RegulonDB RegulonDB 10.8: Gene Form
   

ybiA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dinG rhlE ybiA LexA TSS_961 TSS_961 TSS_960 TSS_960 dinGp dinGp ybiAp6 ybiAp6

Gene      
Name: ybiA    Texpresso search in the literature
Synonym(s): ECK0787, EG11579, b0798
Genome position(nucleotides): 832468 <-- 832950 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.31
External database links:  
ASAP:
 ABE-0002722
ECHOBASE:
 EB1539
OU-MICROARRAY:
 b0798
PortEco:
 ybiA
STRING:
 511145.b0798
COLOMBOS: ybiA


Product      
Name: N-glycosidase YbiA
Synonym(s): YbiA
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 18.669
Isoelectric point: 9.94
Motif(s):
 
Type Positions Sequence
130 -> 130 D
133 -> 133 W
48 -> 48 E
89 -> 89 W
19 -> 156 FYSTSDDYGDFSNFAAWPIKVDGKTWPTSEHYFQAQKFLDEKYREEIRRVSSPMVAARMGRDRSKPLRKNWESVKEQVMRKALRAKFEQHAELRALLLATAPAKLVEHTENDAYWGDGGHGKGKNRLGYLLMELREQL

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.6 - protection --> 5.6.2 - detoxification
Gene Ontology Terms (GO)  
molecular_function GO:0016787 - hydrolase activity
GO:0016798 - hydrolase activity, acting on glycosyl bonds
GO:0016799 - hydrolase activity, hydrolyzing N-glycosyl compounds
biological_process GO:0034656 - nucleobase-containing small molecule catabolic process
GO:0008152 - metabolic process
GO:0009231 - riboflavin biosynthetic process
GO:0071978 - bacterial-type flagellum-dependent swarming motility
GO:1901135 - carbohydrate derivative metabolic process
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-11424N
ECOCYC:
 EG11579-MONOMER
ECOLIWIKI:
 b0798
INTERPRO:
 IPR012816
INTERPRO:
 IPR037238
PDB:
 2B3W
PFAM:
 PF08719
PRIDE:
 P30176
REFSEQ:
 NP_415319
SMR:
 P30176
UNIPROT:
 P30176


Operon      
Name: ybiA         
Operon arrangement:
Transcription unit        Promoter
ybiA


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 ybiAp6 832960 reverse Similarity to the consensus
Read more > 		[ICWHO] [1]
  promoter TSS_960 833795 forward nd [RS-EPT-CBR] [2]
  promoter TSS_961 835181 forward nd [RS-EPT-CBR] [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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