udk: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

udk

Gene Synonym(s)

ECK2060, b2066, JW2051[1], JW2051

Product Desc.

UDK[2][3]

Uridine/cytidine kinase[4]

Product Synonyms(s)

uridine/cytidine kinase[1], B2066[2][1], Udk[2][1] , ECK2060, JW2051, b2066

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): udk-dcd[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

udk

Mnemonic

Uridine kinase

Synonyms

ECK2060, b2066, JW2051[1], JW2051

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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

46.13 minutes 

MG1655: 2140972..2140331
<gbrowseImage> name=NC_000913:2140331..2140972 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2076154..2075513
<gbrowseImage> name=NC_012967:2075513..2076154 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2032814..2033455
<gbrowseImage> name=NC_012759:2032814..2033455 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2145085..2144444
<gbrowseImage> name=NC_007779:2144444..2145085 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2231980..2231339
<gbrowseImage> name=NC_010473:2231339..2231980 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
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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

Δudk (Keio:JW2051)

deletion

deletion

PMID:16738554

Shigen

udk::Tn5KAN-2 (FB20603)

Insertion at nt 385 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20603

contains pKD46

udk-2

CGSC:7315

udk-30

CGSC:16947


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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

JW2051

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACTGATCAGTCTCATCAGTG

Primer 2:CCTTCAAAGAACTGACTTATTTT

2E1

Kohara Phage

Genobase

PMID:3038334

3G4

Kohara Phage

Genobase

PMID:3038334

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[5]

est. P1 cotransduction: 6% [6]
Synonyms:zee-3129::Tn10

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[5]

est. P1 cotransduction: 23% [6]
Synonyms:zbc-3105::Tn10, zbd-3105::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:EG11701

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11701

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001644

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946597

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1652

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006840

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

Udk

Synonyms

uridine/cytidine kinase[1], B2066[2][1], Udk[2][1] , ECK2060, JW2051, b2066

Product description

UDK[2][3]

Uridine/cytidine kinase[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: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:0004849

uridine kinase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00551

F

Seeded from EcoCyc (v14.0)

complete

GO:0004849

uridine kinase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.1.48

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00551

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000764

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006083

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:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00551

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006083

P

Seeded from EcoCyc (v14.0)

complete

GO:0008655

pyrimidine salvage

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00551

P

Seeded from EcoCyc (v14.0)

complete

GO:0016301

kinase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006083

F

Seeded from EcoCyc (v14.0)

complete

GO:0016301

kinase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0418

F

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0016773

phosphotransferase activity, alcohol group as acceptor

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000764

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

grxB

PMID:16606699

Experiment(s):EBI-1141833

Protein

hyaE

PMID:16606699

Experiment(s):EBI-1141833
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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 

MALRRPLPNI QVNQVAKYMT DQSHQCVIIG IAGASASGKS LIASTLYREL REQVGDEHIG
VIPEDCYYKD QSHLSMEERV KTNYDHPSAM DHSLLLEHLQ ALKRGSAIDL PVYSYVEHTR
MKETVTVEPK KVIILEGILL LTDARLRDEL NFSIFVDTPL DICLMRRIKR DVNERGRSMD
SVMAQYQKTV RPMFLQFIEP SKQYADIIVP RGGKNRIAID ILKAKISQFF E
Length

231

Mol. Wt

26.447 kDa

pI

8.0 (calculated)

Extinction coefficient

13,410 - 13,785 (calc based on 9 Y, 0 W, and 3 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

Modification Site

106

phosphorylation site at T106

probability less than 75%

PMID:17938405

Modification Site

108

phosphorylation site at T108

probability less than 75%

PMID:17938405

Domain

10..200

PF00485 Phosphoribulokinase / Uridine kinase 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=udk taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Need to check evidence for the N-terminus of this protein. Alignment with other genomes (e.g. Haemophilus) suggests the possibility of a downstream start. EcoGene shows the downstream start.

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:90111379

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946597

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006840

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A8F4

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11701

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11701

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946597

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001644

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1652

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

1.86E+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

E. coli K-12 MG1655

3151

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

468

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

1144

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)

udk-dcd

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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_000913:2140952..2140992 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:b2066 (EcoliWiki Page)

NCBI GEO profiles for udk

microarray

GenExpDB:b2066 (EcoliWiki Page)

Summary of data for udk 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 (2140925..2141313) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ06; Well:H9[7]

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Notes

Accessions Related to udk Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11701

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1652

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2066

EcoGene

EcoGene:EG11701

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001644

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006840

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

  • ENSANGP00000028090 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000032846 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT3G27190 (score: 1.000; bootstrap: 99%)
  • AT5G40870 (score: 0.882)
  • AT1G55810 (score: 0.674)
  • AT4G26510 (score: 0.624)
  • AT3G27440 (score: 0.614)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000020981 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000015623 (score: 0.078)
  • ENSBTAP00000014316 (score: 0.059)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00026196 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00008948 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000019858 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000029480 (score: 0.500)
  • ENSCAFP00000019316 (score: 0.215)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000007458 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000014825 (score: 0.061)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-030131-7158 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-1585 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-1004 (score: 0.743)
  • ZDB-GENE-030131-5265 (score: 0.743)
  • ZDB-CDNA-040912-115 (score: 0.556)
  • ZDB-GENE-040912-113 (score: 0.556)
  • ZDB-GENE-040724-238 (score: 0.171)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0230208 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0022029 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA19542-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000009713 (score: 1.000; bootstrap: 100%)
  • ENSGALP00000005542 (score: 0.060)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000271395 (score: 1.000; bootstrap: 100%)
  • ENSP00000253015 (score: 0.560)
  • ENSP00000346155 (score: 0.202)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000000760 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000013056 (score: 0.493)
  • ENSMMUP00000020403 (score: 0.202)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000021258 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000001634 (score: 0.065)

From Inparanoid:20070104

Mus musculus

  • MGI:1931744 (score: 1.000; bootstrap: 100%)
  • MGI:98904 (score: 0.568)
  • MGI:1915806 (score: 0.205)

From Inparanoid:20070104

Oryza gramene

  • Q53LT4 (score: 1.000; bootstrap: 99%)
  • Q6K7V0 (score: 1.000; bootstrap: 99%)
  • Q6ZIA3 (score: 0.619)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000002709 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000036774 (score: 0.560)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000015792 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000005213 (score: 0.446)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YNR012W (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPCC1621c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000135528 (score: 1.000; bootstrap: 99%)
  • NEWSINFRUP00000128558 (score: 0.556)
  • NEWSINFRUP00000128310 (score: 0.183)
  • NEWSINFRUP00000168407 (score: 0.123)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00013361001 (score: 1.000; bootstrap: 99%)
  • GSTENP00014402001 (score: 0.546)
  • GSTENP00023499001 (score: 0.120)
  • GSTENP00009786001 (score: 0.090)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000037794 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000003108 (score: 0.470)

From Inparanoid:20070104

Shigella flexneri

UDK

From SHIGELLACYC

E. coli O157

UDK

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:52540

Panther (EcoliWiki Page)

PTHR10285:SF6

Pfam (EcoliWiki Page)

PF00485 Phosphoribulokinase / Uridine kinase family

EcoCyc

EcoCyc:EG11701

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11701

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001644

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1652

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006840

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 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 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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