RegulonDB RegulonDB 10.9: Gene Form
   

topA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

topA cysB yciN CysB PhoP Fis Fis Fis Fis Fis Fis Fis Fis Fis Fis Fis terminator TSS_1721 TSS_1721 TSS_1720 TSS_1720 TSS_1719 TSS_1719 cysBp cysBp TSS_1718 TSS_1718 TSS_1717 TSS_1717 TSS_1716 TSS_1716 TSS_1715 TSS_1715 topAp1 topAp1 topAp2 topAp2 topAp3 topAp3 topAp4 topAp4 yciNp5 yciNp5 TSS_1713 TSS_1713 yciNp11 yciNp11 topAp5 topAp5 yciNp9 yciNp9 TSS_1712 TSS_1712 yciNp8 yciNp8 yciNp10 yciNp10 TSS_1711 (cluster) TSS_1711 (cluster) TSS_1710 TSS_1710

Gene      
Name: topA    Texpresso search in the literature
Synonym(s): ECK1268, EG11013, b1274, supX
Genome position(nucleotides): 1331048 --> 1333645 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.77
External database links:  
ASAP:
ABE-0004275
CGSC:
89
ECHOBASE:
EB1006
ECOLIHUB:
topA
OU-MICROARRAY:
b1274
STRING:
511145.b1274
COLOMBOS: topA


Product      
Name: DNA topoisomerase 1
Synonym(s): DNA topoisomerase I (omega; protein), SupX, TopA, Topo I
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 97.35
Isoelectric point: 8.639
Motif(s):
 
Type Positions Sequence
3 -> 142 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEI
9 -> 9 E
319 -> 319 Y
496 -> 496 T
709 -> 745 VECEKCGSEMHLKMGRFGKYMACTNEECKNTRKILRN

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0005694 - chromosome
molecular_function GO:0003677 - DNA binding
GO:0003916 - DNA topoisomerase activity
GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0046872 - metal ion binding
GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity
biological_process GO:0006265 - DNA topological change
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11011N
ECOCYC:
EG11013-MONOMER
ECOLIWIKI:
b1274
INTERPRO:
IPR013826
INTERPRO:
IPR013825
INTERPRO:
IPR013824
INTERPRO:
IPR013498
INTERPRO:
IPR013497
INTERPRO:
IPR013263
INTERPRO:
IPR006171
INTERPRO:
IPR005733
INTERPRO:
IPR003602
INTERPRO:
IPR003601
INTERPRO:
IPR000380
INTERPRO:
IPR023405
INTERPRO:
IPR023406
INTERPRO:
IPR034149
INTERPRO:
IPR028612
MODBASE:
P06612
PANTHER:
PTHR42785
PDB:
4RUL
PDB:
3PX7
PDB:
3PWT
PDB:
1YUA
PDB:
1MW9
PDB:
1MW8
PDB:
1ECL
PDB:
1CYY
PDB:
1CY9
PDB:
1CY8
PDB:
1CY7
PDB:
1CY6
PDB:
1CY4
PDB:
1CY2
PDB:
1CY1
PDB:
1CY0
PFAM:
PF08272
PFAM:
PF01751
PFAM:
PF01396
PFAM:
PF01131
PRIDE:
P06612
PRINTS:
PR00417
PROSITE:
PS00396
PROSITE:
PS50880
REFSEQ:
NP_415790
SMART:
SM00437
SMART:
SM00436
SMART:
SM00493
SMR:
P06612
UNIPROT:
P06612


Operon      
Name: topA         
Operon arrangement:
Transcription unit        Promoter
topA
topA
topA
topA
topA
topA


Transcriptional Regulation      
Display Regulation             
Activated by: Fis
Repressed by: Fis


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_1710 1330684 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1711 (cluster) 1330687 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter yciNp10 1330689 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yciNp8 1330702 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1712 1330714 reverse nd [RS-EPT-CBR] [1]
  promoter yciNp9 1330757 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yciNp11 1330790 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1713 1330791 forward nd [RS-EPT-CBR] [1]
  promoter yciNp5 1330803 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1715 1331232 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1716 1331471 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1717 1332403 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1718 1333761 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1719 1334133 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1720 1334254 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1721 1334325 forward nd [RS-EPT-CBR] [1]


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] 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.

 [2] 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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