RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

ybdL gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	ybdL
Synonym(s):	ECK0594, G6329, b0600
Genome position(nucleotides):	633586 --> 634746 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.83
External database links:

ASAP:	ABE-0002069
ECHOBASE:	EB3302
OU-MICROARRAY:	b0600
PortEco:	ybdL
STRING:	511145.b0600
COLOMBOS:	ybdL

Product

Name:

methionine-oxo-acid transaminase, PLP-dependent

Synonym(s):

YbdL

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

42.963

Isoelectric point:

6.148

Motif(s):

Type	Positions	Sequence
	32 -> 383	AINLSQGFPDFDGPRYLQERLAHHVAQGANQYAPMTGVQALREAIAQKTERLYGYQPDADSDITVTAGATEALYAAITALVRNGDEVICFDPSYDSYAPAIALSGGIVKRMALQPPHFRVDWQEFAALLSERTRLVILNTPHNPSATVWQQADFAALWQAIAGHEIFVISDEVYEHINFSQQGHASVLAHPQLRERAVAVSSFGKTYHMTGWKVGYCVAPAPISAEIRKVHQYLTFSVNTPAQLALADMLRAEPEHYLALPDFYRQKRDILVNALNESRLEILPCEGTYFLLVDYSAVSTLDDVEFCQWLTQEHGVAAIPLSVFCADPFPHKLIRLCFAKKESTLLAAAERL

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0005737 - cytoplasm GO:0005829 - cytosol
	molecular_function	GO:0016212 - kynurenine-oxoglutarate transaminase activity GO:0003824 - catalytic activity GO:0005515 - protein binding GO:0016740 - transferase activity GO:0008483 - transaminase activity GO:0030170 - pyridoxal phosphate binding GO:0010326 - methionine-oxo-acid transaminase activity
	biological_process	GO:0097052 - L-kynurenine metabolic process GO:0009058 - biosynthetic process

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MINT:

MODBASE:

PDB:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ybdL

Operon arrangement:

Transcription unit	Promoter
ybdL

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	ybdHp6	633517		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.566. P-value: 3.297e-5 Read more >	[ICWHO]	[1]
	promoter	ybdHp7	633524		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.086. P-value: 4.191e-5 Read more >	[ICWHO]	[1]
	promoter	ybdLp3	633557		forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.383. P-value: 3.802e-6 Read more >	[ICWHO], [RS-EPT-CBR]	[1], [2]

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.

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