cspD: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

cspD

Gene Synonym(s)

ECK0871, b0880, JW0864, ybjA[1], cspH, ybjA

Product Desc.

DNA replication inhibitor[2][3];

Component of cold shock protein homolog[3]

Inhibitor of DNA replication; cold shock protein homolog, not cold shock inducible; stationary phase and starvation inducible; lethal when overproduced[4]

Product Synonyms(s)

cold shock protein homolog[1], B0880[2][1], YbjA[2][1], CspD[2][1] , cspH, ECK0871, JW0864, ybjA, b0880

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): cspD[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

cspD

Mnemonic

Cold shock protein

Synonyms

ECK0871, b0880, JW0864, ybjA[1], cspH, ybjA

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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

19.86 minutes 

MG1655: 921813..921589
<gbrowseImage> name=NC_000913:921589..921813 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 939296..939072
<gbrowseImage> name=NC_012967:939072..939296 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 824557..824781
<gbrowseImage> name=NC_012759:824557..824781 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 923012..922788
<gbrowseImage> name=NC_007779:922788..923012 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 975741..975517
<gbrowseImage> name=NC_010473:975517..975741 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

921589

Edman degradation

PMID:9868784


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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

ΔcspD (Keio:JW0864)

deletion

deletion

PMID:16738554

Shigen
CGSC8896[5]

ΔcspD781::kan

PMID:16738554

CGSC:100426


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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

1E5

Kohara Phage

Genobase

PMID:3038334

1H1

Kohara Phage

Genobase

PMID:3038334

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[5]

est. P1 cotransduction: % [6]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: 39% [6]
Synonyms:zbj-1230::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:EG11111

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11111

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001097

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945669

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1102

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002991

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

CspD

Synonyms

cold shock protein homolog[1], B0880[2][1], YbjA[2][1], CspD[2][1] , cspH, ECK0871, JW0864, ybjA, b0880

Product description

DNA replication inhibitor[2][3];

Component of cold shock protein homolog[3]

Inhibitor of DNA replication; cold shock protein homolog, not cold shock inducible; stationary phase and starvation inducible; lethal when overproduced[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:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011129

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012156

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012751

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002059

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012751

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:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002059

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012751

P

Seeded from EcoCyc (v14.0)

complete

GO:0006950

response to stress

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012751

P

Seeded from EcoCyc (v14.0)

complete

GO:0008156

negative regulation of DNA replication

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0236

P

Seeded from EcoCyc (v14.0)

