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carB:On One Page

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Standard Name

carB

Gene Synonym(s)

ECK0034, b0033, JW0031, arg+ura, cap, pyrA[1]

Product Desc.

CarB[2][3];

Component of carbamoyl phosphate synthetase[2][3]

Carbamoyl phosphate synthase, ammonia, large subunit; tetramer of heterodimers[4]

Product Synonyms(s)

carbamoyl-phosphate synthase large subunit[1], B0033[2][1], Cap[2][1], PyrA[2][1], β chain[2][1], large chain[2][1], CarB[2][1]

Function from GO

Molecular Function

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): carB[2], carAB[2], OP00150, pyrA

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(carB)    Textpresso(carB)

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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

carB

Mnemonic

Carbamoyl P

Synonyms

ECK0034, b0033, JW0031, arg+ura, cap, pyrA[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

0.66 minutes 

MG1655: 30817..34038
gbrowse_img.php?coord=30817..34038&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 34888..38109
gbrowse_img.php?coord=34888..38109&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 30817..34038
gbrowse_img.php?coord=30817..34038&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 30817..34038
gbrowse_img.php?coord=30817..34038&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 30817..34038
gbrowse_img.php?coord=30817..34038&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

ΔcarB (Keio:JW0031)

deletion

deletion

PMID:16738554

Shigen
CGSC8349[5]

carB96::Tn10

Insertion at 33,963 bp in MG1655 (NC_000913)

adapted from Nichols et al.[6]

CAG12093 = CGSC7322[5]

Synonyms: car-96::Tn10

carB671

PMID:4373646

CGSC:5037

ΔcarB8

CGSC:6595

carB96::Tn10

CGSC:7106

carB3092::Tn10kan

CGSC:38009

ΔcarB745::kan

PMID:16738554

CGSC:100240


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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

JW0031

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCCAAAACGTACAGATATAAA

Primer 2:CCTTTGATCTGTGCGTGCATTTC

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[5]

est. P1 cotransduction: 30% [6]
Synonyms:thr-34::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 8% [6]
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:EG10135

EchoBASE (EcoliWiki Page)

EchoBASE:EB0133

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0033

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0041

EcoGene (EcoliWiki Page)

EcoGene:EG10135

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:CARB

CGSC (EcoliWiki Page)

CGSC:935

ASAP (EcoliWikiPage)

ASAP:ABE-0000121


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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

CarB

Synonyms

carbamoyl-phosphate synthase large subunit[1], B0033[2][1], Cap[2][1], PyrA[2][1], β chain[2][1], large chain[2][1], CarB[2][1]

Product description

CarB[2][3];

Component of carbamoyl phosphate synthetase[2][3]

Carbamoyl phosphate synthase, ammonia, large subunit; tetramer of heterodimers[4]

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:0046872

metal ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc [7]

complete

GO:0030145

manganese ion binding

GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464
HAMAP:MF_01210

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0019856

pyrimidine base biosynthetic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005480

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0008652

amino acid biosynthetic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0028

P

Seeded from EcoCyc [7]

complete

GO:0016874

ligase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR005481
SP_KW:KW-0436

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0008152

metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005481

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0006807

nitrogen compound metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006275

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0006526

arginine biosynthetic process

GO_REF:0000002
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR005480
SP_KW:KW-0055
HAMAP:MF_01210

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0006221

pyrimidine nucleotide biosynthetic process

GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

SP_KW:KW-0665
HAMAP:MF_01210

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0005737

cytoplasm

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005480

C

Seeded from EcoCyc 12.5 [8]

complete

GO:0000166

nucleotide binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc [7]

complete

GO:0003824

catalytic activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011761
InterPro:IPR013816
InterPro:IPR013817

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0004086

carbamoyl-phosphate synthase activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005480
InterPro:IPR005483
InterPro:IPR006275

F

Seeded from EcoCyc [7]

complete

GO:0004088

carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity

GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

EC:6.3.5.5
HAMAP:MF_01210

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0005524

ATP binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR005479
InterPro:IPR011761
InterPro:IPR013816
InterPro:IPR013817
SP_KW:KW-0067
HAMAP:MF_01210

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0005515

protein binding

PMID:15690043

IPI: Inferred from Physical Interaction

UniProtKB:P0A6F1

F

Seeded from EcoCyc [7]

complete

GO:0005524

ATP binding

PMID:14718657

IMP: Inferred from Mutant Phenotype

F

complete

Contributes to

GO:0004086

carbamoyl-phosphate synthase activity

PMID:14718657

IDA: Inferred from Direct Assay

F

complete

GO:0005515

protein binding

PMID:4358555

IDA: Inferred from Direct Assay

F

CarA

complete

GO:0004086

carbamoyl-phosphate synthase activity

PMID:3549732

IDA: Inferred from Direct Assay

F

complete

GO:0046872

metal ion binding

PMID:229896

IDA: Inferred from Direct Assay

F

complete

GO:0019856

pyrimidine base biosynthetic process

PMID:1737023

IMP: Inferred from Mutant Phenotype

P

complete

GO:0008652

amino acid biosynthetic process

PMID:1737023

IMP: Inferred from Mutant Phenotype

P

complete

Contributes to

GO:0004088

carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity

PMID:1737023

IGI: Inferred from Genetic Interaction

EcoliWiki:carA

F

complete

GO:0000166

nucleotide binding

PMID:10843852

IMP: Inferred from Mutant Phenotype

F

complete

GO:0000166

nucleotide binding

PMID:7648201

IDA: Inferred from Direct Assay

F

UMP (CHEBI:16695) & IMP (CHEBI:17202)

complete

GO:0000166

nucleotide binding

PMID:15322282

IPI: Inferred from Physical Interaction

F

IMP (CHEBI:17202)

complete

GO:0016597

amino acid binding

PMID:7648201

IDA: Inferred from Direct Assay

F

ornithine (CHEBI:18257)

complete

GO:0016597

amino acid binding

PMID:10047492

IPI: Inferred from Physical Interaction

F

ornithine (CHEBI:18257)

