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MetaCyc Enzyme: L-glutamine:D-fructose-6-phosphate aminotransferase

Gene: glmS Accession Numbers: EG10382 (MetaCyc), b3729, ECK3722

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of L-glutamine:D-fructose-6-phosphate aminotransferase = [GlmS]2

Summary:
L-glutamine:D-fructose-6-phosphate aminotransferase, or GFAT, catalyzes the first step in hexosamine biosynthesis. The enzyme uses a nucleophilic attack by the thiol group of Cys1 on the δ-carbonyl group of glutamine to form ammonia, which is then channeled through the enzyme to the acceptor group on fructose-6-phosphate. The enzyme can not use exogenous ammonia as the nitrogen donor [Badet87].

The N-terminal domain contains the glutamine amidohydrolase activity, and the C-terminal domain contains the ketose/aldose isomerase activity [Denisot91]. Crystal structures of the isolated domains and the full length enzyme have been solved [Isupov96, Teplyakov98, Teplyakov99, Teplyakov01, Mouilleron06, Mouilleron08]. An 18 Å hydrophobic channel provides a conduit for the transfer of ammonia from the glutamine amidohydrolase active site to the isomerase active site [Teplyakov01]. Molecular dynamics simulations and kinetic analysis of mutants identified roles for W74, A602 and V605 in the opening and closing of the ammonia channel [Floquet07]. Major structural changes occur during the catalytic cycle [Mouilleron08].

Mutants of GlmS that show reduced sensitivity to product inhibition by glucosamine-6-phosphate have been isolated [Deng06].

Expression of GlmS is controlled at several levels. glmS mRNA and protein levels are decreased by growth on amino sugars [Plumbridge93]. glmS is cotranscribed together with glmU in the glmUS operon. Expression of GlmS is uncoupled from the expression of GlmU in various ways. RNase E processes the glmUS transcript at sites between glmU and glmS, generating a monocistronic 1.9 kb glmS transcript. This transcript is very unstable, with a half life of 0.72 minutes [Joanny07]. The small RNAs GlmY [Urban07] and GlmZ [Kalamorz07] regulate glmS expression posttranscriptionally. Via a regulatory cascade involving processing and stabilization of transcripts, the unprocessed form of GlmZ small regulatory RNA binds to glmS mRNA, uncovering the ribosome binding site and allowing translation [Reichenbach08, Urban08]. Although [Mohanty06] reported that glmS mRNA is polyadenylated, epistasis experiments and direct assays for polyadenylation show that glmS mRNA is not polyadenylated, and the effect of poly(A) polymerase I [Joanny07] on the stability of glmS mRNA is indirect, via polyadenylation of GlmY small regulatory RNA [Reichenbach08, Urban08].

A glmS mutant requires glucosamine or N-acetylglucosamine for growth [Wu71]. Overexpression of the catabolic D-glucosamine-6-phosphate isomerase, NagB, can suppress the requirement for glmS [Vogler89].

The transcription terminator region of glmS contains the unique insertion site for the transposon Tn7 [Gay86].

GlmS: "glucosamine"

Reviews: [Teplyakov02, Gopel14]

Locations: cytosol

Map Position: [3,909,862 <- 3,911,691]

Molecular Weight of Polypeptide: 66.894 kD (from nucleotide sequence), 70.8 kD (experimental) [Badet87 ]

Molecular Weight of Multimer: 127.0 kD (experimental) [Badet87]

pI: 5.8, 4.9 [Badet87]

Unification Links: ASAP:ABE-0012198 , CGSC:706 , DIP:DIP-9775N , EchoBASE:EB0377 , EcoGene:EG10382 , EcoliWiki:b3729 , Mint:MINT-1238536 , ModBase:P17169 , OU-Microarray:b3729 , PortEco:glmS , PR:PRO_000022781 , Pride:P17169 , Protein Model Portal:P17169 , RefSeq:NP_418185 , RegulonDB:EG10382 , SMR:P17169 , String:511145.b3729 , UniProt:P17169

