RegulonDB RegulonDB 10.9: Gene Form
   

ybdL gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybdL hcxA ybdM ybdN ybdLp3 ybdLp3 ybdHp7 ybdHp7 ybdHp6 ybdHp6

Gene      
Name: ybdL    Texpresso search in the literature
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
ECOLIHUB:
ybdL
OU-MICROARRAY:
b0600
STRING:
511145.b0600
COLOMBOS: ybdL


Product      
Name: methionine transaminase
Synonym(s): YbdL, methionine-oxo-acid transaminase, PLP-dependent
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:0042803 - protein homodimerization activity
GO:0010326 - methionine-oxo-acid transaminase activity
biological_process GO:0097052 - L-kynurenine metabolic process
GO:0009058 - biosynthetic process
External database links:  
DIP:
DIP-11350N
ECOCYC:
G6329-MONOMER
ECOLIWIKI:
b0600
INTERPRO:
IPR015421
INTERPRO:
IPR015424
INTERPRO:
IPR015422
INTERPRO:
IPR004839
MODBASE:
P77806
PDB:
1U08
PFAM:
PF00155
PRIDE:
P77806
REFSEQ:
NP_415133
SMR:
P77806
UNIPROT:
P77806


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
Read more >
[ICWHO] [1]
  promoter ybdHp7 633524 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter ybdLp3 633557 forward Similarity to the consensus
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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