RegulonDB RegulonDB 11.0: Gene Form
   

pdxI gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydbD insI2 pdxI NsrR terminator anti-terminator anti-anti-terminator terminator anti-terminator anti-anti-terminator ydbDp ydbDp TSS_1799 (cluster) TSS_1799 (cluster) pdxIp1 pdxIp1 TSS_1798 TSS_1798 TSS_1797 TSS_1797 TSS_1796 TSS_1796 TSS_1795 TSS_1795

Gene      
Name: pdxI    Texpresso search in the literature
Synonym(s): ECK1399, EG11309, b1406, ydbC
Genome position(nucleotides): 1474221 --> 1475081
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.08
External database links:  
ASAP:
 ABE-0004698
ECHOBASE:
 EB1285
ECOLIHUB:
 ydbC
OU-MICROARRAY:
 b1406
STRING:
 511145.b1406
COLOMBOS: pdxI


Product      
Name: pyridoxal reductase
Synonym(s): PdxI, YdbC
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 30.706
Isoelectric point: 5.283
Motif(s):
 
Type Positions Sequence Comment
15 -> 283 RLGYGAMQLAGPGVFGPPRDRHVAITVLREALALGVNHIDTSDFYGPHVTNQIIREALYPYSDDLTIVTKIGARRGEDASWLPAFSPAELQKAVHDNLRNLGLDVLDVVNLRVMMGDGHGPAEGSIEASLTVLAEMQQQGLVKHIGLSNVTPTQVAEARKIAEIVCVQNEYNIAHRADDAMIDALAHDGIAYVPFFPLGGFTPLQSSTLSDVAASLGATPMQVALAWLLQRSPNILLIPGTSSVAHLRENMAAEKLHLSEEVLSTLDGI
210 -> 218 FPLGGFTPL UniProt: NADP.

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.6 - pyridoxal 5'phosphate
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0050236 - pyridoxine:NADP 4-dehydrogenase activity
GO:0016491 - oxidoreductase activity
GO:0004033 - aldo-keto reductase (NADP) activity
biological_process GO:0009443 - pyridoxal 5'-phosphate salvage
Note(s): Note(s): ...[more].
Reference(s): [1] Ito T., et al., 2020
External database links:  
ALPHAFOLD:
 P25906
DIP:
 DIP-11632N
ECOCYC:
 EG11309-MONOMER
ECOLIWIKI:
 b1406
INTERPRO:
 IPR023210
INTERPRO:
 IPR036812
MODBASE:
 P25906
PFAM:
 PF00248
PRIDE:
 P25906
REFSEQ:
 NP_415924
SMR:
 P25906
UNIPROT:
 P25906


Operon      
Name: pdxI         
Operon arrangement:
Transcription unit        Promoter
pdxI


RNA cis-regulatory element    
Attenuation: Transcriptional


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 TSS_1795 1470141 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1796 1470761 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1797 1471321 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1798 1472340 forward nd [RS-EPT-CBR] [2]
  promoter pdxIp1 1474188 forward nd [ICWHO] [3]
  promoter TSS_1799 (cluster) 1474189 forward nd [RS-EPT-CBR] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Ito T., Downs DM., 2020, Pyridoxal Reductase, PdxI, Is Critical for Salvage of Pyridoxal in Escherichia coli., J Bacteriol 202(12)

 [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.

 [3] 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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