RegulonDB

Gene
Name:	yajD
Synonym(s):	ECK0404, EG11097, b0410
Genome position(nucleotides):	430605 --> 430952
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	47.13
External database links:

ASAP:	ABE-0001422
ECHOBASE:	EB1089
ECOLIHUB:	yajD
OU-MICROARRAY:	b0410
STRING:	511145.b0410
COLOMBOS:	yajD

Product

Name:

HNH nuclease family protein YajD

Synonym(s):

YajD

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

13.364

Isoelectric point:

6.62

Motif(s):

Type	Positions	Sequence	Comment
	27 -> 75	CGRCSREFVYSNLRELTVHHIDHDHTNNPEDGSNWELLCLYCHDHEHSK
	109 -> 115	AMMNKKK	UniProt: In Ref. 1; CAA39636..

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003676 - nucleic acid binding GO:0004518 - nuclease activity GO:0004519 - endonuclease activity GO:0016787 - hydrolase activity
	biological_process	GO:0090305 - nucleic acid phosphodiester bond hydrolysis

Note(s):

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

External database links:

ALPHAFOLD:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMART:

UNIPROT:

Operon

Name:

yajD

Operon arrangement:

Transcription unit	Promoter
yajD

RNA cis-regulatory element

Attenuation:	Transcriptional

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_518	429682	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_519	430048	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_520 (cluster)	430051	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_521	430054	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_522	430059	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_523 (cluster)	430063	forward	nd	[RS-EPT-CBR]	[1]
promoter	yajDp6	430469	forward	nd	[COMP-AINF]	[2]
promoter	yajDp5	430530	forward	nd	[COMP-AINF]	[2]
promoter	TSS_524	432002	reverse	nd	[RS-EPT-CBR]	[1]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[COMP-AINF] 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