RegulonDB

Gene
Name:	ybjD
Synonym(s):	ECK0867, G6459, b0876
Genome position(nucleotides):	916473 --> 918131
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.1
External database links:

ASAP:	ABE-0002980
ECHOBASE:	EB3199
ECOLIHUB:	ybjD
OU-MICROARRAY:	b0876
STRING:	511145.b0876
COLOMBOS:	ybjD

Product

Name:

DUF2813 domain-containing protein YbjD

Synonym(s):

YbjD, conserved protein with a nucleotide triphosphate hydrolase domain YbjD

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

63.589

Isoelectric point:

9.619

Motif(s):

Type	Positions	Sequence	Comment
	1 -> 375	MILERVEIVGFRGINRLSLMLEQNNVLIGENAWGKSSLLDALTLLLSPESDLYHFERDDFWFPPGDINGREHHLHIILTFRESLPGRHRVRRYRPLEACWTPCTDGYHRIFYRLEGESAEDGSVMTLRSFLDKDGHPIDVEDINDQARHLVRLMPVLRLRDARFMRRIRNGTVPNVPNVEVTARQLDFLARELSSHPQNLSDGQIRQGLSAMVQLLEHYFSEQGAGQARYRLMRRRASNEQRSWRYLDIINRMIDRPGGRSYRVILLGLFATLLQAKGTLRLDKDARPLLLIEDPETRLHPIMLSVAWHLLNLLPLQRIATTNSGELLSLTPVEHVCRLVRESSRVAAWRLGPSGLSTEDSRRISFHIRFNRPSS
	29 -> 36	GENAWGKS	UniProt: ATP.
	376 -> 440	LFARCWLLVEGETETWVINELARQCGHHFDAEGIKVIEFAQSGLKPLVKFARRMGIEWHVLVDGD
	379 -> 469	RCWLLVEGETETWVINELARQCGHHFDAEGIKVIEFAQSGLKPLVKFARRMGIEWHVLVDGDEAGKKYAATVRSLLNNDREAEREHLTALP	UniProt: Toprim.

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0000166 - nucleotide binding GO:0005524 - ATP binding
	biological_process	GO:0006302 - double-strand break repair GO:0000731 - DNA synthesis involved in DNA repair

Note(s):

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

External database links:

ALPHAFOLD:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

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	aqpZp3	916133	reverse	nd	[COMP-AINF]	[1]
promoter	aqpZp2	916212	reverse	nd	[COMP-AINF]	[1]
promoter	macBp1	920094	forward	The sigma factor was determined by transcription profiling experiments and a bioinformatics approach Zhao K,2005. We assigned a putative transcriptional start site to this promoter based on the observation that the majority of the promoters, whose transcriptional start sites were determined experimentally, present a distance of 6 nucleotides between the transcriptional start site and the -10 box. Read more >	[COMP-AINF], [COMP-AINF-POSITIONAL-IDENTIFICATION], [COMP-AINF-SIMILAR-TO-CONSENSUS]	[1], [2]
promoter	macBp2	920337	forward	The sigma factor was determined by transcription profiling experiments and a bioinformatics approach Zhao K,2005 We assigned a putative transcriptional start site to this promoter based on the observation that the majority of the promoters, whose transcriptional start sites were determined experimentally, show a distance of 6 nucleotides between the transcriptional start site and the -10 box. Read more >	[COMP-AINF], [COMP-AINF-POSITIONAL-IDENTIFICATION], [COMP-AINF-SIMILAR-TO-CONSENSUS]	[1], [2]

Evidence
[COMP-AINF] Inferred computationally without human oversight
[COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position
[COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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] Zhao K., Liu M., Burgess RR., 2005, The global transcriptional response of Escherichia coli to induced sigma 32 protein involves sigma 32 regulon activation followed by inactivation and degradation of sigma 32 in vivo., J Biol Chem 280(18):17758-68