RegulonDB

Gene
Name:	yafD
Synonym(s):	ECK0209, EG11650, b0209
Genome position(nucleotides):	231122 --> 231922 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.68
External database links:

ASAP:	ABE-0000700
ECHOBASE:	EB1603
ECOLIHUB:	yafD
OU-MICROARRAY:	b0209
STRING:	511145.b0209
COLOMBOS:	yafD

Product

Name:

endonuclease/exonuclease/phosphatase domain-containing protein YafD

Synonym(s):

YafD

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

29.992

Isoelectric point:

9.94

Motif(s):

Type	Positions	Sequence
	112 -> 112	T
	49 -> 252	WNIYKQQRAEWLSVLKNYGKDAHLVLLQEAQTTPELVQFATANYLAADQVPAFVLPQHPSGVMTLSAAHPVYCCPLREREPILRLAKSALVTVYPLPDTRLLMVVNIHAVNFSLGVDVYSKQLLPIGDQIAHHSGPVIMAGDFNAWSRRRMNALYRFAREMSLRQVRFTDDQRRRAFGRPLDFVFYRGLNVSEASVLVTRASDH
	223 -> 223	R

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0005737 - cytoplasm

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PRIDE:

REFSEQ:

UNIPROT:

Operon

Name:

yafDE

Operon arrangement:

Transcription unit	Promoter
yafDE	yafDp

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_422	230910	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_423	230912	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_424	230918	reverse	nd	[RS-EPT-CBR]	[1]
promoter	yafCp6	231083	reverse	nd	[ICWHO]	[2]
promoter	TSS_425	231274	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_426	231276	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_427	231280	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_428	231299	forward	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