RegulonDB RegulonDB 10.6.3: Gene Form
   

tomB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

acrB tomB hha BasR PdhR CpxR TSS_622 TSS_622 TSS_621 TSS_621 TSS_620 TSS_620 TSS_619 TSS_619 TSS_618 TSS_618 TSS_617 TSS_617 TSS_616 TSS_616 tomBp1 tomBp1 hhap6 hhap6 TSS_615 (cluster) TSS_615 (cluster) TSS_614 TSS_614 TSS_613 TSS_613

Gene      
Name: tomB    Texpresso search in the literature
Synonym(s): ECK0455, EG12429, b0461, ybaJ
Genome position(nucleotides): 480334 <-- 480708 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
40.53
External database links:  
ASAP:
ABE-0001596
ECHOBASE:
EB2326
ECOCYC:
EG12429
ECOLIHUB:
tomB
OU-MICROARRAY:
b0461
REGULONDB:
b0461
STRING:
511145.b0461
M3D: tomB
COLOMBOS: tomB
PortEco: b0461


Product      
Name: protein that modulates Hha toxicity
Synonym(s): TomB, YbaJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 14.557
Isoelectric point: 4.736
Motif(s):
 
Type Positions Sequence
1 -> 117 MDEYSPKRHDIAQLKFLCETLYHDCLANLEESNHGWVNDPTSAINLQLNELIEHIATFALNYKIKYNEDNKLIEQIDEYLDDTFMLFSSYGINMQDLQKWRKSGNRLFRCFVNATKE

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
molecular_function GO:0003677 - DNA binding
biological_process GO:0044010 - single-species biofilm formation
Note(s): Note(s): ...[more].
Evidence: [IGI] Inferred from genetic interaction
Reference(s): [1] Garcia-Contreras R., et al., 2008
External database links:  
DIP:
DIP-48132N
ECOCYC:
EG12429-MONOMER
ECOLIWIKI:
b0461
INTERPRO:
IPR019693
PFAM:
PF10757
PRIDE:
P0AAR0
PROTEINMODELPORTAL:
P0AAR0
REFSEQ:
NP_414994
SMR:
P0AAR0
UNIPROT:
P0AAR0


Operon      
Name: tomB-hha         
Operon arrangement:
Transcription unit        Promoter
null


Transcriptional Regulation      
Display Regulation             
Activated by: CpxR, BasR
Repressed by: PdhR


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_613 480423 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_614 480431 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_615 (cluster) 480436 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter hhap6 480503 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter TSS_616 480795 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_617 482380 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_618 482514 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_619 482517 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_620 482528 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_621 483377 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_622 483477 reverse 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] Garcia-Contreras R., Zhang XS., Kim Y., Wood TK., 2008, Protein translation and cell death: the role of rare tRNAs in biofilm formation and in activating dormant phage killer genes., PLoS ONE 3(6):e2394

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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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