RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

ycfZ gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	ycfZ
Synonym(s):	ECK1107, G6578, b1121
Genome position(nucleotides):	1180479 <-- 1181267 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	42.59
External database links:

ASAP:	ABE-0003784
ECHOBASE:	EB3218
OU-MICROARRAY:	b1121
PortEco:	ycfZ
STRING:	511145.b1121
COLOMBOS:	ycfZ

Product

Name:

putative inner membrane protein

Synonym(s):

YcfZ

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

28.865

Isoelectric point:

8.99

Motif(s):

Type	Positions	Sequence
	239 -> 258	ISPLWAGLIGVCTFIAALLL
	183 -> 202	TLGFIAWAATFILFSRIFYY
	207 -> 229	IYALKFAVAMTIANMGYQALCLY
	41 -> 152	AEEIAHKAELFRQQTGIAPFIVVLPDINNEASLRQNGKAMLAHASSSLSDVKGSVLLLFTTREPRLIMITNGQVESGLDDKHLGLLIENHTLAYLNADLWYQGINNALAVLQ
	5 -> 27	IILLSLLILLPLTAASKPLIPIM

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane GO:0016021 - integral component of membrane

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ymfA-ycfZ

Operon arrangement:

Transcription unit	Promoter

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_1455	1179908	forward	nd	[RS-EPT-CBR]	[1]
promoter	ycfZp6	1181346	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.275. P-value: 8.272e-5 Read more >	[ICWHO]	[2]
promoter	ycfZp5	1181380	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.195. P-value: 7.636e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1456	1182741	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

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