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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
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Escherichia coli K-12 substr. MG1655 Polypeptide: predicted oxidoreductase, Fe-S subunit



Gene: ygfK Accession Numbers: G7497 (EcoCyc), b2878, ECK2874

Regulation Summary Diagram: ?

Summary:
Preliminary biochemical characterization has shown that YgfK is an iron-sulfur flavoprotein with NADPH:O2 oxidoreductase activity [Sevcenco11].

Based on sequence similarity, YgfK was predicted to be a dihydrothymine dehydrogenase [Reed03].

A transposon insertion mutant in ygfK was unable to reduce selenate to selenium [Bebien02].

Locations: cytosol

Map Position: [3,014,082 -> 3,017,180] (64.96 centisomes)
Length: 3099 bp / 1032 aa

Molecular Weight of Polypeptide: 115.58 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009450 , DIP:DIP-28091N , EchoBASE:EB2873 , EcoGene:EG13061 , EcoliWiki:b2878 , ModBase:Q46811 , OU-Microarray:b2878 , PortEco:ygfK , Pride:Q46811 , Protein Model Portal:Q46811 , RefSeq:NP_417354 , RegulonDB:G7497 , SMR:Q46811 , String:511145.b2878 , UniProt:Q46811

Relationship Links: InterPro:IN-FAMILY:IPR009051 , InterPro:IN-FAMILY:IPR012285 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR017701 , InterPro:IN-FAMILY:IPR017896 , InterPro:IN-FAMILY:IPR017900 , InterPro:IN-FAMILY:IPR023753 , InterPro:IN-FAMILY:IPR028261 , Pfam:IN-FAMILY:PF07992 , Pfam:IN-FAMILY:PF13187 , Pfam:IN-FAMILY:PF14691 , Prosite:IN-FAMILY:PS00198 , Prosite:IN-FAMILY:PS51379

In Paralogous Gene Group: 487 (3 members)

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [GOA01]
Molecular Function: GO:0005506 - iron ion binding Inferred from experiment [Sevcenco11]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Author statement Inferred by computational analysis [GOA01, Sevcenco11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

Gene Class: UNCLASSIFIED

Essentiality data for ygfK 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 ? 02-Feb-2012 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 901
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 905
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 908
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 912
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: potential;
Conserved-Region 928 -> 958
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type;
Metal-Binding-Site 938
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 941
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 944
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 948
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Bebien02: Bebien M, Kirsch J, Mejean V, Vermeglio A (2002). "Involvement of a putative molybdenum enzyme in the reduction of selenate by Escherichia coli." Microbiology 148(Pt 12);3865-72. PMID: 12480890

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

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

GOA01: 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

Reed03: Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)." Genome Biol 4(9);R54. PMID: 12952533

Sevcenco11: Sevcenco AM, Pinkse MW, Wolterbeek HT, Verhaert PD, Hagen WR, Hagedoorn PL (2011). "Exploring the microbial metalloproteome using MIRAGE." Metallomics 3(12);1324-30. PMID: 22094925

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.

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

Other References Related to Gene Regulation

Barrios99: Barrios H, Valderrama B, Morett E (1999). "Compilation and analysis of sigma(54)-dependent promoter sequences." Nucleic Acids Res 27(22);4305-13. PMID: 10536136

Zhao10a: Zhao K, Liu M, Burgess RR (2010). "Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis." Nucleic Acids Res 38(4);1273-83. PMID: 19969540


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 Sun Dec 21, 2014, BIOCYC13B.