Escherichia coli K-12 substr. MG1655 Polypeptide: predicted signal transduction protein (SH3 domain)

Gene: ygiM Accession Numbers: EG12434 (EcoCyc), b3055, ECK3045

Synonyms: ecfG, htrG

Regulation Summary Diagram: ?

Regulation summary diagram for ygiM

Proteomic analysis of membrane preparations suggests that YgiM forms a homo-oligomeric complex [Maddalo11]. The C-terminus of YgiM is located in the cytoplasm [Maddalo11].

Transcription of ygiM is regulated by RpoE (σE) [Dartigalongue01].

EcfG: "extracytoplasmic function G" [Dartigalongue01]

Gene Citations: [Rhodius05]

Locations: cytosol, inner membrane

Map Position: [3,199,229 -> 3,199,849] (68.95 centisomes, 248°)
Length: 621 bp / 206 aa

Molecular Weight of Polypeptide: 23.076 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010028 , EchoBASE:EB2330 , EcoGene:EG12434 , EcoliWiki:b3055 , OU-Microarray:b3055 , PortEco:htrG , Pride:P0ADT8 , Protein Model Portal:P0ADT8 , RefSeq:NP_417527 , RegulonDB:EG12434 , SMR:P0ADT8 , String:511145.b3055 , UniProt:P0ADT8

Relationship Links: InterPro:IN-FAMILY:IPR003646 , InterPro:IN-FAMILY:IPR016476 , Pfam:IN-FAMILY:PF08239 , Smart:IN-FAMILY:SM00287

Genetic Regulation Schematic: ?

Genetic regulation schematic for ygiM

GO Terms:

Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08, Zhang07]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Maddalo11]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

Gene Class: ORFs

Essentiality data for ygiM 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]

Curated 06-Apr-2010 by Keseler I , SRI International
Last-Curated ? 08-Feb-2011 by Mackie A , Macquarie University

Sequence Features

Protein sequence of predicted signal transduction protein (SH3 domain) with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 22
UniProt: Non-Experimental Qualifier: potential;
Chain 23 -> 206
UniProt: Uncharacterized protein ygiM;
Transmembrane-Region 169 -> 191
UniProt: Helical;; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3055 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12434; confirmed by SwissProt match.


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

Dartigalongue01: Dartigalongue C, Missiakas D, Raina S (2001). "Characterization of the Escherichia coli sigma E regulon." J Biol Chem 276(24);20866-75. PMID: 11274153

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

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

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

Maddalo11: Maddalo G, Stenberg-Bruzell F, Gotzke H, Toddo S, Bjorkholm P, Eriksson H, Chovanec P, Genevaux P, Lehtio J, Ilag LL, Daley DO (2011). "Systematic analysis of native membrane protein complexes in Escherichia coli." J Proteome Res 10(4);1848-59. PMID: 21210718

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047

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 the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Gogol11: Gogol EB, Rhodius VA, Papenfort K, Vogel J, Gross CA (2011). "Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon." Proc Natl Acad Sci U S A 108(31);12875-80. PMID: 21768388

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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 19.0 on Tue Oct 13, 2015, biocyc13.