fimB: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

fimB

Gene Synonym(s)

ECK4303, b4312, JW4275, pil[1]

Product Desc.

regulator for fimA[2][3]

Site-specific recombinase, fimA promoter inversion; mediates flagellar phase switching, along with FimE[4]

Product Synonyms(s)

tyrosine recombinase/inversion of on/off regulator of fimA[1], B4312[2][1], Pil[2][1], FimB[2][1] , ECK4303, JW4275, b4312

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): fimB[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

fimB

Mnemonic

Fimbriae

Synonyms

ECK4303, b4312, JW4275, pil[1]

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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

97.83 minutes 

MG1655: 4538980..4539582
<gbrowseImage> name=NC_000913:4538980..4539582 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4545637..4546239
<gbrowseImage> name=NC_007779:4545637..4546239 source=W3110 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

fimB(del) (Keio:JW4275)

deletion

deletion

PMID:16738554

Shigen

CGSC11063[5]

fimB780(del)::kan

PMID:16738554

CGSC:100866


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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

JW4275

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAGAATAAGGCTGATAACAA

Primer 2:CCTAAAACAGCGTGACGCTGTCG

19H10

Kohara Phage

Genobase

PMID:3038334

3F1

Kohara Phage

Genobase

PMID:3038334

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[5]

est. P1 cotransduction: % [6]
Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[5]

est. P1 cotransduction: 7% [6]
Synonyms:zjj-202::Tn10, zji-202::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:EG10309

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10309

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000303

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948832

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0305

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014141

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

FimB

Synonyms

tyrosine recombinase/inversion of on/off regulator of fimA[1], B4312[2][1], Pil[2][1], FimB[2][1] , ECK4303, JW4275, b4312

Product description

regulator for fimA[2][3]

Site-specific recombinase, fimA promoter inversion; mediates flagellar phase switching, along with FimE[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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002104

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011010

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013762

F

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002104

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013762

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0233

P

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0015074

DNA integration

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002104

P

Seeded from EcoCyc (v14.0)

complete

GO:0015074

DNA integration

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013762

P

Seeded from EcoCyc (v14.0)

complete

GO:0015074

DNA integration

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0229

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:11967071

IEP: Inferred from Expression Pattern

P

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

aceF

PMID:15690043

Experiment(s):EBI-887941

Protein

rplB

PMID:15690043

Experiment(s):EBI-887941

Protein

rpsC

PMID:15690043

Experiment(s):EBI-887941, EBI-891005

Protein

rpsD

PMID:15690043

Experiment(s):EBI-887941

Protein

rpsG

PMID:15690043

Experiment(s):EBI-887941, EBI-891005

Protein

rplC

PMID:15690043

Experiment(s):EBI-891005

Protein

rplM

PMID:15690043

Experiment(s):EBI-891005

Protein

rplS

PMID:15690043

Experiment(s):EBI-891005

Protein

rplU

PMID:15690043

Experiment(s):EBI-891005

Protein

rplV

PMID:15690043

Experiment(s):EBI-891005

Protein

rplX

PMID:15690043

Experiment(s):EBI-891005

Protein

rpmB

PMID:15690043

Experiment(s):EBI-891005

Protein

rpsE

PMID:15690043

Experiment(s):EBI-891005

Protein

rpsF

PMID:15690043

Experiment(s):EBI-891005

Protein

rpsH

PMID:15690043

Experiment(s):EBI-891005

Protein

rpsN

PMID:15690043

Experiment(s):EBI-891005

Protein

rpsP

PMID:15690043

Experiment(s):EBI-891005

Protein

rpsR

PMID:15690043

Experiment(s):EBI-891005

Protein

rpsT

PMID:15690043

Experiment(s):EBI-891005

Protein

rplQ

PMID:16606699

Experiment(s):EBI-1147856

Protein

yciH

PMID:16606699

Experiment(s):EBI-1147856

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1147856

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.5

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsH

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753

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

Protein

atpA

PMID:19402753

MALDI(Z-score):24.077980

Protein

yedR

PMID:19402753

LCMS(ID Probability):95.6

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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 

MKNKADNKKR NFLTHSEIES LLKAANTGPH AARNYCLTLL CFIHGFRASE ICRLRISDID
LKAKCIYIHR LKKGFSTTHP LLNKEVQALK NWLSIRTSYP HAESEWVFLS RKGNPLSRQQ
FYHIISTSGG NAGLSLEIHP HMLRHSCGFA LANMGIDTRL IQDYLGHRNI RHTVWYTASN
AGRFYGIWDR ARGRQRHAVL
Length

200

Mol. Wt

22.994 kDa

pI

10.5 (calculated)

Extinction coefficient

32,430 - 33,055 (calc based on 7 Y, 4 W, and 5 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

11..183

PF00589 Phage integrase 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=fimB 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:16132133

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948832

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014141

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ADH5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10309

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10309

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948832

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000303

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0305

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Ecoli K-12

3.274+/-0.067

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.025747508

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

422

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

394

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

407

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)

fimB

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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_000913:4538960..4539000 source=MG1655 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:b4312 (EcoliWiki Page)

NCBI GEO profiles for fimB

microarray

GenExpDB:b4312 (EcoliWiki Page)

Summary of data for fimB 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 fimB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10309

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0305

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4312

EcoGene

EcoGene:EG10309

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000303

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014141

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

Shigella flexneri

FIMB

From SHIGELLACYC

E. coli O157

FIMB

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:56349

Pfam (EcoliWiki Page)

PF00589 Phage integrase family

EcoCyc

EcoCyc:EG10309

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10309

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000303

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0305

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014141

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 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).

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