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

Gene: yhjY Accession Numbers: EG12269 (EcoCyc), b3548, ECK3535

Regulation Summary Diagram: ?

Regulation summary diagram for yhjY

YhjY is predicted to be an outer membrane protein [Casadio03].

yhjY is part of a functional interaction network that includes proteins involved in bacterial adhesion and biofilm formation. A yhjY mutant shows increased biofilm formation [Vlasblom14].

A yhjY null mutant was reported to produce less hydrogen than wild type under fermentation conditions [Mohd12]. No attempt to complement the mutant phenotype with wild-type yhjY is reported.

Citations: [Marani06]

Locations: extracellular space, membrane

Map Position: [3,710,259 <- 3,710,957] (79.97 centisomes, 288°)
Length: 699 bp / 232 aa

Molecular Weight of Polypeptide: 25.951 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011589 , EchoBASE:EB2178 , EcoGene:EG12269 , EcoliWiki:b3548 , OU-Microarray:b3548 , PortEco:yhjY , Protein Model Portal:P37663 , RefSeq:NP_418004 , RegulonDB:EG12269 , String:511145.b3548 , UniProt:P37663

Relationship Links: InterPro:IN-FAMILY:IPR005546 , InterPro:IN-FAMILY:IPR006315 , InterPro:IN-FAMILY:IPR016955 , Pfam:IN-FAMILY:PF03797 , Prosite:IN-FAMILY:PS51208

GO Terms:

Cellular Component: GO:0005576 - extracellular region Inferred by computational analysis [DiazMejia09]
GO:0019867 - outer membrane Inferred by computational analysis [GOA01a]

Gene Class: ORFs Conserved-ORFs

Essentiality data for yhjY 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 21-Feb-2006 by Shearer A , SRI International
Last-Curated ? 27-Oct-2014 by Keseler I , SRI International

Sequence Features

Feature Class Location Citations Comment
Conserved-Region 1 -> 232
UniProt: Autotransporter;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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 ].
10/20/97 Gene b3548 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12269; 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

Casadio03: Casadio R, Fariselli P, Finocchiaro G, Martelli PL (2003). "Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria." Protein Sci 12(6);1158-68. PMID: 12761386

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

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

Marani06: Marani P, Wagner S, Baars L, Genevaux P, de Gier JW, Nilsson I, Casadio R, von Heijne G (2006). "New Escherichia coli outer membrane proteins identified through prediction and experimental verification." Protein Sci 15(4);884-9. PMID: 16522795

Mohd12: Mohd Yusoff MZ, Maeda T, Sanchez-Torres V, Ogawa HI, Shirai Y, Hassan MA, Wood TK (2012). "Uncharacterized Escherichia coli proteins YdjA and YhjY are related to biohydrogen production." Int. J. Hydrogen Energy 37;17778-87.

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

Vlasblom14: Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Kumar A, Leung E, Rizzolo K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry WA, Emili A, Morris Q, Bader G, Babu M (2014). "Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli." Bioinformatics. PMID: 25316676

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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 6, 2015, biocyc14.