RegulonDB

Gene
Name:	ybfA
Synonym(s):	ECK0688, EG11521, b0699
Genome position(nucleotides):	729134 --> 729340 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.24
External database links:

ASAP:	ABE-0002386
ECHOBASE:	EB1483
OU-MICROARRAY:	b0699
PortEco:	ybfA
STRING:	511145.b0699
COLOMBOS:	ybfA

Product

Name:

DUF2517 domain-containing protein YbfA

Synonym(s):

YbfA

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane,cytosol

Molecular weight:

8.275

Isoelectric point:

9.721

Motif(s):

Type	Positions	Sequence
	13 -> 34	FLRRTYAVAAGVLALPFMLFWK
	22 -> 68	AGVLALPFMLFWKDRARFYSYLHRVWSKTSDKPVWMDQAEKATGDFY
	1 -> 21	MELYREYPAWLIFLRRTYAVA
	4 -> 63	YREYPAWLIFLRRTYAVAAGVLALPFMLFWKDRARFYSYLHRVWSKTSDKPVWMDQAEKA

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol GO:0005887 - integral component of plasma membrane
	biological_process	GO:0009314 - response to radiation

Note(s):

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

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

UNIPROT:

Operon

Name:

ybfA

Operon arrangement:

Transcription unit	Promoter

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	ybfAp7	729037	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.6. P-value: 2.232e-5 Read more >	[ICWHO]	[1]
promoter	TSS_828 (cluster)	729071	forward	For this promoter, there is a cluster of 3 transcription start sites,in the interval 729071 to 729073, where the highest frequency is at position 728295. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	ybfAp8	729082	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 6.116. P-value: 1.327e-5 Read more >	[ICWHO], [RS-EPT-CBR]	[1], [2]
promoter	TSS_830	729088	forward	nd	[RS-EPT-CBR]	[2]
promoter	rhsCp3	729379	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.135. P-value: 3.501e-5 Read more >	[ICWHO]	[1]

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)