topA:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

topA

Gene Synonym(s)

ECK1268, b1274, JW1266, supX, asuA?[1][2], asuA?

Product Desc.

DNA topoisomerase I[2][3]

Topoisomerase I[4]

Product Synonyms(s)

DNA topoisomerase I, omega subunit[1], B1274[2][1], SupX[2][1], TopA[2][1], Topo I[2][1], DNA topoisomerase I (ω protein)[2][1] , asuA?, ECK1268, JW1266, supX, b1274

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): topA[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]





Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

topA

Mnemonic

Topoisomerase

Synonyms

ECK1268, b1274, JW1266, supX, asuA?[1][2], asuA?

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

28.65 minutes 

MG1655: 1329072..1331669
<gbrowseImage> name=NC_000913:1329072..1331669 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1329420..1332017
<gbrowseImage> name=NC_012967:1329420..1332017 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1219921..1222518
<gbrowseImage> name=NC_012759:1219921..1222518 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1332762..1335359
<gbrowseImage> name=NC_007779:1332762..1335359 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1418468..1421065
<gbrowseImage> name=NC_010473:1418468..1421065 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

1329075

Edman degradation

PMID:3029379


edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

topA66

PMID:2539359

CGSC:72894

topA10

CGSC:5048

topA75(del)

PMID:15522872

CGSC:80891

topA(del) topB(del)

chromosomal segregation defect is due to a defect in recombination, not decatenation

PMID:11493711

SY791 top-10

Point Mutation

Plasmid Recombination

Decrease in Plasmid recombination

PMID:6094504

See Figure 2 for experimental data.

SY791 top-10

Point Mutation

Supercoiling

Decrease in Super-coiling

PMID:6094504

See Figure 2 for experimental data.

SY791 DE(topA-cysB) 700

deletion

Plasmid Recombination

Decrease in Plasmid Recombination

PMID:6094504

See figure 2 for experimental data.

SY791 DE(topA-cysB) 700

deletion

Supercoiling

Decrease in Supercoiling

PMID:6094504

See figure 2 for experimental data.

edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW1266

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGGTAAAGCTCTTGTCATCGT

Primer 2:CCTTTTTTTCCTTCAACCCATTT

4F1

Kohara Phage

Genobase

PMID:3038334

13F9

Kohara Phage

Genobase

PMID:3038334

trpC83::Tn10

Linked marker

CAG18455 = CGSC7371[5]

est. P1 cotransduction: 67% [6]
Synonyms:trpB83::Tn10

zcj-233::Tn10

Linked marker

CAG12028 = CGSC7373[5]

est. P1 cotransduction: 19% [6]
Synonyms:zci-233::Tn10

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11013

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11013

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001002

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945862

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1006

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004275

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

TopA

Synonyms

DNA topoisomerase I, omega subunit[1], B1274[2][1], SupX[2][1], TopA[2][1], Topo I[2][1], DNA topoisomerase I (ω protein)[2][1] , asuA?, ECK1268, JW1266, supX, b1274

Product description

DNA topoisomerase I[2][3]

Topoisomerase I[4]

EC number (for enzymes)
edit table

<protect></protect>

Notes

Function

[back to top]


<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006154

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000380

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003601

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003602

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005733

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013263

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013497

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013498

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013824

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013826

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003916

DNA topoisomerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003601

F

Seeded from EcoCyc (v14.0)

complete

GO:0003916

DNA topoisomerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003602

F

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

PMID:10713132

IGI: Inferred from Genetic Interaction

EcoliWiki:parC|EcoliWiki:gyrA

P

complete

GO:0003916

DNA topoisomerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013497

F

Seeded from EcoCyc (v14.0)

complete

GO:0003916

DNA topoisomerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013498

F

Seeded from EcoCyc (v14.0)

complete

GO:0003916

DNA topoisomerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013824

F

Seeded from EcoCyc (v14.0)

complete

GO:0003916

DNA topoisomerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013826

F

Seeded from EcoCyc (v14.0)

complete

GO:0003916

DNA topoisomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0799

F

Seeded from EcoCyc (v14.0)

complete

GO:0003917

DNA topoisomerase type I activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000380

F

Seeded from EcoCyc (v14.0)

complete

GO:0003917

DNA topoisomerase type I activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005733

F

Seeded from EcoCyc (v14.0)

complete

GO:0003917

DNA topoisomerase type I activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:5.99.1.2

F

Seeded from EcoCyc (v14.0)

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013263

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000380

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003601

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003602

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005733

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013263

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013497

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013498

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013824

C

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013826

C

Seeded from EcoCyc (v14.0)

complete

GO:0006259

DNA metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006154

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000380

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003601

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003602

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005733

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013263

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013497

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013498

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013824

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013826

P

Seeded from EcoCyc (v14.0)

complete

GO:0006265

DNA topological change

PMID:10713132

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0006268

DNA unwinding involved in replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013824

P

Seeded from EcoCyc (v14.0)

complete

GO:0006268

DNA unwinding involved in replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013826

