RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

ybdK gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	ybdK
Synonym(s):	ECK0573, G6326, b0581
Genome position(nucleotides):	606265 <-- 607383 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.92
External database links:

ASAP:	ABE-0001992
ECHOBASE:	EB3408
ECOLIHUB:	ybdK
OU-MICROARRAY:	b0581
STRING:	511145.b0581
COLOMBOS:	ybdK

Product

Name:

carboxylate-amine ligase

Synonym(s):

YbdK

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

41.688

Isoelectric point:

6.122

Motif(s):

Type	Positions	Sequence
	14 -> 292	LGIELEMQVVNPPGYDLSQDSSMLIDAVKNKITAGEVKHDITESMLELATDVCRDINQAAGQFSAMQKVVLQAATDHHLEICGGGTHPFQKWQRQEVCDNERYQRTLENFGYLIQQATVFGQHVHVGCASGDDAIYLLHGLSRFVPHFIALSAASPYMQGTDTRFASSRPNIFSAFPDNGPMPWVSNWQQFEALFRCLSYTTMIDSIKDLHWDIRPSPHFGTVEVRVMDTPLTLSHAVNMAGLIQATAHWLLTERPFKHQEKDYLLYKFNRFQACRYGL

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		1 - metabolism
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003824 - catalytic activity GO:0016874 - ligase activity GO:0016879 - ligase activity, forming carbon-nitrogen bonds GO:0000166 - nucleotide binding GO:0005524 - ATP binding GO:0004357 - glutamate-cysteine ligase activity
	biological_process	GO:0042398 - cellular modified amino acid biosynthetic process

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

PDB:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ybdK

Operon arrangement:

Transcription unit	Promoter
ybdK

Elements in the selected gene context region unrelated to any object in RegulonDB

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	ybdFp5	606053		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.855. P-value: 6.252e-5 Read more >	[ICWHO]	[1]
	promoter	ybdJp4	606223		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.876. P-value: 5.068e-5 Read more >	[ICWHO]	[1]
	promoter	ybdJp5	606264		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 5.836. P-value: 1.354e-5 Read more >	[ICWHO]	[1]
	promoter	ybdJp2	606405		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.284. P-value: 7.049e-5 Read more >	[ICWHO]	[1]
	promoter	ybdJp3	606411		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.155. P-value: 1.687e-5 Read more >	[ICWHO]	[1]
	promoter	ybdKp3	607561		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.866. P-value: 8.109e-5 Read more >	[ICWHO]	[1]

Evidence
[ICWHO] Inferred computationally without human oversight

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

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