yfiF: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

yfiF

Gene Synonym(s)

ECK2579, b2581, JW2565[1], JW2565

Product Desc.

predicted methyltransferase[2][3]

Putative methyltransferase, function unknown; spoU paralog; non-essential gene[4]

Product Synonyms(s)

predicted methyltransferase[1], B2581[2][1], YfiF[2][1] , ECK2579, JW2565, b2581

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yfiF[2]

Regulation/Activity
Quick Links



        

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Notes

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Ribosome-associated protein (Jiang, 2007).[4]



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

yfiF

Mnemonic

Systematic nomenclature

Synonyms

ECK2579, b2581, JW2565[1], JW2565

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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.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

58.53 minutes 

MG1655: 2716550..2715513
<gbrowseImage> name=NC_000913:2715513..2716550 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2640021..2638984
<gbrowseImage> name=NC_012967:2638984..2640021 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2601318..2602355
<gbrowseImage> name=NC_012759:2601318..2602355 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2717184..2716147
<gbrowseImage> name=NC_007779:2716147..2717184 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2808315..2807278
<gbrowseImage> name=NC_010473:2807278..2808315 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

ΔyfiF (Keio:JW2565)

deletion

deletion

PMID:16738554

Shigen
CGSC10040[5]

ΔyfiF749::kan

PMID:16738554

CGSC:104802


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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

JW2565

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAACGATGAAATGAAAGGTAA

Primer 2:CCGGCTTTATTCTGACGCCACCA

4A12

Kohara Phage

Genobase

PMID:3038334

3F10

Kohara Phage

Genobase

PMID:3038334

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[5]

est. P1 cotransduction: 82% [6]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: 45% [6]

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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:EG11786

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11786

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001720

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947066

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1734

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008497

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

YfiF

Synonyms

predicted methyltransferase[1], B2581[2][1], YfiF[2][1] , ECK2579, JW2565, b2581

Product description

predicted methyltransferase[2][3]

Putative methyltransferase, function unknown; spoU paralog; non-essential gene[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.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001537

F

Seeded from EcoCyc (v14.0)

complete

GO:0006396

RNA processing

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001537

P

Seeded from EcoCyc (v14.0)

complete

GO:0008168

methyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013123

F

Seeded from EcoCyc (v14.0)

complete

GO:0008168

methyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0489

F

Seeded from EcoCyc (v14.0)

complete

GO:0008173

RNA methyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001537

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

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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

holB

PMID:15690043[7]

Experiment(s):EBI-879491

Protein

rplA

PMID:15690043[7]

Experiment(s):EBI-879491, EBI-891424

Protein

rplB

PMID:15690043[7]

Experiment(s):EBI-879491, EBI-891424

Protein

rplC

PMID:15690043[7]

Experiment(s):EBI-879491, EBI-891424

Protein

rplF

PMID:15690043[7]

Experiment(s):EBI-879491

Protein

rplI

PMID:15690043[7]

Experiment(s):EBI-879491

Protein

rpsC

PMID:15690043[7]

Experiment(s):EBI-879491

Protein

rpsD

PMID:15690043[7]

Experiment(s):EBI-879491, EBI-891424

Protein

rpsE

PMID:15690043[7]

Experiment(s):EBI-879491, EBI-891424

Protein

rpsF

PMID:15690043[7]

Experiment(s):EBI-879491, EBI-891424

Protein

rpsG

PMID:15690043[7]

Experiment(s):EBI-879491, EBI-891424

Protein

rpsM

PMID:15690043[7]

Experiment(s):EBI-879491, EBI-891424

Protein

rluB

PMID:15690043[7]

Experiment(s):EBI-879491, EBI-889536

Protein

rpsH

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsK

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsL

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsN

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsO

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsP

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsR

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsS

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

yfhM

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

dacA

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

hupA

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rplP

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rplR

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rplT

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rplV

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsT

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsU

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

sufC

PMID:15690043[7]

Experiment(s):EBI-891424

Protein

rpsD

PMID:16606699[8]

Experiment(s):EBI-1143364

Protein

hybD

PMID:16606699[8]

Experiment(s):EBI-1143364

Protein

ihfA

PMID:16606699[8]

Experiment(s):EBI-1143364

Protein

greB

PMID:16606699[8]

Experiment(s):EBI-1143364

Protein

rplQ

PMID:16606699[8]

Experiment(s):EBI-1143364

Protein

yehZ

PMID:16606699[8]

Experiment(s):EBI-1143364

Protein

rplB

PMID:16606699[8]

Experiment(s):EBI-1143364

Protein

ybgP

PMID:16606699[8]

