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Escherichia coli K-12 substr. MG1655 Polypeptide: protein chain initiation factor IF-3

Gene: infC Accession Numbers: EG10506 (EcoCyc), b1718, ECK1716

Synonyms: fit, srjA, IF3

Regulation Summary Diagram: ?

IF-3 is one of three translation initiation factors in E. coli [Sabol70]. It was also initially identified as a ribosomal dissociation factor [Subramanian68, Subramanian70].

The interaction sites of IF-3 with the 30S subunit have been mapped [Dallas01]. The A790G and U789C mutations in 16S rRNA decreases translation fidelity, which may be due to decreased affinity of the 30S subunit for IF-3 [Qin07, Qin09]. The m2G966 and m5C967 residues of 16S rRNA appear to be important for interaction with IF-3 [Saraiya08].

After the 30S subunit has dissociated from the post-termination ribosome in a process that requires RRF, EF-G, and GTP hydrolysis, IF-3 binds and stimulates dissociation of deacylated tRNA [Karimi99, Peske05, Hirokawa05] and destabilizes binding of all tested tRNAs to the 30S subunit [Antoun06a]. IF-3 also destabilizes incorrect initiation ternary complexes [Risuleo76]. The presence of fMet-tRNAfMet increases the rate of dissociation of IF-3 from the 30S subunit and subsequently increases the rate of docking to the 50S subunit [vanderHofstad78, Antoun06]. In the presence of IF-3, the 30S preinitiation complex can not dock to the 50S subunit [Antoun06]. The path of IF-3 binding to the 30S subunit and its subsequent release upon 30S association with the 50S subunit has been probed [Fabbretti07].

IF-3 also appears to play a role in recycling of stalled ribosomal complexes [Singh05c]. IF-3 appears to facilitate ribosome recycling factor-mediated processing of stalled ribosomes [Singh08c].

infC, the gene encoding IF-3, contains the unusual initiation codon AUU [Sacerdot82]. Expression of infC is negatively autoregulated at the level of translation [Butler86]; this regulation is dependent on the presence of the AUU initiation codon [Butler87]. The mechanism of IF-3 autoregulation was originally thought to be based on its ability to differentiate between typical and atypical initiation codons and discriminate against the atypical initiation codons [Sacerdot96, Sussman96] by recognition of codon-anticodon complementarity [Meinnel99] as well as unique features of the initiator tRNA [OConnor01a]. However, recent experiments suggest that discrimination against the AUU start codon in the presence of IF-3 is a kinetic effect [Antoun06a].

IF-3 consists of two independent domains that are connected via a flexible hydrophilic linker peptide [Fortier94, Hua98]. The solution structures of the full-length protein [Moreau97] as well as that of the N-terminal [Garcia95] and C-terminal domains [Garcia95a] were determined by NMR. Sites of interaction of both domains with the 30S subunit of the ribosome were determined by NMR [Sette99]. The C-terminal domain retains all activities of the full-length IF-3 [Garcia95a, Petrelli01], while the N-terminal domain provides additional binding energy for the interaction with the 30S subunit [Petrelli01]. A physical link between the two domains is required for full function of IF-3 [deCock99]. The phenotypes of a point mutation, Y75N, in the N-terminal domain indicate that this domain is involved in start codon discrimination, initiator tRNA selection, and inhibition of leaderless mRNA translation [Maar08].

Together with IF-1 and CspA, IF-3 plays a role in translational bias during cold acclimation [Giuliodori04, Giuliodori07]. infC transcription and IF-3 synthesis increases during cold shock, and IF-3 increases the rate of initiator tRNA binding to ribosomes programmed with cold shock mRNAs [Giuliodori07].

Overexpression of IF-3 decreases the efficiency of translation re-initiation for the second open reading frame in translationally coupled polycistronic mRNA [Yoo08].

