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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	yidC
Gene Synonym(s)	ECK3698, b3705, JW3683^[1], JW3683, oxaA
Product Desc.	inner-membrane protein insertion factor^[2]^[3]; Component of SecD-SecF-Yajc-YidC Secretion Complex^[2]^[3]; Sec Protein Secretion Complex^[2]^[3] Inner membrane protein (IMP) integration factor; binds TM regions of nascent IMPs; required for Sec-independent IMP integration; associated with the Sec translocase^[4]
Product Synonyms(s)	cytoplasmic insertase into membrane protein, Sec system^[1], B3705^[2]^[1], YidC^[2]^[1] , ECK3698, JW3683, oxaA, b3705
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s):
Regulation/Activity
Quick Links
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Notes

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yidC is an essential gene. YidC depletion activates the Psp response. YidC is required for proper membrane insertion of AtpE and CyoA.^[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	yidC
Mnemonic	Systematic nomenclature
Synonyms	ECK3698, b3705, JW3683^[1], JW3683, oxaA
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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	83.69 minutes	MG1655: 3883099..3884745 <gbrowseImage> name=NC_000913:3883099..3884745 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3845437..3847083 <gbrowseImage> name=NC_012967:3845437..3847083 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3771432..3773078 <gbrowseImage> name=NC_012759:3771432..3773078 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3755339..3753693 <gbrowseImage> name=NC_007779:3753693..3755339 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3980683..3982329 <gbrowseImage> name=NC_010473:3980683..3982329 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
JW3683	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGATTCGCAACGCAATCTTTT Primer 2:CCGGATTTTTTCTTCTCGCGGCT
3F11	Kohara Phage	Genobase	PMID:3038334
3C10	Kohara Phage	Genobase	PMID:3038334
zid-501::Tn10	Linked marker	CAG18499 = CGSC7458^[5]	est. P1 cotransduction: 74% ^[6]
rbsD296::Tn10	Linked marker	CAG18501 = CGSC7460^[5]	est. P1 cotransduction: 12% ^[6] Synonyms:zie-296::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:EG11197	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11197	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001178	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948214	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1183	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012120	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	YidC
Synonyms	cytoplasmic insertase into membrane protein, Sec system^[1], B3705^[2]^[1], YidC^[2]^[1] , ECK3698, JW3683, oxaA, b3705
Product description	inner-membrane protein insertion factor^[2]^[3]; Component of SecD-SecF-Yajc-YidC Secretion Complex^[2]^[3]; Sec Protein Secretion Complex^[2]^[3] Inner membrane protein (IMP) integration factor; binds TM regions of nascent IMPs; required for Sec-independent IMP integration; associated with the Sec translocase^[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:0032977	membrane insertase activity	PMID:10949305	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0016021	integral to membrane	PMID:10675323	IDA: Inferred from Direct Assay		C		complete
	GO:0051205	protein insertion into membrane	PMID:10949305	IDA: Inferred from Direct Assay		P		complete
	GO:0005515	protein binding	PMID:10675323	IPI: Inferred from Physical Interaction	UniProtKB:P0AG96	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:10675323	IPI: Inferred from Physical Interaction	UniProtKB:P0AGA2\|UniProtKB:P0AG96\|UniProtKB:P0AG99	F	YidC co-immunoprecipitates with the SecYEG complex.	complete
	GO:0005515	protein binding	PMID:10675323	IPI: Inferred from Physical Interaction	UniProtKB:P0AG99	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:10675323	IPI: Inferred from Physical Interaction	UniProtKB:P0AGA2	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01810	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001708	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013308	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019998	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020001	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0051205	protein insertion into membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001708	P	Seeded from EcoCyc (v14.0)	complete
	GO:0051205	protein insertion into membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013308	P	Seeded from EcoCyc (v14.0)	complete
	GO:0051205	protein insertion into membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019998	P	Seeded from EcoCyc (v14.0)	complete
	GO:0051205	protein insertion into membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020001	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
Protein	Subunits of SecD-SecF-Yajc-YidC Secretion Complex	could be indirect
Protein	Subunits of Sec Protein Secretion Complex	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
plasma membrane			From EcoCyc^[3]
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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 MDSQRNLLVI ALLFVSFMIW QAWEQDKNPQ PQAQQTTQTT TTAAGSAADQ GVPASGQGKL ISVKTDVLDL TINTRGGDVE QALLPAYPKE LNSTQPFQLL ETSPQFIYQA QSGLTGRDGP DNPANGPRPL YNVEKDAYVL AEGQNELQVP MTYTDAAGNT FTKTFVLKRG DYAVNVNYNV QNAGEKPLEI SSFGQLKQSI TLPPHLDTGS SNFALHTFRG AAYSTPDEKY EKYKFDTIAD NENLNISSKG GWVAMLQQYF ATAWIPHNDG TNNFYTANLG NGIAAIGYKS QPVLVQPGQT GAMNSTLWVG PEIQDKMAAV APHLDLTVDY GWLWFISQPL FKLLKWIHSF VGNWGFSIII ITFIVRGIMY PLTKAQYTSM AKMRMLQPKI QAMRERLGDD KQRISQEMMA LYKAEKVNPL GGCFPLLIQM PIFLALYYML MGSVELRQAP FALWIHDLSA QDPYYILPIL MGVTMFFIQK MSPTTVTDPM QQKIMTFMPV IFTVFFLWFP SGLVLYYIVS NLVTIIQQQL IYRGLEKRGL HSREKKKS
Length	548
Mol. Wt	61.527 kDa
pI	8.2 (calculated)
Extinction coefficient	96,260 - 96,385 (calc based on 24 Y, 11 W, and 1 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	352..536	PF02096 60Kd inner membrane protein		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=yidC taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

