RegulonDB RegulonDB 10.8: Gene Form
   

cspB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cspB cspF ynfU Cis-reg; thermoregulator cspFp8 cspFp8 TSS_1864 TSS_1864 cspFp6 cspFp6 cspBp cspBp cspFp7 cspFp7

Gene      
Name: cspB    Texpresso search in the literature
Synonym(s): ECK1551, EG12203, b1557
Genome position(nucleotides): 1641339 <-- 1641554 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
35.19
External database links:  
ASAP:
ABE-0005199
CGSC:
32231
ECHOBASE:
EB2119
OU-MICROARRAY:
b1557
PortEco:
cspB
STRING:
511145.b1557
COLOMBOS: cspB


Product      
Name: Qin prophage; cold shock-like protein CspB
Synonym(s): CspB, Qin prophage; cold shock protein; putative DNA-binding transcriptional regulator
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 7.717
Isoelectric point: 7.541
Motif(s):
 
Type Positions Sequence
7 -> 67 GLVKWFNADKGFGFISPVDGSKDVFVHFSAIQNDNYRTLFEGQKVTFSIESGAKGPAAANV
5 -> 68 MTGLVKWFNADKGFGFISPVDGSKDVFVHFSAIQNDNYRTLFEGQKVTFSIESGAKGPAAANVI

 

Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0003697 - single-stranded DNA binding
GO:0003723 - RNA binding
GO:0001072 - transcription antitermination factor activity, RNA binding
biological_process GO:0006950 - response to stress
GO:0031564 - transcription antitermination
GO:0009409 - response to cold
GO:0010468 - regulation of gene expression
GO:0060567 - negative regulation of DNA-templated transcription, termination
Note(s): Note(s): ...[more].
Evidence: [AIFS] Automated inference of function from sequence
[APPH] Assay of protein purified to homogeneity
[IMP] Inferred from mutant phenotype
Reference(s): [1] Perez-Rueda E., et al., 2004
[2] Phadtare S., et al., 1999
[3] Sharan M., et al., 2017
[4] Xia B., et al., 2001
External database links:  
DIP:
DIP-9334N
ECOCYC:
EG12203-MONOMER
ECOLIWIKI:
b1557
INTERPRO:
IPR012340
INTERPRO:
IPR019844
INTERPRO:
IPR002059
INTERPRO:
IPR011129
INTERPRO:
IPR012156
MINT:
MINT-1241665
MODBASE:
P36995
PFAM:
PF00313
PRIDE:
P36995
PRINTS:
PR00050
PRODB:
PRO_000022339
PROSITE:
PS00352
PROSITE:
PS51857
REFSEQ:
NP_416075
SMART:
SM00357
SMR:
P36995
SWISSMODEL:
P36995
UNIPROT:
P36995


Operon      
Name: cspB         
Operon arrangement:
Transcription unit        Promoter
cspB


RNA cis-regulatory element    
   
Cis-reg; thermoregulator cspA thermoregulator
   
   


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 cspFp7 1641690 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter cspBp 1641715 reverse nd [AIPP], [RS-EPT-CBR] [6], [7]
  promoter cspFp6 1641765 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter TSS_1864 1641831 forward nd [RS-EPT-CBR] [6]
  promoter cspFp8 1641846 forward Similarity to the consensus
Read more >
[ICWHO] [5]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [AIPP] Automated inference of promoter position

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



Reference(s)    

 [1] 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

 [2] Phadtare S., Inouye M., 1999, Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli., Mol Microbiol 33(5):1004-14

 [3] Sharan M., Forstner KU., Eulalio A., Vogel J., 2017, APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins., Nucleic Acids Res 45(11):e96

 [4] Xia B., Ke H., Inouye M., 2001, Acquirement of cold sensitivity by quadruple deletion of the cspA family and its suppression by PNPase S1 domain in Escherichia coli., Mol Microbiol 40(1):179-88

 [5] 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

 [6] 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.

 [7] Wang N., Yamanaka K., Inouye M., 1999, CspI, the ninth member of the CspA family of Escherichia coli, is induced upon cold shock., J Bacteriol 181(5):1603-9


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