Relationship Links: InterPro:IN-FAMILY:IPR000583 , InterPro:IN-FAMILY:IPR001347 , InterPro:IN-FAMILY:IPR005855 , InterPro:IN-FAMILY:IPR017932 , Panther:IN-FAMILY:PTHR10937:SF0 , PDB:Structure:1JXA , PDB:Structure:1MOQ , PDB:Structure:1MOR , PDB:Structure:1MOS , PDB:Structure:1XFF , PDB:Structure:1XFG , PDB:Structure:2J6H , PDB:Structure:2VF4 , PDB:Structure:2VF5 , PDB:Structure:3OOJ , PDB:Structure:4AMV , Pfam:IN-FAMILY:PF00310 , Pfam:IN-FAMILY:PF01380 , Prosite:IN-FAMILY:PS51278 , Prosite:IN-FAMILY:PS51464

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006048 - UDP-N-acetylglucosamine biosynthetic process Inferred from experiment [Wu71]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA06, GOA01]
GO:0006541 - glutamine metabolic process Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0016051 - carbohydrate biosynthetic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0004360 - glutamine-fructose-6-phosphate transaminase (isomerizing) activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Badet87]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0008483 - transaminase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0030246 - carbohydrate binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: cell structure murein
cell structure surface antigens (ECA, O antigen of LPS)
metabolism biosynthesis of macromolecules (cellular constituents) lipopolysaccharide O antigen
metabolism biosynthesis of macromolecules (cellular constituents) murein (peptidoglycan)
metabolism central intermediary metabolism amino sugar conversions

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: L-glutamine:D-fructose-6-phosphate aminotransferase

Synonyms: glucosamine fructose-6-phosphate aminotransferase (isomerizing), hexosephosphate aminotransferase, D-fructose-6-phosphate amidotransferase, glucosamine-6-phosphate isomerase (glutamine-forming), GFAT, glutamine-fructose-6-phosphate transaminase (isomerizing), glucosamine synthase, L-glutamine-D-fructose 6-P transamidase

EC Number: 2.6.1.16

β-D-fructofuranose 6-phosphate + L-glutamine <=> D-glucosamine 6-phosphate + L-glutamate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Alternative Substrates [Comment 1]:

In Pathways: superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis , O-antigen building blocks biosynthesis (E. coli) , UDP-N-acetyl-D-glucosamine biosynthesis I

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
The enzyme was first purified from E. coli B [Ghosh60].

Inhibitors (Competitive): N3-fumaramoyl-L-2,3-diaminopropanoate [Badet88] , N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoate [Badet88, Kucharczyk90] , 2-deoxy-2-amino glucitol-6-phosphate [BadetDenisot95] , L-glutamate-5-semialdehyde [Bearne95] , pyridoxal 5'-phosphate [GolinelliPimpan91, Comment 2] , 6-diazo-5-oxonorleucine [Ghosh60, Badet87, Comment 3] , L-glutamate [Badet88, Isupov96, Comment 3]

Inhibitors (Irreversible): N-iodoacetylglucosamine 6-phosphate [Bearne96] , glutarate semialdehyde [Bearne95] , iodoacetamide [Badet87]

Inhibitors (Unknown Mechanism): pyridoxal 5'-phosphate [GolinelliPimpan91, Comment 4] , diethylpyrocarbonate [BadetDenisot92]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-glutamate
9.81
[ValerioLepiniec10, BRENDA14]
β-D-fructofuranose 6-phosphate
360.0
[Floquet07]
L-glutamine
170.0
[Deng06, BRENDA14]
L-glutamine
200.0
[Li07, BRENDA14]
L-glutamine
400.0
[Chmara84, BRENDA14]
L-glutamine
650.0
[GHOSH60, BRENDA14]
L-glutamine
270.0
17.2, 0.97, 17.17
[Floquet07, BRENDA14]

pH(opt): 7.9 [BRENDA14, GHOSH60], 7.2 [Badet87]