Reviews: [Boelens02, Laursen05, Seshadri06]

Gene Citations: [Fayat83, Wertheimer88, Lesage90, Springer86]

Locations: cytosol, membrane

Map Position: [1,798,120 <- 1,798,662] (38.76 centisomes)
Length: 543 bp / 180 aa

Molecular Weight of Polypeptide: 20.564 kD (from nucleotide sequence), 21 kD (experimental) [Sabol70 ]

Unification Links: ASAP:ABE-0005734 , CGSC:596 , DIP:DIP-36176N , DisProt:DP00197 , EchoBASE:EB0501 , EcoGene:EG10506 , EcoliWiki:b1718 , Mint:MINT-1221578 , ModBase:P0A707 , OU-Microarray:b1718 , PortEco:infC , PR:PRO_000023014 , Pride:P0A707 , Protein Model Portal:P0A707 , RefSeq:NP_416233 , RegulonDB:EG10506 , SMR:P0A707 , String:511145.b1718 , Swiss-Model:P0A707 , UniProt:P0A707

Relationship Links: InterPro:IN-FAMILY:IPR001288 , InterPro:IN-FAMILY:IPR019813 , InterPro:IN-FAMILY:IPR019814 , InterPro:IN-FAMILY:IPR019815 , Panther:IN-FAMILY:PTHR10938 , PDB:Structure:2IFE , Pfam:IN-FAMILY:PF00707 , Pfam:IN-FAMILY:PF05198 , Prosite:IN-FAMILY:PS00938

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009409 - response to cold Inferred from experiment [Giuliodori04]
GO:0032790 - ribosome disassembly Inferred from experiment [Singh08c]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11]
GO:0006413 - translational initiation Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0003743 - translation initiation factor activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Sabol70]
GO:0005515 - protein binding Inferred from experiment [Lasserre06, Butland05]
GO:0043022 - ribosome binding Inferred from experiment [Dallas01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: information transfer protein related translation

Essentiality data for infC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Last-Curated ? 19-Mar-2009 by Keseler I , SRI International

Sequence Features

Feature Class Location Citations Comment
Methylation-Modification 1
UniProt: N-methylmethionine; in Translation initiation factor IF-3; alternate;
Cleavage-of-Initial-Methionine 1
UniProt: Removed; alternate;
Chain 2 -> 180
UniProt: Translation initiation factor IF-3, N- terminally processed;
Chain 7 -> 180
UniProt: Translation initiation factor IF-3S;
Sequence-Conflict 22
[Brauer77, UniProt10a]
Alternate sequence: Q → E; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 34 -> 36
[Brauer77, UniProt10a]
Alternate sequence: LGI → IGMV; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 47
[Brauer77, UniProt10a]
Alternate sequence: E → Q; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 52
[Brauer77, UniProt10a]
Alternate sequence: D → N; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 61
[Brauer77, UniProt10a]
Alternate sequence: E → Q; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 87
[Brauer77, UniProt10a]
Alternate sequence: K → E; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 90
[Brauer77, UniProt10a]
Alternate sequence: V → K; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 103
[Brauer77, UniProt10a]
Alternate sequence: D → N; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 105
[Brauer77, UniProt10a]
Alternate sequence: G → N; UniProt: (in Ref. 1; AA sequence);
Mutagenesis-Variant 107
[De92b, UniProt11]
Alternate sequence: Y → L; UniProt: Reduced ribosome binding.
Alternate sequence: Y → F; UniProt: Reduced ribosome binding.
Amino-Acid-Site 107
UniProt: Important for 30S binding; Sequence Annotation Type: site;
Mutagenesis-Variant 110
[De92b, UniProt11]
Alternate sequence: K → L; UniProt: Reduced ribosome binding.
Alternate sequence: K → R; UniProt: Reduced ribosome binding.
Amino-Acid-Site 110
UniProt: Important for 30S binding; Sequence Annotation Type: site;
Sequence-Conflict 161
[Miller86a, UniProt10a]
Alternate sequence: F → S; UniProt: (in Ref. 3; AAA51467);
Sequence-Conflict 178
[Brauer77, UniProt10a]
Alternate sequence: K → Q; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 180
[Brauer77, UniProt10a]
Alternate sequence: Q → missing; UniProt: (in Ref. 1; AA sequence);

Gene Local Context (not to scale): ?

Transcription Units:


10/20/97 Gene b1718 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10506; confirmed by SwissProt match.


