RegulonDB

Gene
Name:	cspB
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)
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:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MINT:

MODBASE:

PFAM:

PRIDE:

PRINTS:

PRODB:

PROSITE:

PROSITE:

REFSEQ:

SMART:

SMR:

SWISSMODEL:

UNIPROT:

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	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	cspFp7	1641690	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.32. P-value: 3.330e-5 Read more >	[ICWHO]	[5]
promoter	cspBp	1641715	reverse	nd	[AIPP], [RS-EPT-CBR]	[6], [7]
promoter	cspFp6	1641765	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.22. P-value: 4.821e-5 Read more >	[ICWHO]	[5]
promoter	TSS_1864	1641831	forward	nd	[RS-EPT-CBR]	[6]
promoter	cspFp8	1641846	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.676. P-value: 1.262e-5 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