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Notes

Gene Product Resources

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

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:16131573	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948214	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012120	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P25714	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11197	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11197	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948214	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001178	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1183	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	Reference(s)
Protein	E. coli K-12 MC4100	7.04E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	8807	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	1094	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	2589	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)
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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_000913:3883079..3883119 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

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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:b3705 (EcoliWiki Page)	NCBI GEO profiles for yidC
microarray	GenExpDB:b3705 (EcoliWiki Page)	Summary of data for yidC 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
	GFP Fusion	Intergenic region (3882402..3882756) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ18; Well:E12^[7]
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Notes

Accessions Related to yidC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11197	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1183	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3705
EcoGene	EcoGene:EG11197	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001178	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012120	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
Anopheles gambiae	ENSANGP00000024931 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G62050 (score: 1.000; bootstrap: 100%) AT2G46470 (score: 0.351)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000007094 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00039383 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00007215 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000015718 (score: 1.000; bootstrap: 100%) ENSCINP00000009247 (score: 0.065)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0186234 (score: 1.000; bootstrap: 100%) DDB0204056 (score: 0.072)	From Inparanoid:20070104
Homo sapiens	ENSP00000295890 (score: 1.000; bootstrap: 100%) ENSP00000285848 (score: 0.070)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000001064 (score: 1.000; bootstrap: 100%) ENSMMUP00000000546 (score: 0.077)	From Inparanoid:20070104
Mus musculus	MGI:2448532 (score: 1.000; bootstrap: 100%) MGI:1916339 (score: 0.061)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000027756 (score: 1.000; bootstrap: 100%) ENSPTRP00000039136 (score: 0.070)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000004074 (score: 1.000; bootstrap: 100%) ENSRNOP00000013246 (score: 0.068)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000047859 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YIDC	From SHIGELLACYC
E. coli O157	YIDC	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)	PF02096 60Kd inner membrane protein
Panther (EcoliWiki Page)	PTHR12428:SF11
EcoCyc	EcoCyc:EG11197	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11197	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001178	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1183	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012120	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 ^2.7 ^2.8 ^2.9 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 ^3.4 ^3.5 ^3.6 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yidC: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 yidC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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