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

Gene: ygfM Accession Numbers: G7499 (EcoCyc), b2880, ECK2876

Regulation Summary Diagram

Regulation summary diagram for ygfM

Component of: predicted xanthine dehydrogenase (summary available)

YgfM is consistently found in the same location as XdhD in MIRAGE experiments. Thus the two proteins may form a complex, as has been proposed previously [Sevcenco11].

Map Position: [3,018,562 -> 3,019,341] (65.06 centisomes, 234°)
Length: 780 bp / 259 aa

Molecular Weight of Polypeptide: 28.65 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009456, DIP:DIP-48265N, EchoBASE:EB2875, EcoGene:EG13063, EcoliWiki:b2880, ModBase:P64557, OU-Microarray:b2880, PortEco:ygfM, Protein Model Portal:P64557, RefSeq:NP_417356, RegulonDB:G7499, SMR:P64557, String:511145.b2880, UniProt:P64557

Relationship Links: InterPro:IN-FAMILY:IPR002346, InterPro:IN-FAMILY:IPR005107, InterPro:IN-FAMILY:IPR016166, InterPro:IN-FAMILY:IPR016169, InterPro:IN-FAMILY:IPR017698, Pfam:IN-FAMILY:PF00941, Pfam:IN-FAMILY:PF03450, Prosite:IN-FAMILY:PS51387, Smart:IN-FAMILY:SM01092

Gene-Reaction Schematic

Gene-Reaction Schematic

GO Terms:
Biological Process:
Inferred by computational analysisGO:0055114 - oxidation-reduction process [GOA01]
Molecular Function:
Inferred by computational analysisGO:0016491 - oxidoreductase activity [GOA01]
Inferred by computational analysisGO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [GOA01]
Inferred by computational analysisGO:0050660 - flavin adenine dinucleotide binding [GOA01]


Essentiality data for ygfM knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Last-Curated 02-Feb-2012 by Keseler I, SRI International

Subunit of: predicted xanthine dehydrogenase

Subunit composition of predicted xanthine dehydrogenase = [XdhD][YgfM]
         fused predicted xanthine/hypoxanthine oxidase: molybdopterin-binding subunit and Fe-S binding subunit = XdhD (summary available)
         predicted oxidoreductase = YgfM (summary available)

XdhD and YgfM are predicted to form a complex with xanthine dehydrogenase activity.

Sequence Features

Protein sequence of predicted oxidoreductase with features indicated

Feature Class Location Citations Comment
Conserved-Region 1 -> 159
Inferred by computational analysis[UniProt15]
UniProt: FAD-binding PCMH-type.
Pfam PF00941 4 -> 154
Inferred by computational analysis[Finn14]
FAD_binding_5 : FAD binding domain in molybdopterin dehydrogenase
Pfam PF03450 167 -> 248
Inferred by computational analysis[Finn14]
CO_deh_flav_C : CO dehydrogenase flavoprotein C-terminal domain

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

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 Pathway Tools version 19.5 (software by SRI International) on Sat Nov 28, 2015, biocyc11.