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Escherichia coli K-12 substr. MG1655 Polypeptide: conserved inner membrane protein



Gene: ygdD Accession Numbers: EG11793 (EcoCyc), b2807, ECK2802

Regulation Summary Diagram: ?

Summary:
YgdD is an inner membrane protein with four predicted transmembrane domains. The C terminus is located in the cytoplasm [Daley05].

Citations: [ParadisBleau14]

Locations: inner membrane

Map Position: [2,939,258 <- 2,939,653] (63.35 centisomes)
Length: 396 bp / 131 aa

Molecular Weight of Polypeptide: 14.333 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009199 , EchoBASE:EB1741 , EcoGene:EG11793 , EcoliWiki:b2807 , OU-Microarray:b2807 , PortEco:ygdD , Protein Model Portal:P0ADR2 , RefSeq:NP_417287 , RegulonDB:EG11793 , String:511145.b2807 , UniProt:P0ADR2

Relationship Links: InterPro:IN-FAMILY:IPR006696 , Pfam:IN-FAMILY:PF04241

GO Terms:

Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

Gene Class: ORFs Conserved-Hypothetical-ORFs

Essentiality data for ygdD 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 ? 10-Apr-2008 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 5 -> 25
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 34
[Wilson94, UniProt10a]
Alternate sequence: A → G; UniProt: (in Ref. 1; AAC13743);
Transmembrane-Region 65 -> 85
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 98 -> 118
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
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 ].
10/20/97 Gene b2807 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11793; confirmed by SwissProt match.


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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

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

ParadisBleau14: Paradis-Bleau C, Kritikos G, Orlova K, Typas A, Bernhardt TG (2014). "A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism." PLoS Genet 10(1);e1004056. PMID: 24391520

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Wilson94: Wilson RL, Stauffer GV (1994). "DNA sequence and characterization of GcvA, a LysR family regulatory protein for the Escherichia coli glycine cleavage enzyme system." J Bacteriol 176(10);2862-8. PMID: 8188587


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.