{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	ydiR
Gene Synonym(s)	ECK1696, b1698, JW1688^[1], JW1688
Product Desc.	putative subunit of YdiQ-YdiR flavoprotein^[2]^[3] Function unknown^[4]
Product Synonyms(s)	predicted electron transfer flavoprotein, FAD-binding^[1], B1698^[2]^[1], YdiR^[2]^[1] , ECK1696, JW1688, b1698
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydiQRST-fadK^[2], ydiQRSTD
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

AFMB Structural Genomics target No. 90 (http://afmb.cnrs-mrs.fr/article171.html).^[4]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	ydiR
Mnemonic	Systematic nomenclature
Synonyms	ECK1696, b1698, JW1688^[1], JW1688
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	38.33 minutes	MG1655: 1778425..1779363 <gbrowseImage> name=NC_000913:1778425..1779363 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1757669..1758607 <gbrowseImage> name=NC_012967:1757669..1758607 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1670484..1671422 <gbrowseImage> name=NC_012759:1670484..1671422 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1782115..1783053 <gbrowseImage> name=NC_007779:1782115..1783053 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1868996..1869934 <gbrowseImage> name=NC_010473:1868996..1869934 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

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
ΔydiR (Keio:JW1688)	deletion	deletion			PMID:16738554	Shigen CGSC9429^[5]
ΔydiR::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
ΔydiR772::kan					PMID:16738554	CGSC:104332
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

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

Resource	Resource Type	Source	Notes/Reference
JW1688	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTCAATTAAACAGCGTCTG Primer 2:CCGCGGCTCAACTGGCTAATCAG
8G8	Kohara Phage	Genobase	PMID:3038334
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: 95% ^[6] Synonyms:zdh-925::Tn10
zdj-276::Tn10	Linked marker	CAG18464 = CGSC7387^[5]	est. P1 cotransduction: 7% ^[6] Synonyms:zdi-276::Tn10
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6921	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13977	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003509	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945688	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3734	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005668	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	YdiR
Synonyms	predicted electron transfer flavoprotein, FAD-binding^[1], B1698^[2]^[1], YdiR^[2]^[1] , ECK1696, JW1688, b1698
Product description	putative subunit of YdiQ-YdiR flavoprotein^[2]^[3] Function unknown^[4]
EC number (for enzymes)
edit table

Notes

Function

[back to top]

<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:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001308	F	Seeded from EcoCyc (v14.0)	complete
	GO:0022900	electron transport chain	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0249	P	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001308	F	Seeded from EcoCyc (v14.0)	complete
edit table

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
edit table

</protect>

Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MSQLNSVWVF SDNPERYAEL FGGAQQWGQQ VYAIVQNTDQ AQAVMPYGPK CLYVLAQNDA LQRTENYAES IAALLKDKHP AMLLLAATKR GKALAARLSV QLNAALVNDA TAVDIVDGHI CAEHRMYGGL AFAQEKINSP LAIITLAPGV QEPCTSDTSH QCPTETVPYV APRHEILCRE RRAKAASSVD LSKAKRVVGV GRGLAAQDDL KMVHELAAVL NAEVGCSRPI AEGENWMERE RYIGVSGVLL KSDLYLTLGI SGQIQHMVGG NGAKVIVAIN KDKNAPIFNY ADYGLVGDIY KVVPALISQL SR
Length	312
Mol. Wt	33.769 kDa
pI	7.2 (calculated)
Extinction coefficient	34,380 - 35,130 (calc based on 12 Y, 3 W, and 6 C residues)
edit table

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	188..274	PF00766 Electron transfer flavoprotein FAD-binding domain	PMID:19920124
Domain	6..153	PF01012 Electron transfer flavoprotein domain	PMID:19920124
edit table

<motif_map/>

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

Structures

<beststructure> gene=ydiR taxon=562,83333 </beststructure>

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16129654	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945688	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005668	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77378	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6921	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13977	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945688	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003509	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3734	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	13^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	18	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	4^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
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
ydiQRST-fadK
edit table

Figure courtesy of RegulonDB

</protect>

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

[back to top]

<protect><gbrowseImage> name=NC_000913:1778405..1778445 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

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

Type	Reference	Notes
microarray	GEO Profiles:b1698 (EcoliWiki Page)	NCBI GEO profiles for ydiR
microarray	GenExpDB:b1698 (EcoliWiki Page)	Summary of data for ydiR from multiple microarray studies
edit table

Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
edit table

Notes

Accessions Related to ydiR Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6921	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3734	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1698
EcoGene	EcoGene:EG13977	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003509	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005668	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000014287 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000035078 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G50940 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00023711 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00009187 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000026809 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000013153 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-CDNA-040425-287 (score: 1.000; bootstrap: 100%) ZDB-GENE-030131-4449 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040625-227 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0189158 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0010516 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA21463-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000004621 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000267950 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000014462 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000014996 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:106092 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q75LJ3 (score: 1.000; bootstrap: 100%) Q75LJ2 (score: 0.509)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000012506 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000020544 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YPR004C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC27D76 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000138121 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00015947001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000019967 (score: 1.000; bootstrap: 100%) ENSXETP00000009481 (score: 0.618) ENSXETP00000033499 (score: 0.380)	From Inparanoid:20070104
Shigella flexneri	YDIR	From SHIGELLACYC
E. coli O157	YDIR	From ECOO157CYC
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00766 Electron transfer flavoprotein FAD-binding domain
Pfam (EcoliWiki Page)	PF01012 Electron transfer flavoprotein domain
Panther (EcoliWiki Page)	PTHR10909:SF155
Superfamily (EcoliWiki Page)	SUPERFAMILY:52402
Superfamily (EcoliWiki Page)	SUPERFAMILY:52467
EcoCyc	EcoCyc:G6921	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13977	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003509	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3734	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005668	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

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 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 ^5.2 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).

ydiR:On One Page

Quickview

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 ydiR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search