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Escherichia coli K-12 substr. MG1655 Polypeptide: predicted flavoprotein



Gene: ygcR Accession Numbers: G7436 (EcoCyc), b2770, ECK2765

Regulation Summary Diagram: ?

Summary:
Unlike most other cellular proteins, synthesis of YgcR does not change significantly after induction of the toxin MazF. Under growth conditions causing DNA damage, most of the population of a ygcR mutant survives, phenocopying a ΔmazEF mutant [Amitai09].

fixA, fixB, ydiQ, ydiR, ygcR, and ygcQ form a subsystem based on genome context methods, and may represent a previously uncharacterized electron transfer pathway [Ferrer11].

Locations: cytosol

Map Position: [2,893,798 <- 2,894,577] (62.37 centisomes)
Length: 780 bp / 259 aa

Molecular Weight of Polypeptide: 28.72 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009079 , EchoBASE:EB2926 , EcoGene:EG13125 , EcoliWiki:b2770 , ModBase:Q46908 , OU-Microarray:b2770 , PortEco:ygcR , Pride:Q46908 , Protein Model Portal:Q46908 , RefSeq:NP_417250 , RegulonDB:G7436 , SMR:Q46908 , String:511145.b2770 , UniProt:Q46908

Relationship Links: InterPro:IN-FAMILY:IPR012255 , InterPro:IN-FAMILY:IPR014729 , InterPro:IN-FAMILY:IPR014730 , Panther:IN-FAMILY:PTHR21294 , Pfam:IN-FAMILY:PF01012 , Prosite:IN-FAMILY:PS01065 , Smart:IN-FAMILY:SM00893

In Paralogous Gene Group: 15 (2 members)

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

Gene Class: ORFs Conserved-ORFs

Essentiality data for ygcR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Last-Curated ? 04-Jun-2014 by Keseler I , SRI International


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Amitai09: Amitai S, Kolodkin-Gal I, Hananya-Meltabashi M, Sacher A, Engelberg-Kulka H (2009). "Escherichia coli MazF leads to the simultaneous selective synthesis of both "death proteins" and "survival proteins"." PLoS Genet 5(3);e1000390. PMID: 19282968

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

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

Ferrer11: Ferrer L, Shearer AG, Karp PD (2011). "Discovering novel subsystems using comparative genomics." Bioinformatics 27(18);2478-85. PMID: 21775308

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

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


Report Errors or Provide Feedback
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 Sat Dec 20, 2014, biocyc12.