RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

topA gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	topA
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

Type	Positions	Sequence
	3 -> 142	KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEI
	9 -> 9	E
	319 -> 319	Y
	496 -> 496	T
	709 -> 745	VECEKCGSEMHLKMGRFGKYMACTNEECKNTRKILRN
	787 -> 787	P
	168 -> 168	R
	599 -> 630	CPTCGRKMGIRTASTGVFLGCSGYALPPKERC
	662 -> 689	CPKCGTAMDSYLIDPKRKLHVCGNNPTC
	711 -> 736	CEKCGSEMHLKMGRFGKYMACTNEEC
	111 -> 111	D
	321 -> 321	R
	157 -> 565	LNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLD
	115 -> 115	E
	824 -> 862	GNKTMVRFSRKTKQQYVSSEKDGKATGWSAFYVDGKWVE
	192 -> 197	SAGRVQ
	758 -> 793	LPELPCEKSDAYFVLRDGAAGVFLAANTFPKSRETR
	113 -> 113	D
	172 -> 172	D
	5 -> 142	LVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEI
	365 -> 365	H
	597 -> 622	IDCPTCGRKMGIRTASTGVFLGCSGY

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:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PANTHER:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PFAM:

PFAM:

PFAM:

PFAM:

PRIDE:

PRINTS:

PROSITE:

PROSITE:

REFSEQ:

SMART:

SMART:

SMART:

SMR:

UNIPROT:

Operon

Name:

topA

Operon arrangement:

Transcription unit	Promoter
topA	topAp
topA	topAp5
topA	topAp4
topA	topAp3
topA	topAp2
topA	topAp1

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	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 is a cluster of 2 transcription start sites,in the interval 1330686 to 1330687, where the highest frequency is at position 1328711. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	yciNp10	1330689	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.036. P-value: 6.841e-5 Read more >	[ICWHO]	[2]
promoter	yciNp8	1330702	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.125. P-value: 2.081e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1712	1330714	reverse	nd	[RS-EPT-CBR]	[1]
promoter	yciNp9	1330757	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.005. P-value: 2.300e-5 Read more >	[ICWHO]	[2]
promoter	yciNp11	1330790	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.213. P-value: 5.342e-6 Read more >	[ICWHO]	[2]
promoter	TSS_1713	1330791	forward	nd	[RS-EPT-CBR]	[1]
promoter	yciNp5	1330803	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.29. P-value: 8.356e-5 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

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

RegulonDB