Sequence Features

Feature Class Location Common Name Citations Comment
Cleavage-of-Initial-Methionine 1  
[Badet87]
 
Conserved-Region 2 -> 218  
[UniProt09]
UniProt: Glutamine amidotransferase type-2;
Chain 2 -> 609  
[UniProt09]
UniProt: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing];
Active-Site 2 catalytic nucleophile
[Isupov96]
 
Conserved-Region 286 -> 426  
[UniProt10]
UniProt: SIS 1;
Sequence-Conflict 419 -> 420  
[Walker84, UniProt10a]
Alternate sequence: NV; UniProt: (in Ref. 1; CAA25785);
Conserved-Region 458 -> 599  
[UniProt10]
UniProt: SIS 2;
Active-Site 604  
[UniProt10a]
UniProt: For Fru-6P isomerization activity;

History:
10/20/97 Gene b3729 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10382; confirmed by SwissProt match.


References

Badet87: Badet B, Vermoote P, Haumont PY, Lederer F, LeGoffic F (1987). "Glucosamine synthetase from Escherichia coli: purification, properties, and glutamine-utilizing site location." Biochemistry 1987;26(7);1940-8. PMID: 3297136

Badet88: Badet B, Vermoote P, Le Goffic F (1988). "Glucosamine synthetase from Escherichia coli: kinetic mechanism and inhibition by N3-fumaroyl-L-2,3-diaminopropionic derivatives." Biochemistry 1988;27(7);2282-7. PMID: 3132968

BadetDenisot92: Badet-Denisot MA, Badet B (1992). "Chemical modification of glucosamine-6-phosphate synthase by diethyl pyrocarbonate: evidence of histidine requirement for enzymatic activity." Arch Biochem Biophys 1992;292(2);475-8. PMID: 1731613

BadetDenisot95: Badet-Denisot MA, Leriche C, Massiere F, Badet B (1995). "Nitrogen transfer in E. coli glucosamine-6P synthase. Investigations using substrate and bisubstrate analogs." Bioorg. Med. Chem. Lett. 5(8);815-820.

Bearne00: Bearne SL, Blouin C (2000). "Inhibition of Escherichia coli glucosamine-6-phosphate synthase by reactive intermediate analogues. The role of the 2-amino function in catalysis." J Biol Chem 275(1);135-40. PMID: 10617596

Bearne95: Bearne SL, Wolfenden R (1995). "Glutamate gamma-semialdehyde as a natural transition state analogue inhibitor of Escherichia coli glucosamine-6-phosphate synthase." Biochemistry 34(36);11515-20. PMID: 7547881

Bearne96: Bearne SL (1996). "Active site-directed inactivation of Escherichia coli glucosamine-6-phosphate synthase. Determination of the fructose 6-phosphate binding constant using a carbohydrate-based inactivator." J Biol Chem 271(6);3052-7. PMID: 8621700

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Chmara84: Chmara H, Zahner H (1984). "The inactivation of glucosamine synthetase from bacteria by anticapsin, the C-terminal epoxyamino acid of the antibiotic tetaine." Biochim Biophys Acta 787(1);45-52. PMID: 6426523

Chmara85: Chmara H (1985). "Inhibition of glucosamine synthase by bacilysin and anticapsin." J Gen Microbiol 131(2);265-71. PMID: 3884731

Deng06: Deng MD, Grund AD, Wassink SL, Peng SS, Nielsen KL, Huckins BD, Burlingame RP (2006). "Directed evolution and characterization of Escherichia coli glucosamine synthase." Biochimie 88(5);419-29. PMID: 16871653

Denisot91: Denisot MA, Le Goffic F, Badet B (1991). "Glucosamine-6-phosphate synthase from Escherichia coli yields two proteins upon limited proteolysis: identification of the glutamine amidohydrolase and 2R ketose/aldose isomerase-bearing domains based on their biochemical properties." Arch Biochem Biophys 288(1);225-30. PMID: 1898018

