RegulonDB

Gene
Name:	ynfB
Synonym(s):	ECK1578, G6841, b1583
Genome position(nucleotides):	1655808 --> 1656149 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.17
External database links:

ASAP:	ABE-0005284
ECHOBASE:	EB3601
OU-MICROARRAY:	b1583
PortEco:	ynfB
STRING:	511145.b1583
COLOMBOS:	ynfB

Product

Name:

DUF1283 domain-containing protein YnfB

Synonym(s):

YnfB

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

outer membrane

Molecular weight:

12.909

Isoelectric point:

9.385

Motif(s):

Type	Positions	Sequence
	32 -> 113	KLVIESGDSAQSRQHAAMEKEQWNDTRNLRQKVNKRTEKEWDKADAAFDNRDKCEQSANINAYWEPNTLRCLDRRTGRVITP
	1 -> 28	MKITLSKRIGLLAILLPCALALSTTVHA
	29 -> 113	ETNKLVIESGDSAQSRQHAAMEKEQWNDTRNLRQKVNKRTEKEWDKADAAFDNRDKCEQSANINAYWEPNTLRCLDRRTGRVITP

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0009279 - cell outer membrane
	molecular_function	GO:0005515 - protein binding

Note(s):

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

Reference(s):

[1] Paradis-Bleau C., et al., 2014

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

PRODOM:

REFSEQ:

UNIPROT:

Operon

Name:

ynfB-speG

Operon arrangement:

Transcription unit	Promoter
ynfB-speG	ynfBp

Transcriptional Regulation
	Display Regulation
Repressed by:	GadX

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	ynfAp7	1655679	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.555. P-value: 1.438e-5 Read more >	[ICWHO]	[2]
promoter	ynfAp5	1655690	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.344. P-value: 9.904e-5 Read more >	[ICWHO]	[2]
promoter	ynfAp4	1655699	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.095. P-value: 8.610e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1870	1656041	forward	nd	[RS-EPT-CBR]	[3]
promoter	TSS_1871	1656100	forward	nd	[RS-EPT-CBR]	[3]

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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056
[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
[3] 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.