RegulonDB

Gene
Name:	ydhR
Synonym(s):	ECK1663, G6895, b1667
Genome position(nucleotides):	1746700 --> 1747005 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	44.77
External database links:

ASAP:	ABE-0005572
ECHOBASE:	EB3710
OU-MICROARRAY:	b1667
PortEco:	ydhR
STRING:	511145.b1667
COLOMBOS:	ydhR

Product

Name:

putative monooxygenase YdhR

Synonym(s):

YdhR

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

11.288

Isoelectric point:

4.838

Motif(s):

Type	Positions	Sequence
	4 -> 98	LLQLHFAFNGPFGDAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSALAYLEKHTARLKNLGVEEVVAKVFDVNEPLSQINQA

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0005515 - protein binding GO:0016491 - oxidoreductase activity GO:0042803 - protein homodimerization activity
	biological_process	GO:0055114 - oxidation-reduction process

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PANTHER:

PDB:

PDB:

PDB:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ydhR

Operon arrangement:

Transcription unit	Promoter

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_1956	1746673	forward	nd	[RS-EPT-CBR]	[1]
promoter	ydhSp3	1747068	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.09. P-value: 7.337e-5 Read more >	[ICWHO]	[2]
promoter	ydhSp6	1747082	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.715. P-value: 2.646e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1957	1747091	forward	nd	[RS-EPT-CBR]	[1]
promoter	ydhSp5	1747113	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.816. P-value: 4.067e-5 Read more >	[ICWHO]	[2]

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