Experiment(s):EBI-1143364

Protein

rpsJ

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplP

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsH

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):16.955360

Protein

rplS

PMID:19402753[9]

LCMS(ID Probability):99.4 MALDI(Z-score):4.459057

Protein

rpsM

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):32.877064

Protein

rplU

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsI

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):15.503798

Protein

rpsK

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):3.033690

Protein

rpsF

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):14.882886

Protein

rpsD

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):38.254885

Protein

rpsS

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753[9]

LCMS(ID Probability):97.9 MALDI(Z-score):34.596309

Protein

rplB

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):16.577573

Protein

rpsL

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):36.450286

Protein

rpsR

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsO

PMID:19402753[9]

LCMS(ID Probability):99.2

Protein

rplR

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753[9]

LCMS(ID Probability):98.1 MALDI(Z-score):3.148972

Protein

rpsU

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplT

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

sufC

PMID:19402753[9]

LCMS(ID Probability):99.2

Protein

rplQ

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

dacA

PMID:19402753[9]

LCMS(ID Probability):99.2

Protein

rlmL

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):38.983788

Protein

yhiR

PMID:19402753[9]

MALDI(Z-score):34.110125

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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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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 

MNDEMKGKSG KVKVMYVRSD DDSDKRTHNP RTGKGGGRPG KSRADGGRRP ARDDKQSQPR
DRKWEDSPWR TVSRAPGDET PEKADHGGIS GKSFIDPEVL RRQRAEETRV YGENACQALF
QSRPEAIVRA WFIQSVTPRF KEALRWMAAN RKAYHVVDEA ELTKASGTEH HGGVCFLIKK
RNGTTVQQWV SQAGAQDCVL ALENESNPHN LGGMMRSCAH FGVKGVVVQD AALLESGAAI
RTAEGGAEHV QPITGDNIVN VLDDFRQAGY TVVTTSSEQG KPLFKTSLPA KMVLVLGQEY
EGLPDAARDP NDLRVKIDGT GNVAGLNISV ATGVLLGEWW RQNKA
Length

345

Mol. Wt

37.783 kDa

pI

9.0 (calculated)

Extinction coefficient

45,950 - 46,450 (calc based on 5 Y, 7 W, and 4 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

197..337

PF00588 SpoU rRNA Methylase family

PMID:19920124[10]

Domain

109..183

PF08032 RNA 2'-O ribose methyltransferase substrate binding

PMID:19920124[10]

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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=yfiF taxon=562,83333 </beststructure>

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 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:16130506

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947066

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008497

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AGJ5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11786

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11786

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947066

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001720

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1734

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

3.33E+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

Ecoli K-12

17.936+/-0.109

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.066055931

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

3949

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

1001

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

1945

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

Transcription unit(s)

yfiF

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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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<gbrowseImage> name=NC_000913:2716530..2716570 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> 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

</protect>

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 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:b2581 (EcoliWiki Page)

NCBI GEO profiles for yfiF

microarray

GenExpDB:b2581 (EcoliWiki Page)

Summary of data for yfiF 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 (2716454..2716809) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ08; Well:G1[11]

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<protect>

Notes

Accessions Related to yfiF Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11786

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1734

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2581

EcoGene

EcoGene:EG11786

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001720

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008497

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

Ciona intestinalis

  • ENSCINP00000008350 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0217723 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000034375 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YFIF

From SHIGELLACYC

E. coli O157

YFIF

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.

Database Accession Notes

Panther (EcoliWiki Page)

PTHR12029:SF25

Superfamily (EcoliWiki Page)

SUPERFAMILY:55315

Superfamily (EcoliWiki Page)

SUPERFAMILY:75217

Pfam (EcoliWiki Page)

PF00588 SpoU rRNA Methylase family

Pfam (EcoliWiki Page)

PF08032 RNA 2'-O ribose methyltransferase substrate binding

EcoCyc

EcoCyc:EG11786

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11786

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001720

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1734

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008497

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 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 4.2 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. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 7.15 7.16 7.17 7.18 7.19 7.20 7.21 7.22 7.23 7.24 7.25 7.26 7.27 7.28 7.29 7.30 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  9. ↑ 9.00 9.01 9.02 9.03 9.04 9.05 9.06 9.07 9.08 9.09 9.10 9.11 9.12 9.13 9.14 9.15 9.16 9.17 9.18 9.19 9.20 9.21 9.22 9.23 9.24 9.25 9.26 9.27 9.28 9.29 9.30 9.31 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  10. ↑ 10.0 10.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
  11. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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