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0016853

isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

ssb

PMID:15690043

Experiment(s):EBI-888130

Protein

aceF

PMID:15690043

Experiment(s):EBI-888130, EBI-893705

Protein

alaS

PMID:15690043

Experiment(s):EBI-888130

Protein

macA

PMID:15690043

Experiment(s):EBI-888130

Protein

hns

PMID:15690043

Experiment(s):EBI-888130

Protein

lpdA

PMID:15690043

Experiment(s):EBI-888130

Protein

malP

PMID:15690043

Experiment(s):EBI-888130

Protein

pssA

PMID:15690043

Experiment(s):EBI-888130

Protein

recJ

PMID:15690043

Experiment(s):EBI-888130

Protein

rob

PMID:15690043

Experiment(s):EBI-888130

Protein

rplB

PMID:15690043

Experiment(s):EBI-888130

Protein

rplC

PMID:15690043

Experiment(s):EBI-888130, EBI-893705

Protein

rplS

PMID:15690043

Experiment(s):EBI-888130

Protein

rplV

PMID:15690043

Experiment(s):EBI-888130, EBI-893705

Protein

rpoA

PMID:15690043

Experiment(s):EBI-888130

Protein

rpoB

PMID:15690043

Experiment(s):EBI-888130

Protein

rpoC

PMID:15690043

Experiment(s):EBI-888130, EBI-893705

Protein

rpsC

PMID:15690043

Experiment(s):EBI-888130

Protein

rpsE

PMID:15690043

Experiment(s):EBI-888130

Protein

rpsG

PMID:15690043

Experiment(s):EBI-888130

Protein

rpsM

PMID:15690043

Experiment(s):EBI-888130

Protein

rstA

PMID:15690043

Experiment(s):EBI-888130

Protein

srmB

PMID:15690043

Experiment(s):EBI-888130

Protein

rluB

PMID:15690043

Experiment(s):EBI-888130

Protein

yciA

PMID:16606699

Experiment(s):EBI-1139424

Protein

rplS

PMID:16606699

Experiment(s):EBI-1139424

Protein

hfq

PMID:16606699

Experiment(s):EBI-1139424

Protein

rpsM

PMID:16606699

Experiment(s):EBI-1139424

Protein

rimJ

PMID:16606699

Experiment(s):EBI-1139424

Protein

gabP

PMID:15690043

Experiment(s):EBI-893705

Protein

hupA

PMID:15690043

Experiment(s):EBI-893705

Protein

hupB

PMID:15690043

Experiment(s):EBI-893705

Protein

kdgK

PMID:15690043

Experiment(s):EBI-893705

Protein

rfaL

PMID:15690043

Experiment(s):EBI-893705

Protein

rplM

PMID:15690043

Experiment(s):EBI-893705

Protein

rpmB

PMID:15690043

Experiment(s):EBI-893705

Protein

rpmG

PMID:15690043

Experiment(s):EBI-893705

Protein

rpoZ

PMID:15690043

Experiment(s):EBI-893705

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-893705

Protein

rpsT

PMID:15690043

Experiment(s):EBI-893705

Protein

ybiT

PMID:15690043

Experiment(s):EBI-893705

Protein

srmB

PMID:19402753

MALDI(Z-score):23.372700

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

malP

PMID:19402753

MALDI(Z-score):25.368226

Protein

rpoB

PMID:19402753

LCMS(ID Probability):98.2 MALDI(Z-score):13.655113

Protein

rpoC

PMID:19402753

LCMS(ID Probability):99.4 MALDI(Z-score):8.512704

Protein

rpoZ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rluB

PMID:19402753

MALDI(Z-score):34.761880

Protein

recJ

PMID:19402753

MALDI(Z-score):18.199199

Protein

rplB

PMID:19402753

MALDI(Z-score):36.003310

Protein

ssb

PMID:19402753

MALDI(Z-score):34.039804

Protein

rpoA

PMID:19402753

LCMS(ID Probability):97.9 MALDI(Z-score):35.722433

edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MGKALVIVES PAKAKTINKY LGSDYVVKSS VGHIRDLPTS GSAAKKSADS TSTKTAKKPK
KDERGALVNR MGVDPWHNWE AHYEVLPGKE KVVSELKQLA EKADHIYLAT DLDREGEAIA
WHLREVIGGD DARYSRVVFN EITKNAIRQA FNKPGELNID RVNAQQARRF MDRVVGYMVS
PLLWKKIARG LSAGRVQSVA VRLVVERERE IKAFVPEEFW EVDASTTTPS GEALALQVTH
QNDKPFRPVN KEQTQAAVSL LEKARYSVLE REDKPTTSKP GAPFITSTLQ QAASTRLGFG
VKKTMMMAQR LYEAGYITYM RTDSTNLSQD AVNMVRGYIS DNFGKKYLPE SPNQYASKEN
SQEAHEAIRP SDVNVMAESL KDMEADAQKL YQLIWRQFVA CQMTPAKYDS TTLTVGAGDF
RLKARGRILR FDGWTKVMPA LRKGDEDRIL PAVNKGDALT LVELTPAQHF TKPPARFSEA
SLVKELEKRG IGRPSTYASI ISTIQDRGYV RVENRRFYAE KMGEIVTDRL EENFRELMNY
DFTAQMENSL DQVANHEAEW KAVLDHFFSD FTQQLDKAEK DPEEGGMRPN QMVLTSIDCP
TCGRKMGIRT ASTGVFLGCS GYALPPKERC KTTINLVPEN EVLNVLEGED AETNALRAKR
RCPKCGTAMD SYLIDPKRKL HVCGNNPTCD GYEIEEGEFR IKGYDGPIVE CEKCGSEMHL
KMGRFGKYMA CTNEECKNTR KILRNGEVAP PKEDPVPLPE LPCEKSDAYF VLRDGAAGVF
LAANTFPKSR ETRAPLVEEL YRFRDRLPEK LRYLADAPQQ DPEGNKTMVR FSRKTKQQYV
SSEKDGKATG WSAFYVDGKW VEGKK
Length