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

DutkaMalen88: Dutka-Malen S, Mazodier P, Badet B (1988). "Molecular cloning and overexpression of the glucosamine synthetase gene from Escherichia coli." Biochimie 70(2);287-90. PMID: 3134953

Floquet07: Floquet N, Mouilleron S, Daher R, Maigret B, Badet B, Badet-Denisot MA (2007). "Ammonia channeling in bacterial glucosamine-6-phosphate synthase (Glms): molecular dynamics simulations and kinetic studies of protein mutants." FEBS Lett 581(16);2981-7. PMID: 17559838

Gay86: Gay NJ, Tybulewicz VL, Walker JE (1986). "Insertion of transposon Tn7 into the Escherichia coli glmS transcriptional terminator." Biochem J 234(1);111-7. PMID: 3010949

GHOSH60: GHOSH S, BLUMENTHAL HJ, DAVIDSON E, ROSEMAN S (1960). "Glucosamine metabolism. V. Enzymatic synthesis of glucosamine 6-phosphate." J Biol Chem 235;1265-73. PMID: 13827775

Ghosh60: Ghosh S, Blumenthal HJ, Davidson E, Roseman S (1960). "Glucosamine Metabolism V. Enzymatic synthesis of glucosamine 6-phosphate." J Biol Chem 1960;235(5):1265-1273.

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

GolinelliPimpan91: Golinelli-Pimpaneau B, Badet B (1991). "Possible involvement of Lys603 from Escherichia coli glucosamine-6-phosphate synthase in the binding of its substrate fructose 6-phosphate." Eur J Biochem 1991;201(1);175-82. PMID: 1915361

Gopel14: Gopel Y, Khan MA, Gorke B (2014). "Menage a trois: Post-transcriptional control of the key enzyme for cell envelope synthesis by a base-pairing small RNA, an RNase adaptor protein, and a small RNA mimic." RNA Biol 11(5). PMID: 24667238

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Isupov96: Isupov MN, Obmolova G, Butterworth S, Badet-Denisot MA, Badet B, Polikarpov I, Littlechild JA, Teplyakov A (1996). "Substrate binding is required for assembly of the active conformation of the catalytic site in Ntn amidotransferases: evidence from the 1.8 A crystal structure of the glutaminase domain of glucosamine 6-phosphate synthase." Structure 4(7);801-10. PMID: 8805567

Joanny07: Joanny G, Le Derout J, Brechemier-Baey D, Labas V, Vinh J, Regnier P, Hajnsdorf E (2007). "Polyadenylation of a functional mRNA controls gene expression in Escherichia coli." Nucleic Acids Res 35(8);2494-502. PMID: 17395638

Kalamorz07: Kalamorz F, Reichenbach B, Marz W, Rak B, Gorke B (2007). "Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli." Mol Microbiol 65(6);1518-33. PMID: 17824929

Kucharczyk90: Kucharczyk N, Denisot MA, Le Goffic F, Badet B (1990). "Glucosamine-6-phosphate synthase from Escherichia coli: determination of the mechanism of inactivation by N3-fumaroyl-L-2,3-diaminopropionic derivatives." Biochemistry 1990;29(15);3668-76. PMID: 2111163

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Leriche97: Leriche C, Badet-Denisot MA, Badet B (1997). "Affinity labeling of Escherichia coli glucosamine-6-phosphate synthase with a fructose 6-phosphate analog--evidence for proximity between the N-terminal cysteine and the fructose-6-phosphate-binding site." Eur J Biochem 245(2);418-22. PMID: 9151973

Li07: Li Y, Lopez P, Durand P, Ouazzani J, Badet B, Badet-Denisot MA (2007). "An enzyme-coupled assay for amidotransferase activity of glucosamine-6-phosphate synthase." Anal Biochem 370(2);142-6. PMID: 17880906