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 TypePartnerNotesReferencesEvidence

Protein

Subunits of carbamoyl phosphate synthetase

could be indirect

Protein

ahpF

PMID:16606699

Experiment(s):EBI-1135376

Protein

zwf

PMID:16606699

Experiment(s):EBI-1135376

Protein

groL

PMID:16606699

Experiment(s):EBI-1135376

Protein

glpD

PMID:16606699

Experiment(s):EBI-1135376

Protein

CarA

PMID:4358555

Small Molecule

ATP

PMID:14718657

Small Molecule

Mg2+

PMID:229896


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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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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 

MPKRTDIKSI LILGAGPIVI GQACEFDYSG AQACKALREE GYRVILVNSN PATIMTDPEM
ADATYIEPIH WEVVRKIIEK ERPDAVLPTM GGQTALNCAL ELERQGVLEE FGVTMIGATA
DAIDKAEDRR RFDVAMKKIG LETARSGIAH TMEEALAVAA DVGFPCIIRP SFTMGGSGGG
IAYNREEFEE ICARGLDLSP TKELLIDESL IGWKEYEMEV VRDKNDNCII VCSIENFDAM
GIHTGDSITV APAQTLTDKE YQIMRNASMA VLREIGVETG GSNVQFAVNP KNGRLIVIEM
NPRVSRSSAL ASKATGFPIA KVAAKLAVGY TLDELMNDIT GGRTPASFEP SIDYVVTKIP
RFNFEKFAGA NDRLTTQMKS VGEVMAIGRT QQESLQKALR GLEVGATGFD PKVSLDDPEA
LTKIRRELKD AGADRIWYIA DAFRAGLSVD GVFNLTNIDR WFLVQIEELV RLEEKVAEVG
ITGLNADFLR QLKRKGFADA RLAKLAGVRE AEIRKLRDQY DLHPVYKRVD TCAAEFATDT
AYMYSTYEEE CEANPSTDRE KIMVLGGGPN RIGQGIEFDY CCVHASLALR EDGYETIMVN
CNPETVSTDY DTSDRLYFEP VTLEDVLEIV RIEKPKGVIV QYGGQTPLKL ARALEAAGVP
VIGTSPDAID RAEDRERFQH AVERLKLKQP ANATVTAIEM AVEKAKEIGY PLVVRPSYVL
GGRAMEIVYD EADLRRYFQT AVSVSNDAPV LLDHFLDDAV EVDVDAICDG EMVLIGGIME
HIEQAGVHSG DSACSLPAYT LSQEIQDVMR QQVQKLAFEL QVRGLMNVQF AVKNNEVYLI
EVNPRAARTV PFVSKATGVP LAKVAARVMA GKSLAEQGVT KEVIPPYYSV KEVVLPFNKF
PGVDPLLGPE MRSTGEVMGV GRTFAEAFAK AQLGSNSTMK KHGRALLSVR EGDKERVVDL
AAKLLKQGFE LDATHGTAIV LGEAGINPRL VNKVHEGRPH IQDRIKNGEY TYIINTTSGR
RAIEDSRVIR RSALQYKVHY DTTLNGGFAT AMALNADATE KVISVQEMHA QIK
Length

1,073

Mol. Wt

117.842 kDa

pI

5.1 (calculated)

Extinction coefficient

68,190 - 69,940 (calc based on 31 Y, 4 W, and 14 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

Initiator Methionine

1

Removed

UniProt:P00968


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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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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:CARBPSYN-LARGE

UniProt (EcoliWiki Page)

UniProt:P00968

PFAM (EcoliWiki Page)

PFAM:PF00289

RefSeq (EcoliWiki Page)

RefSeq:NP_414574


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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)

carB

carAB

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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=30797..30837&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&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:b0033 (EcoliWiki Page)

NCBI GEO profiles for carB

microarray

GenExpDB:b0033 (EcoliWiki Page)

Summary of data for carB 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 carB Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10135

EchoBASE (EcoliWiki Page)

EchoBASE:EB0133

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0033

EcoGene (EcoliWiki Page)

EcoGene:EG10135


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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

  • ENSANGP00000014822 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000027743 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G29900 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000022158 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000023783 (score: 0.286)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00023892 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00004259 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000020636 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000007145 (score: 0.302)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000018261 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-021030-4 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0201646 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0003189 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA14996-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000004646 (score: 1.000; bootstrap: 100%)
  • ENSGALP00000026615 (score: 0.148)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000233072 (score: 1.000; bootstrap: 100%)
  • ENSP00000264705 (score: 0.297)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000013775 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000013443 (score: 0.149)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000019706 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000019587 (score: 0.299)

From Inparanoid:20070104

Mus musculus

  • MGI:891996 (score: 1.000; bootstrap: 100%)
  • MGI:1916969 (score: 0.291)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000022022 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000020200 (score: 0.299)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000019021 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000030030 (score: 0.292)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YJL130C (score: 1.000; bootstrap: 100%)
  • YJR109C (score: 0.095)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC22G76c (score: 1.000; bootstrap: 100%)
  • SPBC2158c (score: 0.100)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000168120 (score: 1.000; bootstrap: 100%)
  • NEWSINFRUP00000182666 (score: 0.374)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00009790001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000019810 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

CARB

From SHIGELLACYC

E. coli O157

CARB

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:PF00289


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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 1.15 1.16 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 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 5.3 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 6.2 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. ↑ 7.0 7.1 7.2 7.3 7.4 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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