RegulonDB

Gene
Name:	smrB
Synonym(s):	ECK2325, G7202, b2331, yfcN
Genome position(nucleotides):	2448606 --> 2449157 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.26
External database links:

ASAP:	ABE-0007698
ECHOBASE:	EB3870
OU-MICROARRAY:	b2331
PortEco:	yfcN
STRING:	511145.b2331
COLOMBOS:	smrB

Product

Name:

putative endonuclease SmrB

Synonym(s):

SmrB, YfcN

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

21.013

Isoelectric point:

8.492

Motif(s):

Type	Positions	Sequence
	98 -> 172	LDLHGLTQLQAKQELGALIAACRREHVFCACVMHGHGKHILKQQTPLWLAQHPHVMAFHQAPKEYGGDAALLVLI

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0005829 - cytosol

Note(s):

Note(s): ...[more].

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

smrB

Operon arrangement:

Transcription unit	Promoter
yfcN

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	TSS_2646	2447511	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_2647 (cluster)	2447630	reverse	For this promoter, there is a cluster of 3 transcription start sites,in the interval 2447628 to 2447630, where the highest frequency is at position 2445650. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_2648	2448132	reverse	nd	[RS-EPT-CBR]	[1]
promoter	smrBp6	2448436	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.793. P-value: 8.356e-5 Read more >	[ICWHO]	[2]
promoter	TSS_2649	2448473	reverse	nd	[RS-EPT-CBR]	[1]
promoter	smrBp4	2448568	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 2.695. P-value: 8.697e-5 Read more >	[ICWHO]	[2]
promoter	TSS_2650	2448581	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_2651	2449437	reverse	nd	[RS-EPT-CBR]	[1]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] 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.
[2] 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

Reference(s)

[1] 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.

[2] 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