RegulonDB

Gene
Name:	ybaQ
Synonym(s):	ECK0477, G6259, b0483
Genome position(nucleotides):	508218 --> 508559
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	44.74
External database links:

ASAP:	ABE-0001677
ECHOBASE:	EB3034
ECOLIHUB:	ybaQ
OU-MICROARRAY:	b0483
STRING:	511145.b0483
COLOMBOS:	ybaQ

Product

Name:

DNA-binding transcriptional regulator YbaQ

Synonym(s):

YbaQ

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

13.171

Isoelectric point:

5.792

Motif(s):

Type	Positions	Sequence	Comment
	16 -> 69	LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDF
	27 -> 46	INELAELLHVHRNSVSALIN	UniProt: H-T-H motif.

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
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003677 - DNA binding
	biological_process	GO:0006351 - transcription, DNA-templated

Note(s):

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

Evidence:

[COMP-AINF-FN-FROM-SEQ] Automated inference of function from sequence
[EXP-IPI] Inferred from physical interaction

Reference(s):

[1] Gao Y., et al., 2018
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004

External database links:

ALPHAFOLD:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

PANTHER:

PDB:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

ybaQ

Operon arrangement:

Transcription unit	Promoter
ybaQ	ybaQp

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_649	508097	reverse	nd	[RS-EPT-CBR]	[4]
promoter	ybaQp3	508174	forward	nd	[COMP-AINF]	[5]
promoter	ybaPp3	508262	reverse	nd	[COMP-AINF]	[5]
promoter	ybaPp4	508264	reverse	nd	[COMP-AINF]	[5]
promoter	ybaPp6	508284	reverse	nd	[COMP-AINF]	[5]
promoter	TSS_650	511367	reverse	nd	[RS-EPT-CBR]	[4]
promoter	TSS_651	511370	reverse	nd	[RS-EPT-CBR]	[4]

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] Gao Y., Yurkovich JT., Seo SW., Kabimoldayev I., Drager A., Chen K., Sastry AV., Fang X., Mih N., Yang L., Eichner J., Cho BK., Kim D., Palsson BO., 2018, Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655., Nucleic Acids Res 46(20):10682-10696
[2] 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
[3] 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
[4] 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.
[5] 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