RegulonDB RegulonDB 10.10: Gene Form
   

ribA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

acnA pgpB ribA SoxS pgpBp pgpBp pgpBp7 pgpBp7 pgpBp4 pgpBp4 ribAp2 ribAp2 pgpBp5 pgpBp5 TSS_1724 TSS_1724 ribAp1 ribAp1 TSS_1722 TSS_1722 pgpBp8 pgpBp8 pgpBp9 pgpBp9 pgpBp6 pgpBp6

Gene      
Name: ribA    Texpresso search in the literature
Synonym(s): ECK1272, EG11331, b1277
Genome position(nucleotides): 1338570 <-- 1339160 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.08
External database links:  
ASAP:
 ABE-0004285
CGSC:
 287
ECHOBASE:
 EB1307
ECOLIHUB:
 ribA
OU-MICROARRAY:
 b1277
STRING:
 511145.b1277
COLOMBOS: ribA


Product      
Name: GTP cyclohydrolase 2
Synonym(s): GTP cyclohydrolase II, RibA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 21.836
Isoelectric point: 5.83
Motif(s):
 
Type Positions Sequence
67 -> 67 C
49 -> 53 RVHSE
92 -> 94 EGR
5 -> 170 RVAEAKLPTPWGDFLMVGFEELATGHDHVALVYGDISGHTPVLARVHSECLTGDALFSLRCDCGFQLEAALTQIAEEGRGILLYHRQEGRNIGLLNKIRAYALQDQGYDTVEANHQLGFAADERDFTLCADMFKLLGVNEVRLLTNNPKKVEILTEAGINIVERVP
65 -> 65 C

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.9 - riboflavin
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0003935 - GTP cyclohydrolase II activity
GO:0000166 - nucleotide binding
GO:0005525 - GTP binding
GO:0008270 - zinc ion binding
GO:0000287 - magnesium ion binding
GO:0042803 - protein homodimerization activity
biological_process GO:0009231 - riboflavin biosynthetic process
External database links:  
DIP:
 DIP-36049N
ECOCYC:
 GTP-CYCLOHYDRO-II-MONOMER
ECOLIWIKI:
 b1277
INTERPRO:
 IPR032677
INTERPRO:
 IPR000926
INTERPRO:
 IPR036144
PDB:
 2BZ1
PDB:
 2BZ0
PFAM:
 PF00925
PRIDE:
 P0A7I7
PRODB:
 PRO_000023750
REFSEQ:
 NP_415793
SMR:
 P0A7I7
UNIPROT:
 P0A7I7


Operon      
Name: ribA         
Operon arrangement:
Transcription unit        Promoter
ribA
ribA


Transcriptional Regulation      
Display Regulation             
Activated by: SoxS


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 pgpBp6 1339162 forward nd [ICWHO] [1]
  promoter pgpBp9 1339165 forward nd [ICWHO] [1]
  promoter pgpBp8 1339182 forward nd [ICWHO] [1]
  promoter TSS_1722 1339188 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1724 1339192 reverse nd [RS-EPT-CBR] [2]
  promoter pgpBp5 1339193 forward nd [ICWHO] [1]
  promoter pgpBp4 1339235 forward nd [ICWHO] [1]
  promoter pgpBp7 1339308 forward nd [ICWHO] [1]


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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