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Escherichia coli K-12 substr. MG1655 Polypeptide: fused predicted DNA-binding transcriptional regulator and predicted amino transferase



Gene: ydcR Accession Numbers: G6750 (EcoCyc), b1439, ECK1433

Regulation Summary Diagram: ?

Summary:
YdcR is a member of the GntR family of transcriptional regulators. This family is known to be associated with regulation of carbon metabolism [PerezRueda00]. It has a HTH motif near its N-terminus and an aminotransferase domain.

Locations: cytosol

Map Position: [1,508,027 -> 1,509,433] (32.5 centisomes)
Length: 1407 bp / 468 aa

Molecular Weight of Polypeptide: 52.793 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004800 , DIP:DIP-28077N , EchoBASE:EB3524 , EcoGene:EG13761 , EcoliWiki:b1439 , ModBase:P77730 , OU-Microarray:b1439 , PortEco:ydcR , Pride:P77730 , Protein Model Portal:P77730 , RefSeq:NP_415956 , RegulonDB:G6750 , SMR:P77730 , String:511145.b1439 , UniProt:P77730

Relationship Links: InterPro:IN-FAMILY:IPR000524 , InterPro:IN-FAMILY:IPR004839 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015424 , Pfam:IN-FAMILY:PF00155 , Pfam:IN-FAMILY:PF00392 , Prosite:IN-FAMILY:PS50949 , Smart:IN-FAMILY:SM00345

In Paralogous Gene Group: 491 (2 members)

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, PerezRueda00, PerezRueda04]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0009058 - biosynthetic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0008483 - transaminase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0030170 - pyridoxal phosphate binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level

Essentiality data for ydcR 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]

Sequence Features

Feature Class Location Citations Comment
Conserved-Region 1 -> 69
[UniProt09]
UniProt: HTH gntR-type;
N6-pyridoxal-phosphate-Lys-Modification 312
[UniProt11]
UniProt: N6-(pyridoxal phosphate)lysine; Non-Experimental Qualifier: by similarity.


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

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

GOA01: 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

PerezRueda00: Perez-Rueda E, Collado-Vides J (2000). "The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12." Nucleic Acids Res 28(8);1838-47. PMID: 10734204

PerezRueda04: Perez-Rueda E, Collado-Vides J, Segovia L (2004). "Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea." Comput Biol Chem 28(5-6);341-50. PMID: 15556475

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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 Thu Nov 27, 2014, BIOCYC13A.