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Standard Name	ygfM
Gene Synonym(s)	ECK2876, b2880, JW2848^[1], JW2848
Product Desc.	predicted oxidoreductase; possible component of selenate reductase^[2]^[3]; Component of putative selenate reductase^[3] Function unknown^[4]
Product Synonyms(s)	predicted oxidoreductase^[1], B2880^[2]^[1], YgfM^[2]^[1] , ECK2876, JW2848, b2880
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ygfM^[2]
Regulation/Activity
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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	ygfM
Mnemonic	Systematic nomenclature
Synonyms	ECK2876, b2880, JW2848^[1], JW2848
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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	65.06 minutes	MG1655: 3018562..3019341 <gbrowseImage> name=NC_000913:3018562..3019341 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2906294..2907073 <gbrowseImage> name=NC_012967:2906294..2907073 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2905710..2906489 <gbrowseImage> name=NC_012759:2905710..2906489 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3019196..3019975 <gbrowseImage> name=NC_007779:3019196..3019975 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3112432..3113211 <gbrowseImage> name=NC_010473:3112432..3113211 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
ΔygfM (Keio:JW2848)	deletion	deletion			PMID:16738554	Shigen
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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
JW2848	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATTGAACAATTTTTCAGGCC Primer 2:CCTACGGCTTCCTCCCCAGCCTG
6A1	Kohara Phage	Genobase	PMID:3038334
5B4	Kohara Phage	Genobase	PMID:3038334
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[5]	est. P1 cotransduction: 2% ^[6]
speA210::Tn10	Linked marker	CAG12168 = CGSC7431^[5]	est. P1 cotransduction: 2% ^[6] Synonyms:zgd-210::Tn10, zgf-210::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:G7499	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13063	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004062	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949071	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2875	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009456	Escherichia coli str. K-12 substr. MG1655
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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	YgfM
Synonyms	predicted oxidoreductase^[1], B2880^[2]^[1], YgfM^[2]^[1] , ECK2876, JW2848, b2880
Product description	predicted oxidoreductase; possible component of selenate reductase^[2]^[3]; Component of putative selenate reductase^[3] Function unknown^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016166	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016169	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002346	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016166	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016169	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002346	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016169	P	Seeded from EcoCyc (v14.0)	complete
	GO:0071949	FAD binding	PMID:12480890	IC: Inferred by Curator		F		Missing: with/from
	GO:0003674	molecular function	PMID:12480890	ND: No biological Data available		F		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 putative selenate reductase	could be indirect
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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 MIEQFFRPDS VEQALELKRR YQDEAVWFAG GSKLNATPTR TDKKIAISLQ DLELDWVDWD NGALRIGAMS RLQPLRDARF IPAALREALG FVYSRHVRNQ STIGGEIAAR QEESVLLPVL LALDAELVFG NGETLSIEDY LACPCDRLLT EIIIKDPYRT CATRKISRSQ AGLTVVTAAV AMTDHDGMRI ALDGVASKAL RLHDVEKQNL EGNALEQAVA NAIFPQEDLR GSVAYKRYIT GVLVADLYAD CQQAGEEAV
Length	259
Mol. Wt	28.649 kDa
pI	4.9 (calculated)
Extinction coefficient	26,930 - 27,430 (calc based on 7 Y, 3 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	161..251	PF03450 CO dehydrogenase flavoprotein C-terminal domain	PMID:19920124
Domain	1..156	PF00941 FAD binding domain in molybdopterin dehydrogenase	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=ygfM 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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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:16130782	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949071	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009456	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P64557	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7499	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13063	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949071	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004062	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2875	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	11^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	8	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	5^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)
ygfM
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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_000913:3018542..3018582 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:b2880 (EcoliWiki Page)	NCBI GEO profiles for ygfM
microarray	GenExpDB:b2880 (EcoliWiki Page)	Summary of data for ygfM 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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Accessions Related to ygfM Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7499	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2875	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2880
EcoGene	EcoGene:EG13063	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004062	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009456	Escherichia coli str. K-12 substr. MG1655
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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
Anopheles gambiae	ENSANGP00000027634 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	Z4219	From ECOO157CYC
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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)	PF03450 CO dehydrogenase flavoprotein C-terminal domain
Pfam (EcoliWiki Page)	PF00941 FAD binding domain in molybdopterin dehydrogenase
Panther (EcoliWiki Page)	PTHR11908:SF19
Superfamily (EcoliWiki Page)	SUPERFAMILY:55447
Superfamily (EcoliWiki Page)	SUPERFAMILY:56176
EcoCyc	EcoCyc:G7499	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13063	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004062	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2875	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009456	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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
↑ ^4.0 ^4.1 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).

ygfM:On One Page

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Notes

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 ygfM Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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