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ribF:On One Page

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Standard Name

ribF

Gene Synonym(s)

ECK0026, b0025, JW0023, yaaC[1]

Product Desc.

RIBF[2]; bifunctional riboflavin kinase / FMN adenylyltransferase[3]

Riboflavin kinase and FAD synthase, riboflavin biosynthesis[4]

Product Synonyms(s)

bifunctional riboflavin kinase and FAD synthetase[1], B0025[2][1], YaaC[2][1], RibF[2][1]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ribF-ileS-lspA-fkpB-ispH[2], ileS-lsp, ileS-lspA-lytB, ribF-ileS-lspA-slpA-lytB

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(ribF)    Textpresso(ribF)

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Notes

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The riboflavin kinase is the N-terminal domain; the FAD synthase is the C-terminal domain. RibF is homologous to and can substitute for the essential B. subtilis RibC. ribF is a non-essential gene. Also known as protein X. Biochemical characterization described in Kitatsuji, K., S. Ishino, S. Teshiba, and M. Arimoto, 1993, Process for producing flavine nucleotides, European patent application: 0 542 240 A2.[4]



Gene

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Nomenclature

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Standard name

ribF

Mnemonic

Riboflavin

Synonyms

ECK0026, b0025, JW0023, yaaC[1]

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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.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

0.46 minutes 

MG1655: 21407..22348
gbrowse_img.php?coord=21407..22348&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 25479..26420
gbrowse_img.php?coord=25479..26420&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 21407..22348
gbrowse_img.php?coord=21407..22348&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 21407..22348
gbrowse_img.php?coord=21407..22348&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 21407..22348
gbrowse_img.php?coord=21407..22348&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW0023

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAGCTGATACGCGGCATACA

Primer 2:CCAGCCGGTTTTGTTAGCCCAAA

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[5]

est. P1 cotransduction: 46% [6]
Synonyms:thr-34::Tn10

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 68% [6]
Synonyms:car-96::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11079

EchoBASE (EcoliWiki Page)

EchoBASE:EB1071

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0025

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0029

EcoGene (EcoliWiki Page)

EcoGene:EG11079

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:RIBF

CGSC (EcoliWiki Page)

CGSC:35833

ASAP (EcoliWikiPage)

ASAP:ABE-0000091


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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

RibF

Synonyms

bifunctional riboflavin kinase and FAD synthetase[1], B0025[2][1], YaaC[2][1], RibF[2][1]

Product description

RIBF[2]; bifunctional riboflavin kinase / FMN adenylyltransferase[3]

Riboflavin kinase and FAD synthase, riboflavin biosynthesis[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.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0003919

FMN adenylyltransferase activity

PMID:9473052

IGI: Inferred from Genetic Interaction

UniProtKB:P54575

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0005515

protein binding

PMID:15690043

IPI: Inferred from Physical Interaction

UniProtKB:P0AFG8

F

Seeded from EcoCyc [8]

complete

GO:0008531

riboflavin kinase activity

PMID:9473052

IGI: Inferred from Genetic Interaction

UniProtKB:P54575

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0009231

riboflavin biosynthetic process

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002606
InterPro:IPR015864
InterPro:IPR015865

P

Seeded from EcoCyc [8]

complete

GO:0008531

riboflavin kinase activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000003

IEA: Inferred from Electronic Annotation

InterPro:IPR002606
InterPro:IPR015865
EC:2.7.1.26

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0003919

FMN adenylyltransferase activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000003

IEA: Inferred from Electronic Annotation

InterPro:IPR002606
InterPro:IPR015864
EC:2.7.7.2

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0003824

catalytic activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0511

F

Seeded from EcoCyc [8]

complete

GO:0016740

transferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc [8]

complete

GO:0016779

nucleotidyltransferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0548

F

Seeded from EcoCyc [8]

complete

GO:0006747

FAD biosynthetic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0009398

FMN biosynthetic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0003919

FMN adenylyltransferase activity

PMID:9473052

IGI

F

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0008531

riboflavin kinase activity

PMID:9473052

IGI

F

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

Protein

phnN

PMID:16606699

Experiment(s):EBI-1135327

Protein

adhE

PMID:16606699

Experiment(s):EBI-1135327

Protein

nadE

PMID:16606699

Experiment(s):EBI-1135327

Protein

rplD

PMID:16606699

Experiment(s):EBI-1135327

Protein

glpD

PMID:16606699

Experiment(s):EBI-1135327

Protein

groL

PMID:16606699

Experiment(s):EBI-1135327

Protein

aceE

PMID:15690043

Experiment(s):EBI-889192

Protein

acrD

PMID:15690043

Experiment(s):EBI-894280

Protein

recD

PMID:15690043

Experiment(s):EBI-894280

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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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.

Sequence

at EcoCyc 

MKLIRGIHNL SQAPQEGCVL TIGNFDGVHR GHRALLQGLQ EEGRKRNLPV MVMLFEPQPL
ELFATDKAPA RLTRLREKLR YLAECGVDYV LCVRFDRRFA ALTAQNFISD LLVKHLRVKF
LAVGDDFRFG AGREGDFLLL QKAGMEYGFD ITSTQTFCEG GVRISSTAVR QALADDNLAL
AESLLGHPFA ISGRVVHGDE LGRTIGFPTA NVPLRRQVSP VKGVYAVEVL GLGEKPLPGV
ANIGTRPTVA GIRQQLEVHL LDVAMDLYGR HIQVVLRKKI RNEQRFASLD ELKAQIARDE
LTAREFFGLT KPA
Length

313

Mol. Wt

34.734 kDa

pI

9.6 (calculated)

Extinction coefficient

7,450 - 7,950 (calc based on 5 Y, 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.

TypeResiduesDescriptionNotesReferences
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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:RIBF-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0AG40

PFAM (EcoliWiki Page)

PFAM:PF06574

RefSeq (EcoliWiki Page)

RefSeq:NP_414566


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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)

ribF-ileS-lspA-fkpB-ispH

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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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gbrowse_img.php?coord=21387..21427&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.png
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

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 NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b0025 (EcoliWiki Page)

NCBI GEO profiles for ribF

microarray

GenExpDB:b0025 (EcoliWiki Page)

Summary of data for ribF 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to ribF Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11079

EchoBASE (EcoliWiki Page)

EchoBASE:EB1071

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0025

EcoGene (EcoliWiki Page)

EcoGene:EG11079


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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.

OrganismHomologs (Statistics)Comments

Arabidopsis thaliana

  • AT5G08340 (score: 1.000; bootstrap: 100%)
  • AT5G23330 (score: 0.617)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00030179 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00011224 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000012931 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RIBF

From SHIGELLACYC

E. coli O157

RIBF

From ECOO157CYC

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Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF06574


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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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 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 3.4 3.5 3.6 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 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. ↑ 7.0 7.1 7.2 7.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 8.4 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70

Categories

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