intA:On One Page

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

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Standard Name

intA

Gene Synonym(s)

ECK2618, b2622, JW2602, slpA, intX[1], intX

Product Desc.

prophage CP4-57; integrase[2][3]

Integrase gene, CP4-57 putative defective prophage[4]

Product Synonyms(s)

CP4-57 prophage; integrase[1], B2622[2][1], IntX[2][1], IntA[2][1] , ECK2618, intX, JW2602, slpA, b2622

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): intA[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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Notes

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Gene

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Nomenclature

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

Standard name

intA

Mnemonic

Integrase

Synonyms

ECK2618, b2622, JW2602, slpA, intX[1], intX

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Notes

Location(s) and DNA Sequence

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<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

59.36 minutes 

MG1655: 2754181..2755422
<gbrowseImage> name=NC_000913:2754181..2755422 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2639993..2641234
<gbrowseImage> name=NC_012759:2639993..2641234 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2754815..2756056
<gbrowseImage> name=NC_007779:2754815..2756056 source=W3110 preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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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

Strain DH10B

R273Q

Nonsynonomous mutation

PMID:18245285

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔintA (Keio:JW2602)

deletion

deletion

PMID:16738554

Shigen
CGSC10059[5]

intA::Tn5KAN-I-SceI (FB20869)

Insertion at nt 671 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20869

does not contain pKD46

intA::Tn5KAN-I-SceI (FB20870)

Insertion at nt 671 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20870

contains pKD46

ΔintA777::kan

PMID:16738554

CGSC:101570


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Notes

Genetic Interactions

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

Genetic Resources

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

Resource Resource Type Source Notes/Reference

JW2602

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCAAGAAAAACCAAGCCGTT

Primer 2:CCTCCGACAAGACGAATTTTGCT

22D7

Kohara Phage

Genobase

PMID:3038334

24G1

Kohara Phage

Genobase

PMID:3038334

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: 55% [6]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: 1% [6]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

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Notes

Accessions in Other Databases

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

Database Accession Notes

EcoCyc

EcoCyc:EG11783

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11783

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001717

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946160

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1731

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008630

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

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

Standard name

IntA

Synonyms

CP4-57 prophage; integrase[1], B2622[2][1], IntX[2][1], IntA[2][1] , ECK2618, intX, JW2602, slpA, b2622

Product description

prophage CP4-57; integrase[2][3]

Integrase gene, CP4-57 putative defective prophage[4]

EC number (for enzymes)


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Notes

Function

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<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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002104

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011010

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013762

F

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002104

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013762

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0233

P

Seeded from EcoCyc (v14.0)

complete

GO:0015074

DNA integration

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002104

P

Seeded from EcoCyc (v14.0)

complete

GO:0015074

DNA integration

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013762

P

Seeded from EcoCyc (v14.0)

complete

GO:0015074

DNA integration

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0229

P

Seeded from EcoCyc (v14.0)

complete

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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

