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caiA:On One Page

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Standard Name

caiA

Gene Synonym(s)

ECK0040, b0039, JW0038, yaaO[1]

Product Desc.

Crotonobetaine reductase, CII component[2]

Product Synonyms(s)

crotonobetaine reductase subunit II, FAD-binding[1], B0039[3][1], YaaO[3][1], CaiA[3][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): caiTABCDE[3]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(caiA)    Textpresso(caiA)

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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

caiA

Mnemonic

Carnitine inducible

Synonyms

ECK0040, b0039, JW0038, yaaO[1]

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Notes

Location(s) and DNA Sequence

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

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

0.85 minutes 

MG1655: 40386..39244
gbrowse_img.php?coord=39244..40386&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 44579..43437
gbrowse_img.php?coord=43437..44579&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 40386..39244
gbrowse_img.php?coord=39244..40386&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 40386..39244
gbrowse_img.php?coord=39244..40386&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 39244..40386
gbrowse_img.php?coord=39244..40386&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔcaiA (Keio:JW0038)

deletion

deletion

PMID:16738554

Shigen


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Notes

Genetic Resources

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

ResourceResource TypeSourceNotes/Reference

JW0038

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGATTTTAATTTAAATGATGA

Primer 2:CCGCGGTATTGCTTCAGCACCGC

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[4]

est. P1 cotransduction: 80% [5]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[4]

est. P1 cotransduction: 14% [5]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11560

EchoBASE (EcoliWiki Page)

EchoBASE:EB1521

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0039

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0048

EcoGene (EcoliWiki Page)

EcoGene:EG11560

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:CAIA

CGSC (EcoliWiki Page)

CGSC:36825

ASAP (EcoliWikiPage)

ASAP:ABE-0000139


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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

CaiA

Synonyms

crotonobetaine reductase subunit II, FAD-binding[1], B0039[3][1], YaaO[3][1], CaiA[3][1]

Product description

Crotonobetaine reductase, CII component[2]

EC number (for enzymes)
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Notes

Function

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

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0050660

FAD binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013786

F

Seeded from EcoCyc [6]

complete

GO:0003995

acyl-CoA dehydrogenase activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR006089
InterPro:IPR006091
InterPro:IPR006092
HAMAP:MF_01052

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0008152

metabolic process

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009100
InterPro:IPR013786

P

Seeded from EcoCyc [6]

complete

GO:0016491

oxidoreductase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR013764
SP_KW:KW-0560

F

Seeded from EcoCyc [6]

complete

GO:0016627

oxidoreductase activity, acting on the CH-CH group of donors

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006090
InterPro:IPR009075
InterPro:IPR009100
InterPro:IPR013786

F

Seeded from EcoCyc [6]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[8].

required fields missing

GO:0009055

electron carrier activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013764

F

Seeded from EcoCyc [6]

complete

GO:0055114

oxidation reduction

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc [6]

complete

GO:0006097

glyoxylate cycle

P

Seeded from Riley et al 2006 [1].

required fields missing

GO:0009310

amine catabolic process

P

Seeded from Riley et al 2006 [1].

required fields missing

GO:0042413

carnitine catabolic process

P

Seeded from EcoCyc 11.1[8].

required fields missing

GO:0009054

electron acceptor activity

F

Seeded from EcoCyc 11.1[8].

required fields missing

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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 TypePartnerNotesReferencesEvidence

Protein

slyD

PMID:16606699

Experiment(s):EBI-1135403

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1135403

Protein

fdoI

PMID:16606699

Experiment(s):EBI-1135403

Protein

hemA

PMID:16606699

Experiment(s):EBI-1135403

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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes

cytoplasm

From EcoCyc[8]


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Notes

Structure and Physical Properties

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

Sequence

at EcoCyc 

MDFNLNDEQE LFVAGIRELM ASENWEAYFA ECDRDSVYPE RFVKALADMG IDSLLIPEEH
GGLDAGFVTL AAVWMELGRL GAPTYVLYQL PGGFNTFLRE GTQEQIDKIM AFRGTGKQMW
NSAITEPGAG SDVGSLKTTY TRRNGKIYLN GSKCFITSSA YTPYIVVMAR DGASPDKPVY
TEWFVDMSKP GIKVTKLEKL GLRMDSCCEI TFDDVELDEK DMFGREGNGF NRVKEEFDHE
RFLVALTNYG TAMCAFEDAA RYANQRVQFG EAIGRFQLIQ EKFAHMAIKL NSMKNMLYEA
AWKADNGTIT SGDAAMCKYF CANAAFEVVD SAMQVLGGVG IAGNHRISRF WRDLRVDRVS
GGSDEMQILT LGRAVLKQYR
Length

380

Mol. Wt

42.558 kDa

pI

5.0 (calculated)

Extinction coefficient

53,860 - 54,735 (calc based on 14 Y, 6 W, and 7 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.

