RegulonDB

Gene
Name:	ydgH
Synonym(s):	ECK1599, G6860, b1604
Genome position(nucleotides):	1678427 --> 1679371 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.11
External database links:

ASAP:	ABE-0005359
ECHOBASE:	EB3688
OU-MICROARRAY:	b1604
PortEco:	ydgH
STRING:	511145.b1604
COLOMBOS:	ydgH

Product

Name:

DUF1471 domain-containing protein YdgH

Synonym(s):

YdgH

Sequence:

Get amino acid sequence Fasta Format

Molecular weight:

33.903

Isoelectric point:

9.765

Motif(s):

Type	Positions	Sequence
	35 -> 90	KPFDRVVVTGRFNAIGEAVKAVSRRADKEGAASFYVVDTSDFGNSGNWRVVADLYK
	1 -> 19	MKLKNTLLASALLSAMAFS
	259 -> 314	MVPFDSIKFSGNYGNMTEVSYQVAKRAAKKGAKYYHITRQWQERGNNLTVSADLYK
	20 -> 314	VNAATELTPEQAAAVKPFDRVVVTGRFNAIGEAVKAVSRRADKEGAASFYVVDTSDFGNSGNWRVVADLYKADAEKAEETSNRVINGVVELPKDQAVLIEPFDTVTVQGFYRSQPEVNDAITKAAKAKGAYSFYIVRQIDANQGGNQRITAFIYKKDAKKRIVQSPDVIPADSEAGRAALAAGGEAAKKVEIPGVATTASPSSEVGRFFETQSSKGGRYTVTLPDGTKVEELNKATAAMMVPFDSIKFSGNYGNMTEVSYQVAKRAAKKGAKYYHITRQWQERGNNLTVSADLYK
	119 -> 174	EPFDTVTVQGFYRSQPEVNDAITKAAKAKGAYSFYIVRQIDANQGGNQRITAFIYK

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ydgH

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	pntBp6	1676548	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.565. P-value: 5.381e-5 Read more >	[ICWHO]	[1]
promoter	TSS_1888	1676849	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_1889	1677293	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_1890	1678014	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_1891	1678308	forward	nd	[RS-EPT-CBR]	[2]
promoter	TSS_1892	1678368	forward	nd	[RS-EPT-CBR]	[2]
promoter	TSS_1893	1678370	forward	nd	[RS-EPT-CBR]	[2]
promoter	ydgHp5	1678377	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.425. P-value: 5.017e-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)

[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.