Antoun06: Antoun A, Pavlov MY, Lovmar M, Ehrenberg M (2006). "How initiation factors tune the rate of initiation of protein synthesis in bacteria." EMBO J 25(11);2539-50. PMID: 16724118

Antoun06a: Antoun A, Pavlov MY, Lovmar M, Ehrenberg M (2006). "How initiation factors maximize the accuracy of tRNA selection in initiation of bacterial protein synthesis." Mol Cell 23(2);183-93. PMID: 16857585

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Boelens02: Boelens R, Gualerzi CO (2002). "Structure and function of bacterial initiation factors." Curr Protein Pept Sci 3(1);107-19. PMID: 12370015

Brauer77: Brauer D, Wittmann-Liebold B (1977). "The primary structure of the initiation factor IF-3 from Escherichia coli." FEBS Lett 79(2);269-75. PMID: 330233

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

Butler86: Butler JS, Springer M, Dondon J, Graffe M, Grunberg-Manago M (1986). "Escherichia coli protein synthesis initiation factor IF3 controls its own gene expression at the translational level in vivo." J Mol Biol 192(4);767-80. PMID: 2438418

Butler87: Butler JS, Springer M, Grunberg-Manago M (1987). "AUU-to-AUG mutation in the initiator codon of the translation initiation factor IF3 abolishes translational autocontrol of its own gene (infC) in vivo." Proc Natl Acad Sci U S A 84(12);4022-5. PMID: 2954162

Dallas01: Dallas A, Noller HF (2001). "Interaction of translation initiation factor 3 with the 30S ribosomal subunit." Mol Cell 8(4);855-64. PMID: 11684020

De92b: De Bellis D, Liveris D, Goss D, Ringquist S, Schwartz I (1992). "Structure-function analysis of Escherichia coli translation initiation factor IF3: tyrosine 107 and lysine 110 are required for ribosome binding." Biochemistry 31(48);11984-90. PMID: 1457399

deCock99: de Cock E, Springer M, Dardel F (1999). "The interdomain linker of Escherichia coli initiation factor IF3: a possible trigger of translation initiation specificity." Mol Microbiol 32(1);193-202. PMID: 10216872

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

Fabbretti07: Fabbretti A, Pon CL, Hennelly SP, Hill WE, Lodmell JS, Gualerzi CO (2007). "The real-time path of translation factor IF3 onto and off the ribosome." Mol Cell 25(2);285-96. PMID: 17244535

Fayat83: Fayat G, Mayaux JF, Sacerdot C, Fromant M, Springer M, Grunberg-Manago M, Blanquet S (1983). "Escherichia coli phenylalanyl-tRNA synthetase operon region. Evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20." J Mol Biol 171(3);239-61. PMID: 6317865

Fortier94: Fortier PL, Schmitter JM, Garcia C, Dardel F (1994). "The N-terminal half of initiation factor IF3 is folded as a stable independent domain." Biochimie 76(5);376-83. PMID: 7849101

Garcia95: Garcia C, Fortier PL, Blanquet S, Lallemand JY, Dardel F (1995). "1H and 15N resonance assignments and structure of the N-terminal domain of Escherichia coli initiation factor 3." Eur J Biochem 228(2);395-402. PMID: 7705354

Garcia95a: Garcia C, Fortier PL, Blanquet S, Lallemand JY, Dardel F (1995). "Solution structure of the ribosome-binding domain of E. coli translation initiation factor IF3. Homology with the U1A protein of the eukaryotic spliceosome." J Mol Biol 254(2);247-59. PMID: 7490747

Giuliodori04: Giuliodori AM, Brandi A, Gualerzi CO, Pon CL (2004). "Preferential translation of cold-shock mRNAs during cold adaptation." RNA 10(2);265-76. PMID: 14730025

Giuliodori07: Giuliodori AM, Brandi A, Giangrossi M, Gualerzi CO, Pon CL (2007). "Cold-stress-induced de novo expression of infC and role of IF3 in cold-shock translational bias." RNA 13(8);1355-65. PMID: 17592046