Mohanty06: Mohanty BK, Kushner SR (2006). "The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells." Nucleic Acids Res 34(19);5695-704. PMID: 17040898

Mouilleron06: Mouilleron S, Badet-Denisot MA, Golinelli-Pimpaneau B (2006). "Glutamine binding opens the ammonia channel and activates glucosamine-6P synthase." J Biol Chem 281(7);4404-12. PMID: 16339762

Mouilleron08: Mouilleron S, Badet-Denisot MA, Golinelli-Pimpaneau B (2008). "Ordering of C-terminal loop and glutaminase domains of glucosamine-6-phosphate synthase promotes sugar ring opening and formation of the ammonia channel." J Mol Biol 377(4);1174-85. PMID: 18295797

Plumbridge93: Plumbridge JA, Cochet O, Souza JM, Altamirano MM, Calcagno ML, Badet B (1993). "Coordinated regulation of amino sugar-synthesizing and -degrading enzymes in Escherichia coli K-12." J Bacteriol 1993;175(16);4951-6. PMID: 8349539

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Reichenbach08: Reichenbach B, Maes A, Kalamorz F, Hajnsdorf E, Gorke B (2008). "The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli." Nucleic Acids Res 36(8);2570-80. PMID: 18334534

Teplyakov01: Teplyakov A, Obmolova G, Badet B, Badet-Denisot MA (2001). "Channeling of ammonia in glucosamine-6-phosphate synthase." J Mol Biol 313(5);1093-102. PMID: 11700065

Teplyakov02: Teplyakov A, Leriche C, Obmolova G, Badet B, Badet-Denisot MA (2002). "From Lobry de Bruyn to enzyme-catalyzed ammonia channelling: molecular studies of D-glucosamine-6P synthase." Nat Prod Rep 19(1);60-9. PMID: 11902440

Teplyakov98: Teplyakov A, Obmolova G, Badet-Denisot MA, Badet B, Polikarpov I (1998). "Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain." Structure 6(8);1047-55. PMID: 9739095

Teplyakov99: Teplyakov A, Obmolova G, Badet-Denisot MA, Badet B (1999). "The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase." Protein Sci 8(3);596-602. PMID: 10091662

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Urban07: Urban JH, Papenfort K, Thomsen J, Schmitz RA, Vogel J (2007). "A Conserved Small RNA Promotes Discoordinate Expression of the glmUS Operon mRNA to Activate GlmS Synthesis." J Mol Biol 373(3);521-8. PMID: 17854828

Urban08: Urban JH, Vogel J (2008). "Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation." PLoS Biol 6(3);e64. PMID: 18351803

ValerioLepiniec10: Valerio-Lepiniec M, Aumont-Nicaise M, Roux C, Raynal B, England P, Badet B, Badet-Denisot MA, Desmadril M (2010). "Analysis of the Escherichia coli glucosamine-6-phosphate synthase activity by isothermal titration calorimetry and differential scanning calorimetry." Arch Biochem Biophys 498(2);95-104. PMID: 20416269

Vogler89: Vogler AP, Trentmann S, Lengeler JW (1989). "Alternative route for biosynthesis of amino sugars in Escherichia coli K-12 mutants by means of a catabolic isomerase." J Bacteriol 1989;171(12);6586-92. PMID: 2687246

Walker84: Walker JE, Gay NJ, Saraste M, Eberle AN (1984). "DNA sequence around the Escherichia coli unc operon. Completion of the sequence of a 17 kilobase segment containing asnA, oriC, unc, glmS and phoS." Biochem J 224(3);799-815. PMID: 6395859

Wu71: Wu HC, Wu TC (1971). "Isolation and characterization of a glucosamine-requiring mutant of Escherichia coli K-12 defective in glucosamine-6-phosphate synthetase." J Bacteriol 105(2);455-66. PMID: 5541523


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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