complete

GO:0003697

single-stranded DNA binding

PMID:11260474

IDA: Inferred from Direct Assay

F

Figure 4

complete

GO:0042594

response to starvation

PMID:9260955

IDA: Inferred from Direct Assay

P

Figure 4

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 cold shock protein homolog

could be indirect

Protein

aceE

PMID:15690043

Experiment(s):EBI-879539

Protein

cspC

PMID:15690043

Experiment(s):EBI-879539, EBI-883767, EBI-883980

Protein

cspE

PMID:15690043

Experiment(s):EBI-879539

Protein

deaD

PMID:15690043

Experiment(s):EBI-879539

Protein

pnp

PMID:15690043

Experiment(s):EBI-879539

Protein

rho

PMID:15690043

Experiment(s):EBI-879539

Protein

rplA

PMID:15690043

Experiment(s):EBI-879539

Protein

rplB

PMID:15690043

Experiment(s):EBI-879539

Protein

rplC

PMID:15690043

Experiment(s):EBI-879539, EBI-883767

Protein

rpsA

PMID:15690043

Experiment(s):EBI-879539

Protein

rpsB

PMID:15690043

Experiment(s):EBI-879539, EBI-883767

Protein

rpsC

PMID:15690043

Experiment(s):EBI-879539

Protein

rpsE

PMID:15690043

Experiment(s):EBI-879539, EBI-883767

Protein

rpsG

PMID:15690043

Experiment(s):EBI-879539, EBI-883767

Protein

rpsM

PMID:15690043

Experiment(s):EBI-879539

Protein

tehB

PMID:15690043

Experiment(s):EBI-879539

Protein

rnr

PMID:15690043

Experiment(s):EBI-879539

Protein

ycbY

PMID:15690043

Experiment(s):EBI-879539

Protein

rluC

PMID:15690043

Experiment(s):EBI-879539

Protein

rluB

PMID:15690043

Experiment(s):EBI-879539

Protein

accA

PMID:15690043

Experiment(s):EBI-879539

Protein

rpsD

PMID:15690043

Experiment(s):EBI-879539, EBI-883767

Protein

acrD

PMID:15690043

Experiment(s):EBI-883767

Protein

aspA

PMID:15690043

Experiment(s):EBI-883767

Protein

ddpB

PMID:15690043

Experiment(s):EBI-883767

Protein

ddlA

PMID:15690043

Experiment(s):EBI-883767

Protein

dppD

PMID:15690043

Experiment(s):EBI-883767

Protein

skp

PMID:15690043

Experiment(s):EBI-883767

Protein

hupA

PMID:15690043

Experiment(s):EBI-883767

Protein

rplM

PMID:15690043

Experiment(s):EBI-883767

Protein

rplS

PMID:15690043

Experiment(s):EBI-883767

Protein

rplX

PMID:15690043

Experiment(s):EBI-883767

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-883767

Protein

rpsN

PMID:15690043

Experiment(s):EBI-883767

Protein

rpsT

PMID:15690043

Experiment(s):EBI-883767

Protein

rpsU

PMID:15690043

Experiment(s):EBI-883767

Protein

ydiA

PMID:15690043

Experiment(s):EBI-883767

Protein

yfiF

PMID:15690043

Experiment(s):EBI-883767

Protein

rho

PMID:19402753

MALDI(Z-score):37.446310

Protein

ddlA

PMID:19402753

LCMS(ID Probability):99.0

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):5.368742

Protein

skp

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753

MALDI(Z-score):24.834488

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):4.578737

Protein

rpsU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):5.962325

Protein

rpsC

PMID:19402753

MALDI(Z-score):25.075789

Protein

aspA

PMID:19402753

LCMS(ID Probability):99.0

Protein

rpsM

PMID:19402753

MALDI(Z-score):26.386877

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753

MALDI(Z-score):29.727578

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):35.563879

Protein

ppsR

PMID:19402753

LCMS(ID Probability):99.0

Protein

rplA

PMID:19402753

LCMS(ID Probability):95.4 MALDI(Z-score):31.394353

Protein

rlmL

PMID:19402753

MALDI(Z-score):20.841640

Protein

acrD

PMID:19402753

LCMS(ID Probability):99.0

Protein

cspE

PMID:19402753

LCMS(ID Probability):97.9 MALDI(Z-score):17.053160

Protein

yfiF

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):19.466810

Protein

rnr

PMID:19402753

MALDI(Z-score):23.323615

Protein

rluC

PMID:19402753

MALDI(Z-score):26.672161

Protein

deaD

PMID:19402753

MALDI(Z-score):25.179680

Protein

rluB

PMID:19402753

MALDI(Z-score):35.756062

Protein

cspC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

dppD

PMID:19402753

LCMS(ID Probability):99.0

Protein

ddpB

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

Nucleoid

PMID:11520610


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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 

MEKGTVKWFN NAKGFGFICP EGGGEDIFAH YSTIQMDGYR TLKAGQSVQF DVHQGPKGNH
ASVIVPVEVE AAVA
Length

74

Mol. Wt

7.968 kDa

pI

6.2 (calculated)

Extinction coefficient

8,480 - 8,605 (calc based on 2 Y, 1 W, and 1 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

1..67

PF00313 'Cold-shock' DNA-binding domain

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=cspD 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:16128848

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945669

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002991

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A968

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11111

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11111

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945669

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001097

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1102

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

2.11E+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

53.579+/-0.434

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.799107143

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

743

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

2643

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

658

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)

cspD

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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_000913:921793..921833 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:b0880 (EcoliWiki Page)

NCBI GEO profiles for cspD

microarray

GenExpDB:b0880 (EcoliWiki Page)

Summary of data for cspD 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 (921730..922146) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ16; Well:B11[7]

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<protect></protect>

Notes

Accessions Related to cspD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11111