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

Hirokawa05: Hirokawa G, Nijman RM, Raj VS, Kaji H, Igarashi K, Kaji A (2005). "The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits." RNA 11(8);1317-28. PMID: 16043510

Hua98: Hua Y, Raleigh DP (1998). "On the global architecture of initiation factor IF3: a comparative study of the linker regions from the Escherichia coli protein and the Bacillus stearothermophilus protein." J Mol Biol 278(4);871-8. PMID: 9614948

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

Karimi99: Karimi R, Pavlov MY, Buckingham RH, Ehrenberg M (1999). "Novel roles for classical factors at the interface between translation termination and initiation." Mol Cell 3(5);601-9. PMID: 10360176

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

Laursen05: Laursen BS, Sorensen HP, Mortensen KK, Sperling-Petersen HU (2005). "Initiation of protein synthesis in bacteria." Microbiol Mol Biol Rev 69(1);101-23. PMID: 15755955

Lesage90: Lesage P, Truong HN, Graffe M, Dondon J, Springer M (1990). "Translated translational operator in Escherichia coli. Auto-regulation in the infC-rpmI-rplT operon." J Mol Biol 213(3);465-75. PMID: 2191140

Maar08: Maar D, Liveris D, Sussman JK, Ringquist S, Moll I, Heredia N, Kil A, Blasi U, Schwartz I, Simons RW (2008). "A single mutation in the IF3 N-terminal domain perturbs the fidelity of translation initiation at three levels." J Mol Biol 383(5);937-44. PMID: 18805426

Meinnel99: Meinnel T, Sacerdot C, Graffe M, Blanquet S, Springer M (1999). "Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules." J Mol Biol 290(4);825-37. PMID: 10398584

Miller86a: Miller H.I. (1986). Data submission to EMBL/GenBank/DDBJ databases on 1986-11.

Moreau97: Moreau M, de Cock E, Fortier PL, Garcia C, Albaret C, Blanquet S, Lallemand JY, Dardel F (1997). "Heteronuclear NMR studies of E. coli translation initiation factor IF3. Evidence that the inter-domain region is disordered in solution." J Mol Biol 266(1);15-22. PMID: 9054966

OConnor01a: O'Connor M, Gregory ST, Rajbhandary UL, Dahlberg AE (2001). "Altered discrimination of start codons and initiator tRNAs by mutant initiation factor 3." RNA 7(7);969-78. PMID: 11453069

Peske05: Peske F, Rodnina MV, Wintermeyer W (2005). "Sequence of steps in ribosome recycling as defined by kinetic analysis." Mol Cell 18(4);403-12. PMID: 15893724

Petrelli01: Petrelli D, LaTeana A, Garofalo C, Spurio R, Pon CL, Gualerzi CO (2001). "Translation initiation factor IF3: two domains, five functions, one mechanism?." EMBO J 20(16);4560-9. PMID: 11500382

Qin07: Qin D, Abdi NM, Fredrick K (2007). "Characterization of 16S rRNA mutations that decrease the fidelity of translation initiation." RNA 13(12);2348-55. PMID: 17942743

Qin09: Qin D, Fredrick K (2009). "Control of translation initiation involves a factor-induced rearrangement of helix 44 of 16S ribosomal RNA." Mol Microbiol 71(5);1239-49. PMID: 19154330

Risuleo76: Risuleo G, Gualerzi C, Pon C (1976). "Specificity and properties of the destabilization, induced by initiation factor IF-3, of ternary complexes of the 30-S ribosomal subunit, aminoacyl-tRNA and polynucleotides." Eur J Biochem 67(2);603-13. PMID: 9282

Sabol70: Sabol S, Sillero MA, Iwasaki K, Ochoa S (1970). "Purification and properties of initiation factor F3." Nature 228(5278);1269-73. PMID: 4922687

Sacerdot82: Sacerdot C, Fayat G, Dessen P, Springer M, Plumbridge JA, Grunberg-Manago M, Blanquet S (1982). "Sequence of a 1.26-kb DNA fragment containing the structural gene for E.coli initiation factor IF3: presence of an AUU initiator codon." EMBO J 1(3);311-5. PMID: 6325158

