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Escherichia coli K-12 substr. MG1655 Polypeptide: predicted phosphatase, inner membrane protein



Gene: ynbD Accession Numbers: G6730 (EcoCyc), b1411, ECK1404

Regulation Summary Diagram: ?

Summary:
No information about this protein was found by a literature search conducted on October 4, 2006.

Locations: inner membrane

Map Position: [1,478,933 -> 1,480,225] (31.88 centisomes)
Length: 1293 bp / 430 aa

Molecular Weight of Polypeptide: 49.563 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004710 , DIP:DIP-12745N , EchoBASE:EB3514 , EcoGene:EG13751 , EcoliWiki:b1411 , Mint:MINT-1248050 , ModBase:P76093 , OU-Microarray:b1411 , PortEco:ynbD , Protein Model Portal:P76093 , RefSeq:NP_415929 , RegulonDB:G6730 , SMR:P76093 , String:511145.b1411 , UniProt:P76093

Relationship Links: InterPro:IN-FAMILY:IPR000326 , InterPro:IN-FAMILY:IPR000340 , InterPro:IN-FAMILY:IPR000387 , InterPro:IN-FAMILY:IPR016130 , InterPro:IN-FAMILY:IPR020422 , InterPro:IN-FAMILY:IPR024950 , Panther:IN-FAMILY:PTHR10159 , Pfam:IN-FAMILY:PF00782 , Pfam:IN-FAMILY:PF01569 , Prosite:IN-FAMILY:PS00383 , Prosite:IN-FAMILY:PS50056 , Smart:IN-FAMILY:SM00195

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006470 - protein dephosphorylation Inferred by computational analysis [GOA01a, Gaudet10]
GO:0016311 - dephosphorylation Inferred by computational analysis [GOA01a]
GO:0035335 - peptidyl-tyrosine dephosphorylation Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0004725 - protein tyrosine phosphatase activity Inferred by computational analysis [GOA01a]
GO:0008138 - protein tyrosine/serine/threonine phosphatase activity Inferred by computational analysis [GOA01a, Gaudet10]
GO:0016791 - phosphatase activity Inferred by computational analysis [GOA01a]
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, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

Gene Class: ORFs

Essentiality data for ynbD 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 ? 04-Oct-2006 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 2 -> 22
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 46 -> 66
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 85 -> 105
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 175 -> 195
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 209 -> 229
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 230 -> 250
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 372 -> 392
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

UniProt10a: 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."

Other References Related to Gene Regulation

Salscheider14: Salscheider SL, Jahn A, Schnetz K (2014). "Transcriptional regulation by BglJ-RcsB, a pleiotropic heteromeric activator in Escherichia coli." Nucleic Acids Res 42(5);2999-3008. PMID: 24335284


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 Nov 23, 2014, BIOCYC14B.