RegulonDB RegulonDB 10.7: Gene Form
   

ydcR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydcR ydcS hicB Nac ydcSp1 ydcSp1 TSS_1815 TSS_1815 ydcSp7 ydcSp7 ydcSp9 ydcSp9 ydcRp ydcRp

Gene      
Name: ydcR    Texpresso search in the literature
Synonym(s): ECK1433, G6750, b1439
Genome position(nucleotides): 1510003 --> 1511409 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.39
External database links:  
ASAP:
ABE-0004800
ECHOBASE:
EB3524
OU-MICROARRAY:
b1439
PORTECO:
ydcR
REGULONDB:
b1439
STRING:
511145.b1439
M3D: ydcR
COLOMBOS: ydcR
PortEco: b1439


Product      
Name: fused putative DNA-binding transcriptional regulator/putative aminotransferase YdcR
Synonym(s): YdcR
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 52.793
Isoelectric point: 8.96
Motif(s):
 
Type Positions Sequence
1 -> 69 MKKYQQLAEQLREQIASGIWQPGDRLPSLRDQVALSGMSFMTVSHAYQLLESQGYIIARPQSGYYVAPQ
3 -> 66 KYQQLAEQLREQIASGIWQPGDRLPSLRDQVALSGMSFMTVSHAYQLLESQGYIIARPQSGYYV
145 -> 445 PGNAELRQAIARRYALQGITISPDEIVITAGALEALNLSLQAVTEPGDWVIVENPCFYGALQALERLRLKALSVATDVKEGIDLQALELALQEYPVKACWLMTNSQNPLGFTLTPQKKAQLVALLNQYNVTLIEDDVYSELYFGREKPLPAKAWDRHDGVLHCSSFSKCLVPGFRIGWVAAGKHARKIQRLQLMSTLSTSSPMQLALVDYLSTRRYDAHLRRLRRQLAERKQRAWQALLRYLPAEVKIHHNDSGYFLWLELPEPLDAGELSLAALTHHISIAPGKMFSTGENWSRFFRFNT

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0016740 - transferase activity
GO:0008483 - transaminase activity
GO:0003700 - DNA-binding transcription factor activity
GO:0030170 - pyridoxal phosphate binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0009058 - biosynthetic process
GO:1901605 - alpha-amino acid metabolic process
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
[IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Nakata K., et al., 2010
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
External database links:  
DIP:
DIP-28077N
ECOCYC:
G6750-MONOMER
ECOLIWIKI:
b1439
INTERPRO:
IPR015422
INTERPRO:
IPR036388
INTERPRO:
IPR036390
INTERPRO:
IPR015421
INTERPRO:
IPR004839
INTERPRO:
IPR000524
INTERPRO:
IPR015424
MODBASE:
P77730
PFAM:
PF00392
PFAM:
PF00155
PRIDE:
P77730
PROSITE:
PS50949
PROTEINMODELPORTAL:
P77730
REFSEQ:
NP_415956
SMART:
SM00345
SMR:
P77730
UNIPROT:
P77730


Operon      
Name: ydcR         
Operon arrangement:
Transcription unit        Promoter
 


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter ydcSp9 1511453 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ydcSp7 1511515 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_1815 1511596 forward nd [RS-EPT-CBR] [5]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Nakata K., Koh MM., Tsuchido T., Matsumura Y., 2010, All genomic mutations in the antimicrobial surfactant-resistant mutant, Escherichia coli OW66, are involved in cell resistance to surfactant., Appl Microbiol Biotechnol 87(5):1895-905

 [2] 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

 [3] 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

 [4] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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