RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

ygbI gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	ygbI
Synonym(s):	ECK2730, G7416, b2735
Genome position(nucleotides):	2860467 <-- 2861234 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.56
External database links:

ASAP:	ABE-0008982
ECHOBASE:	EB2906
ECOLIHUB:	ygbI
OU-MICROARRAY:	b2735
STRING:	511145.b2735
COLOMBOS:	ygbI

Product

Name:

putative DeoR-type DNA-binding transcriptional regulator YgbI

Synonym(s):

YgbI

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

27.435

Isoelectric point:

6.781

Motif(s):

Type	Positions	Sequence
	20 -> 39	VSIAELTDRMNVSHMTIRRD
	6 -> 59	RRQIILEMVAEKGIVSIAELTDRMNVSHMTIRRDLQKLEQQGAVVLVSGGVQSP
	76 -> 231	MTQKAAIGKLAASLVQPGSCIYLDAGTTTLAIAQHLIHMESLTVVTNDFVIADYLLDNSNCTIIHTGGAVCRENRSCVGEAAATMLRSLMIDQAFISASSWSVRGISTPAEDKVTVKRAIASASRQRVLVCDATKYGQVATWLALPLSEFDQIITD
	3 -> 58	PVERRQIILEMVAEKGIVSIAELTDRMNVSHMTIRRDLQKLEQQGAVVLVSGGVQS

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003677 - DNA binding GO:0003700 - DNA-binding transcription factor activity
	biological_process	GO:0006351 - transcription, DNA-templated GO:0006355 - regulation of transcription, DNA-templated

Note(s):

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

Evidence:

[HIFS] Human inference of function from sequence

Reference(s):

[1] Perez-Rueda E., et al., 2000
[2] Perez-Rueda E., et al., 2004

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PFAM:

PRIDE:

PRINTS:

PROSITE:

PROSITE:

REFSEQ:

SMART:

UNIPROT:

Operon

Name:

ygbI

Operon arrangement:

Transcription unit	Promoter
ygbI

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_3025	2861256	reverse	nd	[RS-EPT-CBR]	[3]
promoter	ygbIp6	2861362	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.078. P-value: 4.821e-5 Read more >	[ICWHO]	[4]
promoter	ygbIp5	2861441	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.623. P-value: 9.904e-5 Read more >	[ICWHO]	[4]

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] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47
[2] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50
[3] 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.
[4] 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

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