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Escherichia coli K-12 substr. MG1655 Polypeptide: predicted truncated N-acetylgalactosamine-6-phosphate deacetylase



Gene: agaA Accession Numbers: EG12766 (EcoCyc), b3135, ECK3123

Synonyms: yraA

Regulation Summary Diagram: ?

Summary:
Though AgaA is predicted to be an N-acetylgalactosamine-6-phosphate deacetylase, it also appears to be nonfunctional by dint of having an amino-terminal deletion [Reizer96, Homma02].

Gene Citations: [Brinkkotter00]

Locations: cytosol

Map Position: [3,279,144 -> 3,279,647] (70.68 centisomes)
Length: 504 bp / 167 aa

Molecular Weight of Polypeptide: 17.519 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010302 , EchoBASE:EB2619 , EcoGene:EG12766 , EcoliWiki:b3135 , ModBase:P42906 , OU-Microarray:b3135 , PortEco:agaA , Protein Model Portal:P42906 , RefSeq:YP_026206 , RegulonDB:EG12766 , SMR:P42906 , String:316407.agaA , Swiss-Model:P42906 , UniProt:P42906

Relationship Links: EcoO157Cyc:Homolog:Z4489 , EcoO157Cyc:Homolog:Z4489-MONOMER , InterPro:IN-FAMILY:IPR006680 , Pfam:IN-FAMILY:PF01979

In Paralogous Gene Group: 496 (2 members)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: All-Genes Pseudo-Genes
MultiFun transport Group Translocators Phosphotransferase Systems (PEP-dependent PTS)

Essentiality data for agaA 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 ? 01-Aug-2006 by Shearer A , SRI International


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 145
[Blattner97, UniProt10a]
Alternate sequence: S → R; UniProt: (in Ref. 1; AAA57938);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3135 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12766; 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

Blattner97: Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997). "The complete genome sequence of Escherichia coli K-12." Science 277(5331);1453-74. PMID: 9278503

Brinkkotter00: Brinkkotter A, Kloss H, Alpert C, Lengeler JW (2000). "Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli." Mol Microbiol 2000;37(1);125-35. PMID: 10931310

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."

Homma02: Homma K, Fukuchi S, Kawabata T, Ota M, Nishikawa K (2002). "A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome." Gene 294(1-2);25-33. PMID: 12234664

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

Reizer96: Reizer J, Ramseier TM, Reizer A, Charbit A, Saier MH (1996). "Novel phosphotransferase genes revealed by bacterial genome sequencing: a gene cluster encoding a putative N-acetylgalactosamine metabolic pathway in Escherichia coli." Microbiology 1996;142 ( Pt 2);231-50. PMID: 8932697

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

Ray04: Ray WK, Larson TJ (2004). "Application of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in N-acetylgalactosamine metabolism in Escherichia coli K-12." Mol Microbiol 51(3);813-26. PMID: 14731281


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 Fri Dec 19, 2014, BIOCYC13B.