Sacerdot96: Sacerdot C, Chiaruttini C, Engst K, Graffe M, Milet M, Mathy N, Dondon J, Springer M (1996). "The role of the AUU initiation codon in the negative feedback regulation of the gene for translation initiation factor IF3 in Escherichia coli." Mol Microbiol 21(2);331-46. PMID: 8858588

Saraiya08: Saraiya AA, Lamichhane TN, Chow CS, SantaLucia J, Cunningham PR (2008). "Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA." J Mol Biol 376(3);645-57. PMID: 18177894

Seshadri06: Seshadri A, Varshney U (2006). "Mechanism of recycling of post-termination ribosomal complexes in eubacteria: a new role of initiation factor 3." J Biosci 31(2);281-9. PMID: 16809861

Sette99: Sette M, Spurio R, van Tilborg P, Gualerzi CO, Boelens R (1999). "Identification of the ribosome binding sites of translation initiation factor IF3 by multidimensional heteronuclear NMR spectroscopy." RNA 5(1);82-92. PMID: 9917068

Singh05c: Singh NS, Das G, Seshadri A, Sangeetha R, Varshney U (2005). "Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs in Escherichia coli." Nucleic Acids Res 33(17);5591-601. PMID: 16199751

Singh08c: Singh NS, Ahmad R, Sangeetha R, Varshney U (2008). "Recycling of ribosomal complexes stalled at the step of elongation in Escherichia coli." J Mol Biol 380(3);451-64. PMID: 18565340

Springer86: Springer M, Graffe M, Butler JS, Grunberg-Manago M (1986). "Genetic definition of the translational operator of the threonine-tRNA ligase gene in Escherichia coli." Proc Natl Acad Sci U S A 83(12);4384-8. PMID: 3086882

Subramanian68: Subramanian AR, Ron EZ, Davis BD (1968). "A factor required for ribosome dissociation in Escherichia coli." Proc Natl Acad Sci U S A 61(2);761-7. PMID: 4879403

Subramanian70: Subramanian AR, Davis BD (1970). "Activity of initiation factor F3 in dissociating Escherichia coli ribosomes." Nature 228(5278);1273-5. PMID: 4922688

Sussman96: Sussman JK, Simons EL, Simons RW (1996). "Escherichia coli translation initiation factor 3 discriminates the initiation codon in vivo." Mol Microbiol 21(2);347-60. PMID: 8858589

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

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

vanderHofstad78: van der Hofstad GA, Buitenhek A, Bosch L, Voorma HO (1978). "Initiation factor IF-3 and the binary complex between initiation factor IF-2 and formylmethionyl-tRNA are mutually exclusive on the 30-S ribosomal subunit." Eur J Biochem 89(1);213-20. PMID: 359327

Wertheimer88: Wertheimer SJ, Klotsky RA, Schwartz I (1988). "Transcriptional patterns for the thrS-infC-rplT operon of Escherichia coli." Gene 63(2);309-20. PMID: 2838394

Yoo08: Yoo JH, RajBhandary UL (2008). "Requirements for translation re-initiation in Escherichia coli: roles of initiator tRNA and initiation factors IF2 and IF3." Mol Microbiol 67(5);1012-26. PMID: 18221266

Other References Related to Gene Regulation

Lemke11: Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL (2011). "Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA." Proc Natl Acad Sci U S A 108(14);5712-7. PMID: 21402902

Liveris91: Liveris D, Klotsky RA, Schwartz I (1991). "Growth rate regulation of translation initiation factor IF3 biosynthesis in Escherichia coli." J Bacteriol 173(12);3888-93. PMID: 2050639

Mayaux83: Mayaux JF, Fayat G, Fromant M, Springer M, Grunberg-Manago M, Blanquet S (1983). "Structural and transcriptional evidence for related thrS and infC expression." Proc Natl Acad Sci U S A 80(20);6152-6. PMID: 6353409

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

Pramanik86: Pramanik A, Wertheimer SJ, Schwartz JJ, Schwartz I (1986). "Expression of Escherichia coli infC: identification of a promoter in an upstream thrS coding sequence." J Bacteriol 168(2);746-51. PMID: 3536858

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 28, 2014, biocyc14.