recF: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

recF

Gene Synonym(s)

ECK3692, b3700, JW3677, uvrF[1], uvrF

Product Desc.

ssDNA and dsDNA binding, ATP binding[2][3];

Component of RecFOR complex[2][3]

Recombination and repair; antagonizes RecX inhibition of RecA filament formation[4]

Product Synonyms(s)

gap repair protein[1], B3700[2][1], UvrF[2][1], RecF[2][1] , ECK3692, JW3677, uvrF, b3700

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): recF[2], dnaN-recF[2], dnaAN-recF[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

recF

Mnemonic

Recombination

Synonyms

ECK3692, b3700, JW3677, uvrF[1], uvrF

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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

83.59 minutes, 83.59 minutes 

MG1655: 3879244..3878171
<gbrowseImage> name=NC_000913:3878171..3879244 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3841582..3840509
<gbrowseImage> name=NC_012967:3840509..3841582 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3766504..3767577
<gbrowseImage> name=NC_012759:3766504..3767577 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3759194..3760267
<gbrowseImage> name=NC_007779:3759194..3760267 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3976828..3975755
<gbrowseImage> name=NC_010473:3975755..3976828 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

3878174

Edman degradation

PMID:2228960


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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

recF(del) (Keio:JW3677)

deletion

deletion

PMID:16738554

Shigen

recF::Tn5KAN-I-SceI (FB21402)

Insertion at nt 370 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21402

does not contain pKD46

recF::Tn5KAN-I-SceI (FB21403)

Insertion at nt 370 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21403

contains pKD46

recFK36R

K36R

Weakly active

seeded from UniProt:P0A7H0

recF143

CGSC:10318

recF400::Tn5

PMID:2841294

CGSC:67402

recF

deletion

Sensitivity to

decreases sensitivity to Bicyclomycin

PMID:21357484

fig 2

recF349

Growth Phenotype

Mutations show approximately 50% decrease in viability relative to the wild type, table 1.

PMID:8820655

JC18536

recF4101 priA2:kan

Growth Phenotype

Double mutation decreases cell viability from wildtype, table 1.

PMID:8820655

experimental strain: JC18991

recF4115 priA2:kan

Growth Phenotype

Double mutation decreases cell viability, table 1.

PMID:8820655

JC18996

recF143 priA2::kan

Growth Phenotype

Double mutation causes decreased cell viability, table 1.

PMID:8820655

JC18989

recF143

Sensitivity to

mutant shows attenuated UV-inducible SOS expression compared to wildtype, fig 1B.

PMID:8820655


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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

JW3677

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCCCTCACCCGCTTGTTGAT

Primer 2:CCATCCGTTATTTTACCCTTTTC

3C10

Kohara Phage

Genobase

PMID:3038334

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[5]

est. P1 cotransduction: 87% [6]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[5]

est. P1 cotransduction: 9% [6]
Synonyms:zie-296::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:EG10828

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10828

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000819

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948209

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0821

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012095

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

RecF

Synonyms

gap repair protein[1], B3700[2][1], UvrF[2][1], RecF[2][1] , ECK3692, JW3677, uvrF, b3700

Product description

ssDNA and dsDNA binding, ATP binding[2][3];

Component of RecFOR complex[2][3]

Recombination and repair; antagonizes RecX inhibition of RecA filament formation[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: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:0003697

single-stranded DNA binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00365

F

Seeded from EcoCyc (v14.0)

complete

GO:0003697

single-stranded DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003697

single-stranded DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018078

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00365

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001238

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003395

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018078

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:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003395

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00365

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:0000731

DNA synthesis involved in DNA repair

PMID:9108043

IMP: Inferred from Mutant Phenotype

P

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0009411

response to UV

PMID:9108043

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006260

DNA replication

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00365

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0235

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00365

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001238

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018078

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00365

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0009432

SOS response

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00365

P

Seeded from EcoCyc (v14.0)

complete

GO:0009432

SOS response

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0742

P

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

Subunits of RecFOR complex

could be indirect

Protein

groL

PMID:15690043

Experiment(s):EBI-882102, EBI-889518

Protein

groL

PMID:16606699

Experiment(s):EBI-1146517

Protein

spoT

PMID:16606699

Experiment(s):EBI-1146517

Protein

glpD

PMID:16606699

Experiment(s):EBI-1146517

Protein

dnaA

PMID:16606699

Experiment(s):EBI-1146517

Protein

mlc

PMID:16606699

Experiment(s):EBI-1146517

Protein

uidC

PMID:15690043

Experiment(s):EBI-889518

Protein

groL

PMID:19402753

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

Protein

groS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.366927

Protein

uidC

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
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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 

MSLTRLLIRD FRNIETADLA LSPGFNFLVG ANGSGKTSVL EAIYTLGHGR AFRSLQIGRV
IRHEQEAFVL HGRLQGEERE TAIGLTKDKQ GDSKVRIDGT DGHKVAELAH LMPMQLITPE
GFTLLNGGPK YRRAFLDWGC FHNEPGFFTA WSNLKRLLKQ RNAALRQVTR YEQLRPWDKE
LIPLAEQIST WRAEYSAGIA ADMADTCKQF LPEFSLTFSF QRGWEKETEY AEVLERNFER
DRQLTYTAHG PHKADLRIRA DGAPVEDTLS RGQLKLLMCA LRLAQGEFLT RESGRRCLYL
IDDFASELDD ERRGLLASRL KATQSQVFVS AISAEHVIDM SDENSKMFTV EKGKITD
Length

357

Mol. Wt

40.515 kDa

pI

7.2 (calculated)

Extinction coefficient

37,930 - 38,430 (calc based on 7 Y, 5 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

Initiator Methionine

1

Removed

UniProt:P0A7H0

Domain

2..356

PF02463 RecF/RecN/SMC N terminal 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=recF 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:16131568

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948209

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012095

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A7H0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10828

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10828

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948209

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000819

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0821

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 MG1655

149

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

41

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

68

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)

recF

dnaN-recF

dnaAN-recF

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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_000913:3879224..3879264 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:b3700 (EcoliWiki Page)

NCBI GEO profiles for recF

microarray

GenExpDB:b3700 (EcoliWiki Page)

Summary of data for recF 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
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Notes

Accessions Related to recF Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10828

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0821

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3700

EcoGene

EcoGene:EG10828

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000819

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012095

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

  • ENSANGP00000000334 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RECF

From SHIGELLACYC

E. coli O157

RECF

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

Pfam (EcoliWiki Page)

PF02463 RecF/RecN/SMC N terminal domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR18937:SF15

EcoCyc

EcoCyc:EG10828

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10828

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000819

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0821

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012095

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. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 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 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).

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