aceF

PMID:15690043

Experiment(s):EBI-889517, EBI-886344

Protein

yihI

PMID:15690043

Experiment(s):EBI-886344

Protein

frmA

PMID:15690043

Experiment(s):EBI-887783

Protein

ebgA

PMID:15690043

Experiment(s):EBI-887783

Protein

eda

PMID:15690043

Experiment(s):EBI-887783

Protein

flgI

PMID:15690043

Experiment(s):EBI-887783

Protein

glvG

PMID:15690043

Experiment(s):EBI-887783

Protein

hupA

PMID:15690043

Experiment(s):EBI-887783

Protein

nuoI

PMID:15690043

Experiment(s):EBI-887783

Protein

rplI

PMID:15690043

Experiment(s):EBI-887783

Protein

rpsA

PMID:15690043

Experiment(s):EBI-887783

Protein

rpsE

PMID:15690043

Experiment(s):EBI-887783

Protein

rpsG

PMID:15690043

Experiment(s):EBI-887783

Protein

rpsM

PMID:15690043

Experiment(s):EBI-887783

Protein

rpsN

PMID:15690043

Experiment(s):EBI-887783

Protein

rpsP

PMID:15690043

Experiment(s):EBI-887783

Protein

ycgX

PMID:15690043

Experiment(s):EBI-887783

Protein

puuP

PMID:15690043

Experiment(s):EBI-887783

Protein

ydhU

PMID:15690043

Experiment(s):EBI-887783

Protein

ygiQ

PMID:15690043

Experiment(s):EBI-887783

Protein

yhbY

PMID:15690043

Experiment(s):EBI-887783

Protein

rplB

PMID:16606699

Experiment(s):EBI-1143528

Protein

yihI

PMID:19402753

LCMS(ID Probability):99.6

Protein

ppc

PMID:19402753

LCMS(ID Probability):99.5

Protein

puuP

PMID:19402753

LCMS(ID Probability):99.0

Protein

ydhU

PMID:19402753

LCMS(ID Probability):99.0

Protein

frmA

PMID:19402753

LCMS(ID Probability):99.0

Protein

ebgA

PMID:19402753

LCMS(ID Probability):99.0

Protein

nuoI

PMID:19402753

LCMS(ID Probability):99.0

Protein

flgI

PMID:19402753

LCMS(ID Probability):99.0

Protein

ycgX

PMID:19402753

LCMS(ID Probability):99.0

Protein

eda

PMID:19402753

LCMS(ID Probability):99.0

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Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<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 

MARKTKPLTD TEIKAAKPKD ADYQLYDGDG LTLLIKSSGS KLWQFRYYRP LTKQRTKQSF
GAYPAVSLSD ARKLRAESKV LLAKDIDPQE HQKEQVRNSQ EAKTNTFLLV AERWWNVKKT
SVTEDYADDI WRSLERDIFP AIGDISITEI KAHTLVKAVQ PVQARGALET VRRLCQRINE
VMIYAQNTGL IDAVPSVNIG KAFEKPQKKN MPSIRPDQLP QLMHTMRTAS ISMSTRCLFM
WQLLTITRPA EAAEARWDEI DFNASEWKIP AARMKMNRDH TVPLSDGALA ILEMMKPLSG
GREFIFPSRI KPNQPMNSQT VNAALKRAGL GGVLVSHGLR SIASTALNEE GFPPDVIEAA
LAHVDKNEVR RAYNRSDYLE QRRPMMQWWA DLVKAADSGS IVLTHLSKIR LVG
Length

413

Mol. Wt

46.652 kDa

pI

10.0 (calculated)

Extinction coefficient

62,910 - 63,160 (calc based on 9 Y, 9 W, and 2 C residues)

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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

212..380

PF00589 Phage integrase family

PMID:19920124

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<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130540

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946160

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008630

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P32053

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11783

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11783

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946160

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001717

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1731

Escherichia coli str. K-12 substr. MG1655

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Notes

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Expression

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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

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See Help:Cellular levels

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

Protein

E. coli K-12 MG1655

286

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

232

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

372

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

intA

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Figure courtesy of RegulonDB

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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

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<protect><gbrowseImage> name=NC_000913:2754161..2754201 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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

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

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b2622 (EcoliWiki Page)

NCBI GEO profiles for intA

microarray

GenExpDB:b2622 (EcoliWiki Page)

Summary of data for intA from multiple microarray studies

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

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (2753887..2754254) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ02; Well:D3[7]

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Notes

Accessions Related to intA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11783

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1731

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2622

EcoGene

EcoGene:EG11783

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001717

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008630

Escherichia coli str. K-12 substr. MG1655

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Notes

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Evolution

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Homologs in Other Organisms

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

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000001970 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000015167 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

S2859

From SHIGELLACYC

E. coli O157

Z5890

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Superfamily (EcoliWiki Page)

SUPERFAMILY:56349

Pfam (EcoliWiki Page)

PF00589 Phage integrase family

PFAM (EcoliWiki Page)

PFAM:PF00589

EcoCyc

EcoCyc:EG11783

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11783

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001717

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1731

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008630

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 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 5.2 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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