RegulonDB

Gene
Name:	ydhI
Synonym(s):	ECK1639, G6883, b1643
Genome position(nucleotides):	1721025 --> 1721261 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	48.95
External database links:

ASAP:	ABE-0005499
ECHOBASE:	EB3701
OU-MICROARRAY:	b1643
PortEco:	ydhI
STRING:	511145.b1643
COLOMBOS:	ydhI

Product

Name:

DUF1656 domain-containing protein YdhI

Synonym(s):

YdhI

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

8.891

Isoelectric point:

8.229

Motif(s):

Type	Positions	Sequence
	19 -> 70	ASVYFPPFFKAFAFGFVIWLVVHRLLRGWIYAGDIWHPLLMDLSLFAICVCL
	57 -> 77	LLMDLSLFAICVCLALAILIA
	20 -> 40	SVYFPPFFKAFAFGFVIWLVV

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:

REFSEQ:

UNIPROT:

Operon

Name:

ydhIJK

Operon arrangement:

Transcription unit	Promoter
ydhIJK	ydhIp

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	slyAp13	1720849	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.143. P-value: 6.315e-5 Read more >	[ICWHO]	[1]
promoter	slyAp14	1720865	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.606. P-value: 9.805e-5 Read more >	[ICWHO]	[1]
promoter	TSS_1927 (cluster)	1720870	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1720869 to 1720870, where the highest frequency is at position 1718894. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_1928	1720879	reverse	nd	[RS-EPT-CBR]	[2]
promoter	slyAp10	1721014	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.19. P-value: 9.327e-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)