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

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:CROBETREDUCT-MONOMER

UniProt (EcoliWiki Page)

UniProt:P60584

PFAM (EcoliWiki Page)

PFAM:PF02771

RefSeq (EcoliWiki Page)

RefSeq:NP_414581


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)

caiTABCDE

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=40366..40406&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

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

TypeReferenceNotes

microarray

GEO Profiles:b0039 (EcoliWiki Page)

NCBI GEO profiles for caiA

microarray

GenExpDB:b0039 (EcoliWiki Page)

Summary of data for caiA 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to caiA Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11560

EchoBASE (EcoliWiki Page)

EchoBASE:EB1521

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0039

EcoGene (EcoliWiki Page)

EcoGene:EG11560


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Notes

Links

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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.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000019082 (score: 1.000; bootstrap: 99%)
  • ENSANGP00000013168 (score: 0.322)
  • ENSANGP00000015771 (score: 0.175)
  • ENSANGP00000021837 (score: 0.133)
  • ENSANGP00000012480 (score: 0.056)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000031197 (score: 1.000; bootstrap: 99%)
  • ENSAPMP00000025701 (score: 0.116)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT3G45300 (score: 1.000; bootstrap: 92%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000024017 (score: 0.162)
  • ENSBTAP00000009844 (score: 1.000; bootstrap: 99%)
  • ENSBTAP00000017188 (score: 0.126)
  • ENSBTAP00000004205 (score: 0.095)
  • ENSBTAP00000005782 (score: 0.074)
  • ENSBTAP00000003999 (score: 0.062)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00039091 (score: 1.000; bootstrap: 94%)
  • WBGene00033562 (score: 0.105)
  • WBGene00033579 (score: 0.096)
  • WBGene00033551 (score: 0.081)
  • WBGene00025544 (score: 0.058)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00015326 (score: 1.000; bootstrap: 94%)
  • WBGene00016943 (score: 0.101)
  • WBGene00019433 (score: 0.075)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000015398 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000018661 (score: 0.148)
  • ENSCAFP00000030246 (score: 0.135)
  • ENSCAFP00000013428 (score: 0.127)
  • ENSCAFP00000014350 (score: 0.094)
  • ENSCAFP00000020422 (score: 0.082)
  • ENSCAFP00000006464 (score: 0.074)
  • ENSCAFP00000023601 (score: 0.066)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000001629 (score: 1.000; bootstrap: 79%)
  • ENSCINP00000017142 (score: 1.000; bootstrap: 61%)
  • ENSCINP00000002142 (score: 0.125)
  • ENSCINP00000003052 (score: 0.093)
  • ENSCINP00000019524 (score: 0.078)
  • ENSCINP00000008564 (score: 0.064)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040808-64 (score: 1.000; bootstrap: 97%)
  • ZDB-GENE-040426-2210 (score: 1.000; bootstrap: 97%)
  • ZDB-CDNA-040425-3157 (score: 1.000; bootstrap: 97%)
  • ZDB-CDNA-040808-67 (score: 1.000; bootstrap: 97%)
  • ZDB-GENE-030616-262 (score: 1.000; bootstrap: 95%)
  • ZDB-CDNA-040425-429 (score: 1.000; bootstrap: 94%)
  • ZDB-CDNA-040625-185 (score: 1.000; bootstrap: 95%)
  • ZDB-CDNA-040425-1697 (score: 0.105)
  • ZDB-GENE-040426-771 (score: 0.105)
  • ZDB-CDNA-040625-47 (score: 0.104)
  • ZDB-CDNA-040425-3014 (score: 0.102)
  • ZDB-CDNA-040425-2892 (score: 0.101)
  • ZDB-GENE-040426-1945 (score: 0.101)
  • ZDB-CDNA-040425-1756 (score: 0.101)
  • ZDB-GENE-040426-828 (score: 0.101)
  • ZDB-CDNA-050522-298 (score: 0.099)
  • ZDB-GENE-041008-219 (score: 0.075)
  • ZDB-CDNA-040425-3118 (score: 0.058)
  • ZDB-GENE-030131-899 (score: 0.058)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0230189 (score: 1.000; bootstrap: 99%)
  • DDB0185291 (score: 0.115)
  • DDB0219367 (score: 0.078)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0038742 (score: 1.000; bootstrap: 99%)
  • FBgn0037999 (score: 0.516)
  • FBgn0036824 (score: 0.170)
  • FBgn0035811 (score: 0.100)
  • FBgn0035911 (score: 0.098)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA18369-PA (score: 1.000; bootstrap: 99%)
  • GA18485-PA (score: 0.543)
  • GA17761-PA (score: 0.187)
  • GA19744-PA (score: 0.124)
  • GA11516-PA (score: 0.114)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000011441 (score: 1.000; bootstrap: 95%)
  • ENSGALP00000015708 (score: 1.000; bootstrap: 83%)
  • ENSGALP00000028954 (score: 0.194)
  • ENSGALP00000007454 (score: 0.156)
  • ENSGALP00000002364 (score: 0.132)
  • ENSGALP00000015482 (score: 0.095)
  • ENSGALP00000008056 (score: 0.092)
  • ENSGALP00000004548 (score: 0.084)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000242592 (score: 1.000; bootstrap: 99%)
  • ENSP00000346877 (score: 0.175)
  • ENSP00000235701 (score: 0.140)
  • ENSP00000249760 (score: 0.131)
  • ENSP00000281182 (score: 0.118)
  • ENSP00000312618 (score: 0.074)
  • ENSP00000233710 (score: 0.055)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000027174 (score: 1.000; bootstrap: 99%)
  • ENSMMUP00000000920 (score: 0.171)
  • ENSMMUP00000009469 (score: 0.144)
  • ENSMMUP00000018989 (score: 0.133)
  • ENSMMUP00000009311 (score: 0.123)
  • ENSMMUP00000008358 (score: 0.079)
  • ENSMMUP00000013785 (score: 0.051)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000003655 (score: 1.000; bootstrap: 95%)
  • ENSMODP00000000393 (score: 0.136)
  • ENSMODP00000023827 (score: 0.128)
  • ENSMODP00000006758 (score: 0.095)
  • ENSMODP00000010524 (score: 0.070)
  • ENSMODP00000008065 (score: 0.069)
  • ENSMODP00000019737 (score: 0.061)

