RegulonDB RegulonDB 10.10: Gene Form
   

rhsD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rhsD ybbP ybbC ybbA TSS_665 TSS_665 rhsDp8 rhsDp8

Gene      
Name: rhsD    Texpresso search in the literature
Synonym(s): ECK0491, EG10849, b0497
Genome position(nucleotides): 523261 --> 527541 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 60.13
External database links:  
ASAP:
 ABE-0001724
ECHOBASE:
 EB0842
ECOLIHUB:
 rhsD
MIM:
 616736
OU-MICROARRAY:
 b0497
STRING:
 511145.b0497
COLOMBOS: rhsD


Product      
Name: protein RhsD
Synonym(s): RhsD
Sequence: Get amino acid sequence Fasta Format
Cellular location: extracellular space,outer membrane
Molecular weight: 159.724
Isoelectric point: 5.715
Motif(s):
 
Type Positions Sequence
539 -> 572 RYGQLLAFTDCSGYQTRYEYDRFGQMTAVHREEG
593 -> 613 GRETRYEYNAAGDLTAVITPD
716 -> 738 GEPAEQWQYDGHGWLTDISHLSE
833 -> 861 GSMAGSNAAYELTSTYTPAGQLQSQHLNS
996 -> 1030 EPLVESRYLYDPLGRRMAKRVWRRERDLTGWMSLS

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0005576 - extracellular region
biological_process GO:0010438 - cellular response to sulfur starvation
Note(s): Note(s): ...[more].
Evidence: [IEP] Inferred from expression pattern
Reference(s): [1] Lin RJ., et al., 1984
[2] van der Ploeg JR., et al., 1996
External database links:  
DIP:
 DIP-10702N
ECOCYC:
 EG10849-MONOMER
ECOLIWIKI:
 b0497
INTERPRO:
 IPR031325
INTERPRO:
 IPR025479
INTERPRO:
 IPR022385
INTERPRO:
 IPR006530
INTERPRO:
 IPR001826
PFAM:
 PF03527
PFAM:
 PF05593
PFAM:
 PF14220
PRIDE:
 P16919
PRINTS:
 PR00394
PRODB:
 PRO_000023746
REFSEQ:
 NP_415030
SMR:
 P16919
UNIPROT:
 P16919


Operon      
Name: rhsD-ybbC-ylbH-ybbD         
Operon arrangement:
Transcription unit        Promoter
rhsD-ybbC-ylbH-ybbD


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 rhsDp8 523066 forward nd [ICWHO] [3]
  promoter TSS_665 526934 forward nd [RS-EPT-CBR] [4]


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] Lin RJ., Capage M., Hill CW., 1984, A repetitive DNA sequence, rhs, responsible for duplications within the Escherichia coli K-12 chromosome., J Mol Biol 177(1):1-18

 [2] van der Ploeg JR., Weiss MA., Saller E., Nashimoto H., Saito N., Kertesz MA., Leisinger T., 1996, Identification of sulfate starvation-regulated genes in Escherichia coli: a gene cluster involved in the utilization of taurine as a sulfur source., J Bacteriol 178(18):5438-46

 [3] 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

 [4] 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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