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Standard Name	rutF
Gene Synonym(s)	ycdH, ECK0998, b1007, JW5138^[1]^[2], JW5138
Product Desc.	predicted flavin reductase^[2]^[3] Gene in rut operon for pyrimidine nitrogen catabolism; putative flavin:NADH reductase^[4]
Product Synonyms(s)	predicted oxidoreductase, flavin:NADH component^[1], YcdH^[2]^[1], B1007^[2]^[1], RutF^[2]^[1] , ECK0998, JW5138, ycdH, b1007
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rutABCDEFG^[2]
Regulation/Activity
Quick Links
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Notes

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NtrC regulon. The rut operon is required for the utilization of thymidine, uridine and cytidine as nitrogen sources at 37C, but not at room temperature.^[4]

Gene

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Nomenclature

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Standard name	rutF
Mnemonic	PyRimidine UTilization
Synonyms	ycdH, ECK0998, b1007, JW5138^[1]^[2], JW5138
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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	23.04 minutes	MG1655: 1069577..1069083 <gbrowseImage> name=NC_000913:1069083..1069577 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1086144..1086638 <gbrowseImage> name=NC_012967:1086144..1086638 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 972051..972545 <gbrowseImage> name=NC_012759:972051..972545 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1070776..1070282 <gbrowseImage> name=NC_007779:1070282..1070776 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1123505..1123011 <gbrowseImage> name=NC_010473:1123011..1123505 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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
5A12	Kohara Phage	Genobase	PMID:3038334
7B5	Kohara Phage	Genobase	PMID:3038334
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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:G6518	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13854	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003118	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946594	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3614	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003403	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	YcdH
Synonyms	predicted oxidoreductase, flavin:NADH component^[1], YcdH^[2]^[1], B1007^[2]^[1], RutF^[2]^[1] , ECK0998, JW5138, ycdH, b1007
Product description	predicted flavin reductase^[2]^[3] Gene in rut operon for pyrimidine nitrogen catabolism; putative flavin:NADH reductase^[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:0010181	FMN binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012349	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	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
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Notes

Localization

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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 MSCMGAAVNI ITTDGPAGRA GFTASAVCSV TDTPPTLLVC LNRGASVWPA FNENRTLCVN TLSAGQEPLS NLFGGKTPME HRFAAARWQT GVTGCPQLEE ALVSFDCRIS QVVSVGTHDI LFCAIEAIHR HTTPYGLVWF DRSYHALMRP AC
Length	152
Mol. Wt	16.328 kDa
pI	7.0 (calculated)
Extinction coefficient	19,480 - 20,480 (calc based on 2 Y, 3 W, and 8 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	13..160	PF01613 Flavin reductase like domain		PMID:19920124^[5]
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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=rutF taxon=562,83333 </beststructure>

Models

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Structure figures

Notes

Gene Product Resources

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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:90111202	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946594	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003403	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75893	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6518	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13854	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946594	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003118	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3614	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	E. coli K-12 MG1655	9^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	23	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	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
rutABCDEFG
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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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<gbrowseImage> name=NC_000913:1069557..1069597 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

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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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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:b1007 (EcoliWiki Page)	NCBI GEO profiles for rutF
microarray	GenExpDB:b1007 (EcoliWiki Page)	Summary of data for rutF 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 rutF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6518	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3614	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1007
EcoGene	EcoGene:EG13854	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003118	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003403	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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Organism	Homologs (Statistics)	Comments
Apis mellifera	ENSAPMP00000028433 (score: 1.000; bootstrap: 100%) ENSAPMP00000034328 (score: 0.478)	From Inparanoid:20070104
Shigella flexneri	S1080	From SHIGELLACYC
E. coli O157	Z1506	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)	PF01613 Flavin reductase like domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:50475
EcoCyc	EcoCyc:G6518	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13854	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003118	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3614	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003403	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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.
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

rutF: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 rutF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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