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Gene |

Product(s) |

Expression|

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Standard Name	ribF
Gene Synonym(s)	ECK0026, b0025, JW0023, yaaC^[1], yaaC
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] , ECK0026, JW0023, yaaC, b0025
Function from GO	<GO_nr />
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
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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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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	ribF
Mnemonic	Riboflavin
Synonyms	ECK0026, b0025, JW0023, yaaC^[1], yaaC
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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	0.46 minutes	MG1655: 21407..22348 <gbrowseImage> name=NC_000913:21407..22348 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 25479..26420 <gbrowseImage> name=NC_012967:25479..26420 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 21407..22348 <gbrowseImage> name=NC_012759:21407..22348 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 21407..22348 <gbrowseImage> name=NC_007779:21407..22348 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 21407..22348 <gbrowseImage> name=NC_010473:21407..22348 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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
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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
JW0023	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGCTGATACGCGGCATACA Primer 2:CCAGCCGGTTTTGTTAGCCCAAA
6H3	Kohara Phage	Genobase	PMID:3038334
22B12	Kohara Phage	Genobase	PMID:3038334
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.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11079	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11079	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001067	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949129	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1071	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000091	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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] , ECK0026, JW0023, yaaC, b0025
Product description	RIBF^[2]; bifunctional riboflavin kinase / FMN adenylyltransferase^[3] Riboflavin kinase and FAD synthase, riboflavin biosynthesis^[4]
EC number (for enzymes)	2.7.1.26^[1] 2.7.7.2^[1]
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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:0003919	FMN adenylyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002606	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003919	FMN adenylyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015864	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003919	FMN adenylyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.7.2	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:0008531	riboflavin kinase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002606	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008531	riboflavin kinase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015865	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008531	riboflavin kinase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.1.26	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009231	riboflavin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002606	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009231	riboflavin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015864	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009231	riboflavin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015865	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	References	Evidence
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
Protein	recD	PMID:19402753	LCMS(ID Probability):99.0
Protein	acrD	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 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, 0 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	References
Domain	184..308	PF01687 Riboflavin kinase	PMID:19920124
Domain	11..168	PF06574 FAD synthetase	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=ribF taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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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:16128019	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000091	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AG40	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11079	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11079	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949129	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001067	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949129	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1071	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	13.22+/-0.09	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.148246546	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	720	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	233	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	435	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)
ribF-ileS-lspA-fkpB-ispH
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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_000913:21387..21427 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: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 Name	Resource Type	Description	Source	Notes
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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.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11079	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1071	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0025
EcoGene	EcoGene:EG11079	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001067	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000091	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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
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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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
Pfam (EcoliWiki Page)	PF01687 Riboflavin kinase
Superfamily (EcoliWiki Page)	SUPERFAMILY:52374
Panther (EcoliWiki Page)	PTHR22749:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:82114
Pfam (EcoliWiki Page)	PF06574 FAD synthetase
EcoCyc	EcoCyc:EG11079	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11079	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001067	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1071	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000091	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^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)
↑ ^2.0 ^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
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^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).

ribF:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to ribF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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