865

Mol. Wt

97.35 kDa

pI

8.7 (calculated)

Extinction coefficient

98,210 - 99,960 (calc based on 29 Y, 10 W, and 14 C residues)

edit table


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

156..565

PF01131 DNA topoisomerase

PMID:19920124

Domain

3..140

PF01751 Toprim domain

PMID:19920124

Domain

596..639

PF01396 Topoisomerase DNA binding C4 zinc finger

PMID:19920124

Domain

708..745

PF01396 Topoisomerase DNA binding C4 zinc finger

PMID:19920124

Domain

757..797

PF08272 Topoisomerase I zinc-ribbon-like

PMID:19920124

Domain

824..865

PF08272 Topoisomerase I zinc-ribbon-like

PMID:19920124

edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=topA taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129235

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945862

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004275

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P06612

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11013

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11013

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945862

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001002

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1006

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

5.56E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

60.165+/-0.38

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.119175972

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

2792

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

677

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

2134

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

topA

edit table
Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

[back to top]


<protect><gbrowseImage> name=NC_000913:1329052..1329092 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
edit table


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b1274 (EcoliWiki Page)

NCBI GEO profiles for topA

microarray

GenExpDB:b1274 (EcoliWiki Page)

Summary of data for topA from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
edit table

<protect></protect>

Notes

Accessions Related to topA Expression

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11013

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1006

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1274

EcoGene

EcoGene:EG11013

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001002

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004275

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000027829 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000017117 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G31210 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000022721 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000022999 (score: 0.134)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00034105 (score: 1.000; bootstrap: 100%)
  • WBGene00039708 (score: 0.144)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00006596 (score: 1.000; bootstrap: 100%)
  • WBGene00012995 (score: 0.141)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000026983 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000022795 (score: 0.136)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000016196 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000000598 (score: 0.151)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0217608 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0040268 (score: 1.000; bootstrap: 100%)
  • FBgn0026015 (score: 0.095)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA10090-PA (score: 1.000; bootstrap: 100%)
  • GA17464-PA (score: 0.100)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000008036 (score: 1.000; bootstrap: 100%)
  • ENSGALP00000002248 (score: 0.116)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000215840 (score: 1.000; bootstrap: 100%)
  • ENSP00000353166 (score: 0.155)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000019022 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000017797 (score: 0.121)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000017120 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000022073 (score: 0.131)

From Inparanoid:20070104

Mus musculus

  • MGI:1197527 (score: 1.000; bootstrap: 100%)
  • MGI:1333803 (score: 0.135)

From Inparanoid:20070104

Oryza gramene

  • Q5VMY4 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000024315 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000046426 (score: 0.154)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000002524 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000006848 (score: 0.129)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YLR234W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC16G52c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000156273 (score: 1.000; bootstrap: 100%)
  • NEWSINFRUP00000136008 (score: 0.120)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00011897001 (score: 1.000; bootstrap: 100%)
  • GSTENP00001410001 (score: 0.184)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000040195 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000012696 (score: 0.147)

From Inparanoid:20070104

Shigella flexneri

TOPA

From SHIGELLACYC

E. coli O157

TOPA

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Panther (EcoliWiki Page)

PTHR11390:SF17

Superfamily (EcoliWiki Page)

SUPERFAMILY:56712

Superfamily (EcoliWiki Page)

SUPERFAMILY:57783

Superfamily (EcoliWiki Page)

SUPERFAMILY:57783

Superfamily (EcoliWiki Page)

SUPERFAMILY:57783

Superfamily (EcoliWiki Page)

SUPERFAMILY:57783

Pfam (EcoliWiki Page)

PF01131 DNA topoisomerase

Pfam (EcoliWiki Page)

PF01751 Toprim domain

Pfam (EcoliWiki Page)

PF01396 Topoisomerase DNA binding C4 zinc finger

Pfam (EcoliWiki Page)

PF01396 Topoisomerase DNA binding C4 zinc finger

Pfam (EcoliWiki Page)

PF08272 Topoisomerase I zinc-ribbon-like

Pfam (EcoliWiki Page)

PF08272 Topoisomerase I zinc-ribbon-like

EcoCyc

EcoCyc:EG11013

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11013

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001002

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1006

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004275

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=topA:On_One_Page&oldid=219668"