	0	0	[c] : h[p] + zn2[c] --> h[c] + zn2[p]