RegulonDB

Gene
Name:	yfdY
Synonym(s):	ECK2373, G7240, b2377
Genome position(nucleotides):	2495050 <-- 2495292 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	48.15
External database links:

ASAP:	ABE-0007841
ECHOBASE:	EB3899
OU-MICROARRAY:	b2377
PortEco:	yfdY
COLOMBOS:	yfdY

Product

Name:

DUF2545 domain-containing protein YfdY

Synonym(s):

YfdY

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

8.874

Isoelectric point:

8.478

Motif(s):

Type	Positions	Sequence
	55 -> 75	LVTGIFMFLAPACGLMIRFMV
	2 -> 22	INLWMFLALCIVCVSGYIGQV
	32 -> 52	FFGMVILAALIYYFTMWLTGG
	1 -> 80	MINLWMFLALCIVCVSGYIGQVLNVVSAVSSFFGMVILAALIYYFTMWLTGGNELVTGIFMFLAPACGLMIRFMVGYGRR

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:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

PRODOM:

REFSEQ:

UNIPROT:

Operon

Name:

yfdY

Operon arrangement:

Transcription unit	Promoter
yfdY

RNA cis-regulatory element

Attenuation:	Translational

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	yfdYp5	2495333	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.684. P-value: 3.947e-5 Read more >	[ICWHO]	[1]
promoter	yfdYp6	2495336	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.746. P-value: 1.605e-5 Read more >	[ICWHO]	[1]
promoter	TSS_2670	2495493	forward	nd	[RS-EPT-CBR]	[2]

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] 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
[2] 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.

Reference(s)

[1] 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

[2] 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.