From Inparanoid:20070104

Mus musculus

  • MGI:87868 (score: 1.000; bootstrap: 98%)
  • MGI:1914135 (score: 0.156)
  • MGI:87867 (score: 0.154)
  • MGI:1929242 (score: 0.145)
  • MGI:1914198 (score: 0.140)
  • MGI:1914272 (score: 0.083)
  • MGI:87866 (score: 0.067)

From Inparanoid:20070104

Oryza gramene

  • Q75IM9 (score: 1.000; bootstrap: 91%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000009412 (score: 1.000; bootstrap: 96%)
  • ENSPTRP00000001508 (score: 0.137)
  • ENSPTRP00000011814 (score: 0.129)
  • ENSPTRP00000007690 (score: 0.121)
  • ENSPTRP00000026466 (score: 0.074)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000001556 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000027999 (score: 0.148)
  • ENSRNOP00000013238 (score: 0.144)
  • ENSRNOP00000013829 (score: 0.136)
  • ENSRNOP00000017686 (score: 0.076)
  • ENSRNOP00000019108 (score: 0.075)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000131936 (score: 1.000; bootstrap: 99%)
  • NEWSINFRUP00000160477 (score: 1.000; bootstrap: 98%)
  • NEWSINFRUP00000160814 (score: 0.123)
  • NEWSINFRUP00000175290 (score: 0.118)
  • NEWSINFRUP00000169342 (score: 0.105)
  • NEWSINFRUP00000176454 (score: 0.079)
  • NEWSINFRUP00000144126 (score: 0.071)
  • NEWSINFRUP00000158840 (score: 0.051)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00025379001 (score: 1.000; bootstrap: 96%)
  • GSTENP00032196001 (score: 1.000; bootstrap: 95%)
  • GSTENP00012530001 (score: 0.126)
  • GSTENP00030024001 (score: 0.092)
  • GSTENP00012133001 (score: 0.083)
  • GSTENP00014188001 (score: 0.072)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000045054 (score: 1.000; bootstrap: 80%)
  • ENSXETP00000026824 (score: 0.275)
  • ENSXETP00000039754 (score: 0.174)
  • ENSXETP00000017649 (score: 0.155)
  • ENSXETP00000006513 (score: 0.136)
  • ENSXETP00000048685 (score: 0.114)
  • ENSXETP00000043405 (score: 0.114)
  • ENSXETP00000035066 (score: 0.113)
  • ENSXETP00000003600 (score: 0.100)
  • ENSXETP00000021089 (score: 0.093)
  • ENSXETP00000040469 (score: 0.086)
  • ENSXETP00000002367 (score: 0.077)
  • ENSXETP00000018266 (score: 0.060)
  • ENSXETP00000026243 (score: 0.053)

From Inparanoid:20070104

Shigella flexneri

CAIA

From SHIGELLACYC

E. coli O157

CAIA

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF02771


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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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  7. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

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