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1102

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0880

EcoGene

EcoGene:EG11111

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001097

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002991

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000011455 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000035713 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G36020 (score: 1.000; bootstrap: 100%)
  • AT4G38680 (score: 1.000; bootstrap: 100%)
  • AT2G21060 (score: 1.000; bootstrap: 100%)
  • AT2G17870 (score: 0.545)
  • AT5G46730 (score: 0.091)
  • AT2G30560 (score: 0.091)
  • AT4G01985 (score: 0.067)
  • AT2G05440 (score: 0.062)
  • AT2G21660 (score: 0.051)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000023094 (score: 1.000; bootstrap: 80%)
  • ENSBTAP00000012733 (score: 1.000; bootstrap: 80%)
  • ENSBTAP00000023101 (score: 0.327)
  • ENSBTAP00000032304 (score: 0.166)
  • ENSBTAP00000005429 (score: 0.145)
  • ENSBTAP00000016451 (score: 0.071)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00025935 (score: 1.000; bootstrap: 100%)
  • WBGene00032931 (score: 1.000; bootstrap: 100%)
  • WBGene00033626 (score: 1.000; bootstrap: 100%)
  • WBGene00035267 (score: 1.000; bootstrap: 100%)
  • WBGene00025320 (score: 1.000; bootstrap: 100%)
  • WBGene00037745 (score: 0.203)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00000474 (score: 1.000; bootstrap: 100%)
  • WBGene00000472 (score: 1.000; bootstrap: 100%)
  • WBGene00003014 (score: 1.000; bootstrap: 100%)
  • WBGene00000473 (score: 0.667)
  • WBGene00000475 (score: 0.165)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000014863 (score: 1.000; bootstrap: 78%)
  • ENSCAFP00000025464 (score: 1.000; bootstrap: 78%)
  • ENSCAFP00000019752 (score: 1.000; bootstrap: 79%)
  • ENSCAFP00000003704 (score: 1.000; bootstrap: 81%)
  • ENSCAFP00000001245 (score: 1.000; bootstrap: 78%)
  • ENSCAFP00000023761 (score: 0.321)
  • ENSCAFP00000024297 (score: 0.241)
  • ENSCAFP00000024295 (score: 0.237)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000012813 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-000629-3 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-592 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040516-5 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0035626 (score: 1.000; bootstrap: 63%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA14466-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000007728 (score: 1.000; bootstrap: 78%)
  • ENSGALP00000023766 (score: 0.148)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000350456 (score: 0.892)
  • ENSP00000228251 (score: 1.000; bootstrap: 77%)
  • ENSP00000163282 (score: 1.000; bootstrap: 78%)
  • ENSP00000347863 (score: 0.769)
  • ENSP00000331292 (score: 0.426)
  • ENSP00000007699 (score: 0.272)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000022751 (score: 0.705)
  • ENSMMUP00000029562 (score: 1.000; bootstrap: 78%)
  • ENSMMUP00000017257 (score: 1.000; bootstrap: 79%)
  • ENSMMUP00000029908 (score: 0.233)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000022758 (score: 0.366)
  • ENSMODP00000021480 (score: 1.000; bootstrap: 77%)
  • ENSMODP00000021948 (score: 0.294)

From Inparanoid:20070104

Mus musculus

  • MGI:2137670 (score: 1.000; bootstrap: 100%)
  • MGI:99146 (score: 1.000; bootstrap: 100%)
  • MGI:1096372 (score: 0.292)
  • MGI:1925802 (score: 0.289)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000044294 (score: 0.815)
  • ENSPTRP00000010950 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000008009 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000001059 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000014791 (score: 0.276)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000044956 (score: 0.853)
  • ENSRNOP00000048698 (score: 1.000; bootstrap: 78%)
  • ENSRNOP00000007427 (score: 1.000; bootstrap: 79%)
  • ENSRNOP00000045908 (score: 1.000; bootstrap: 81%)
  • ENSRNOP00000047897 (score: 0.664)
  • ENSRNOP00000023003 (score: 0.293)
  • ENSRNOP00000050512 (score: 0.283)
  • ENSRNOP00000047157 (score: 0.164)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000146056 (score: 1.000; bootstrap: 75%)
  • NEWSINFRUP00000158886 (score: 0.194)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00022541001 (score: 1.000; bootstrap: 100%)
  • GSTENP00023133001 (score: 1.000; bootstrap: 100%)
  • GSTENP00018633001 (score: 0.211)
  • GSTENP00019221001 (score: 0.185)
  • GSTENP00038594001 (score: 0.095)
  • GSTENP00009564001 (score: 0.063)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000029443 (score: 1.000; bootstrap: 79%)
  • ENSXETP00000035457 (score: 0.276)

From Inparanoid:20070104

Shigella flexneri

CSPD

From SHIGELLACYC

E. coli O157

CSPD

From ECOO157CYC

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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)

PF00313 'Cold-shock' DNA-binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:50249

EcoCyc

EcoCyc:EG11111

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11111

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001097

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1102

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002991

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 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 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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