atpH: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

atpH

Gene Synonym(s)

ECK3728, b3735, JW3713, papE, uncH, unc[1]

Product Desc.

ATP synthase, F1 complex, δ subunit[2][3];

Component of ATP synthase, F1 complex[2][3]; ATP synthase[2][3]

ATP synthase subunit delta, membrane-bound, F1 sector[4]

Product Synonyms(s)

F1 sector of membrane-bound ATP synthase, delta subunit[1], B3735[2][1], Unc[2][1], UncH[2][1], PapE[2][1], AtpH[2][1] , ECK3728, JW3713, papE, uncH, b3735

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): atpBEFHAGDC[2], atpIBEFHAGDC[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

atpH

Mnemonic

ATP

Synonyms

ECK3728, b3735, JW3713, papE, uncH, unc[1]

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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

84.44 minutes, 84.44 minutes 

MG1655: 3918426..3917893
<gbrowseImage> name=NC_000913:3917893..3918426 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3880769..3880236
<gbrowseImage> name=NC_012967:3880236..3880769 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3806226..3806759
<gbrowseImage> name=NC_012759:3806226..3806759 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3716278..3716811
<gbrowseImage> name=NC_007779:3716278..3716811 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4016010..4015477
<gbrowseImage> name=NC_010473:4015477..4016010 source=DH10B 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

Coding Start (SO:0000323)

MG1655

3917896

Edman degradation

PMID:6278247
PMID:9164460


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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

atpH(del) (Keio:JW3713)

deletion

deletion

PMID:16738554

Shigen

CGSC10714[5]

atpH241

CGSC:64364

atpH764(del)::kan

PMID:16738554

CGSC:100146


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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

JW3713

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTGAATTTATTACGGTAGC

Primer 2:CCAGACTGCAAGACGTCTGCAAG

2A1

Kohara Phage

Genobase

PMID:3038334

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[5]

est. P1 cotransduction: 15% [6]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[5]

est. P1 cotransduction: 66% [6]
Synonyms:zie-296::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:EG10105

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10105

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000101

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948254

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0103

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012215

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

AtpH

Synonyms

F1 sector of membrane-bound ATP synthase, delta subunit[1], B3735[2][1], Unc[2][1], UncH[2][1], PapE[2][1], AtpH[2][1] , ECK3728, JW3713, papE, uncH, b3735

Product description

ATP synthase, F1 complex, δ subunit[2][3];

Component of ATP synthase, F1 complex[2][3]; ATP synthase[2][3]

ATP synthase subunit delta, membrane-bound, F1 sector[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:0005886

plasma membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000711

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020781

C

Seeded from EcoCyc (v14.0)

complete

Contributes to

GO:0046933

hydrogen ion transporting ATP synthase activity, rotational mechanism

PMID:2863270

IDA: Inferred from Direct Assay

F

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0045261

proton-transporting ATP synthase complex, catalytic core F(1)

PMID:6294057

IMP: Inferred from Mutant Phenotype

C

Component of F1 complex, with gene products of uncA (alpha), uncD (beta), uncG (gamma) and uncC (epsilon) - for review see Chap 19 of Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd Edition.

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0015986

ATP synthesis coupled proton transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000711

P

Seeded from EcoCyc (v14.0)

complete

GO:0015986

ATP synthesis coupled proton transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020781

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0019898

extrinsic to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9903

C

Seeded from EcoCyc (v14.0)

complete

GO:0045261

proton-transporting ATP synthase complex, catalytic core F(1)

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000711

C

Seeded from EcoCyc (v14.0)

complete

GO:0045261

proton-transporting ATP synthase complex, catalytic core F(1)

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0139

C

Seeded from EcoCyc (v14.0)

complete

GO:0046933

hydrogen ion transporting ATP synthase activity, rotational mechanism

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01416

F

Seeded from EcoCyc (v14.0)

complete

GO:0046933

hydrogen ion transporting ATP synthase activity, rotational mechanism

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000711

F

Seeded from EcoCyc (v14.0)

complete

GO:0046933

hydrogen ion transporting ATP synthase activity, rotational mechanism

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020781

F

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

Subunits of ATP synthase, F1 complex

could be indirect

Protein

iscS

PMID:16606699

Experiment(s):EBI-1146620

Protein

glpC

PMID:16606699

Experiment(s):EBI-1146620

Protein

atpA

PMID:16606699

Experiment(s):EBI-1146620

Protein

glpD

PMID:16606699

Experiment(s):EBI-1146620

Protein

yjjK

PMID:16606699

Experiment(s):EBI-1146620

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1146620

Protein

atpD

PMID:16606699

Experiment(s):EBI-1146620

Protein

tyrR

PMID:19402753

LCMS(ID Probability):99.4

Protein

Subunits of ATP synthase

could be indirect


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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

plasma membrane

From EcoCyc[3]


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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 

MSEFITVARP YAKAAFDFAV EHQSVERWQD MLAFAAEVTK NEQMAELLSG ALAPETLAES
FIAVCGEQLD ENGQNLIRVM AENGRLNALP DVLEQFIHLR AVSEATAEVD VISAAALSEQ
QLAKISAAME KRLSRKVKLN CKIDKSVMAG VIIRAGDMVI DGSVRGRLER LADVLQS
Length

177

Mol. Wt

19.331 kDa

pI

5.0 (calculated)

Extinction coefficient

6,990 - 7,240 (calc based on 1 Y, 1 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

7..175

PF00213 ATP synthase delta (OSCP) subunit

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=atpH 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:16131603

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948254

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012215

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ABA4

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10105

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10105

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948254

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000101

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0103

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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 MC4100

1.28E+03

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

91.026+/-0.402

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.79412+/-0.28626

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

1.287054409

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

9335

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

2677

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

4796

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)

atpBEFHAGDC

atpIBEFHAGDC

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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_000913:3918406..3918446 source=MG1655 flip=1 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:b3735 (EcoliWiki Page)

NCBI GEO profiles for atpH

microarray

GenExpDB:b3735 (EcoliWiki Page)

Summary of data for atpH 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
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Notes

Accessions Related to atpH Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10105

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0103

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3735

EcoGene

EcoGene:EG10105

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000101

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012215

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

  • ENSANGP00000011882 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000010338 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000024326 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00033275 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00000230 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000014026 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000011862 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-050522-147 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-050522-147 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0016691 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA18097-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000025745 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000290299 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000020340 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000010247 (score: 0.469)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000026329 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000000446 (score: 0.796)

From Inparanoid:20070104

Mus musculus

  • MGI:106341 (score: 1.000; bootstrap: 100%)
  • MGI:3643291 (score: 0.948)

From Inparanoid:20070104

Oryza gramene

  • Q67W57 (score: 1.000; bootstrap: 100%)
  • Q7X9K5 (score: 0.454)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000023882 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000002732 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YDR298C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPCC18406 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000152442 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00017008001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000031010 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

ATPH

From SHIGELLACYC

E. coli O157

ATPH

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

Pfam (EcoliWiki Page)

PF00213 ATP synthase delta (OSCP) subunit

Superfamily (EcoliWiki Page)

SUPERFAMILY:47928

Panther (EcoliWiki Page)

PTHR11910:SF0

EcoCyc

EcoCyc:EG10105

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10105

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000101

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0103

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012215

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. ↑ 1.00 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 2.15 2.16 2.17 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 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).

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