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Standard Name	yccA
Gene Synonym(s)	ECK0961, b0970, JW0953^[1], JW0953
Product Desc.	putative carrier/transport protein; substrate or modulator of FtsH-mediated proteolysis^[2]^[3] Membrane-associated protein that binds to FtsH(HflB) and HflKC proteins; mutant YccA stabilizes SecY(Ts); suppression requires HflKC; YccA is a native substrate for the FtsH(HflB) protease^[4]
Product Synonyms(s)	inner membrane protein^[1], B0970^[2]^[1], YccA^[2]^[1] , ECK0961, JW0953, b0970
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yccA^[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	yccA
Mnemonic	Systematic nomenclature
Synonyms	ECK0961, b0970, JW0953^[1], JW0953
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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	22.2 minutes	MG1655: 1030641..1029982 <gbrowseImage> name=NC_000913:1029982..1030641 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1048509..1047850 <gbrowseImage> name=NC_012967:1047850..1048509 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 932950..933609 <gbrowseImage> name=NC_012759:932950..933609 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1031840..1031181 <gbrowseImage> name=NC_007779:1031181..1031840 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1084569..1083910 <gbrowseImage> name=NC_010473:1083910..1084569 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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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)	Reference	Availability
ΔyccA (Keio:JW0953)	deletion	deletion	PMID:16738554	Shigen CGSC8949^[5]
ΔyccA785::kan			PMID:16738554	CGSC:103944
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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
JW0953	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGATCGTATTGTTAGTTCTTC Primer 2:CCATCGCGGCTAGCGAAGCCCAG
9B10	Kohara Phage	Genobase	PMID:3038334
4H9	Kohara Phage	Genobase	PMID:3038334
zcb-3059::Tn10	Linked marker	CAG12094 = CGSC7358^[5]	est. P1 cotransduction: 34% ^[6]
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[5]	est. P1 cotransduction: 27% ^[6]
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc	EcoCyc:EG11113	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11113	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001099	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946016	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1104	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003280	Escherichia coli str. K-12 substr. MG1655
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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	YccA
Synonyms	inner membrane protein^[1], B0970^[2]^[1], YccA^[2]^[1] , ECK0961, JW0953, b0970
Product description	putative carrier/transport protein; substrate or modulator of FtsH-mediated proteolysis^[2]^[3] Membrane-associated protein that binds to FtsH(HflB) and HflKC proteins; mutant YccA stabilizes SecY(Ts); suppression requires HflKC; YccA is a native substrate for the FtsH(HflB) protease^[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: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:IPR006213	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:0016021	integral to membrane	PMID:9636708	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0042981	regulation of apoptosis	PMID:19661432	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0043066	negative regulation of apoptosis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006213	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

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

Compartment	Description	Evidence	Reference/Source
plasma membrane	C-terminus localized in the cytoplasm with 7 predicted transmembrane domains	Daley et al. (2005) ^[7]
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 MDRIVSSSHD RTSLLSTHKV LRNTYFLLSL TLAFSAITAT ASTVLMLPSP GLILTLVGMY GLMFLTYKTA NKPTGIISAF AFTGFLGYIL GPILNTYLSA GMGDVIAMAL GGTALVFFCC SAYVLTTRKD MSFLGGMLMA GIVVVLIGMV ANIFLQLPAL HLAISAVFIL ISSGAILFET SNIIHGGETN YIRATVSLYV SLYNIFVSLL SILGFASRD
Length	219
Mol. Wt	23.364 kDa
pI	9.0 (calculated)
Extinction coefficient	13,410 - 13,660 (calc based on 9 Y, 0 W, and 2 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	19..215	PF01027 Uncharacterised protein family UPF0005		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=yccA 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:16128937	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946016	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003280	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AAC6	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11113	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11113	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946016	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001099	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1104	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 MG1655	8269	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	3556	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	3541	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)
yccA
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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.

Transcription ofyccA is induced >3-fold 5 min after the addition of 0.5 mM CuSO₄ to exponential phase cultures growing in LB medium at 37°C.^[8] Induction was shown to be dependent upon CpxRA.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1030621..1030661 source=MG1655 flip=1 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:b0970 (EcoliWiki Page)	NCBI GEO profiles for yccA
microarray	GenExpDB:b0970 (EcoliWiki Page)	Summary of data for yccA 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 (1030549..1030852) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:C9^[9]
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Notes

Accessions Related to yccA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11113	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1104	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0970
EcoGene	EcoGene:EG11113	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001099	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003280	Escherichia coli str. K-12 substr. MG1655
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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
Apis mellifera	ENSAPMP00000012808 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000024738 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000007331 (score: 1.000; bootstrap: 100%) ENSCAFP00000012362 (score: 0.965)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0013305 (score: 1.000; bootstrap: 71%) FBgn0025692 (score: 0.454) FBgn0038209 (score: 0.347) FBgn0053673 (score: 0.104)	From Inparanoid:20070104
Drosophila pseudoobscura	GA17704-PA (score: 1.000; bootstrap: 100%) GA17693-PA (score: 0.667) GA15801-PA (score: 0.369)	From Inparanoid:20070104
Homo sapiens	ENSP00000267115 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000007839 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000005268 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:99682 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6ZEY6 (score: 1.000; bootstrap: 50%) Q6F387 (score: 0.751) Q94GN3 (score: 0.708) Q6F386 (score: 0.476) Q6ATX8 (score: 0.455) Q6ZEY7 (score: 0.428)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000008396 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000048834 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00010329001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000021541 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YCCA	From SHIGELLACYC
E. coli O157	YCCA	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)	PF01027 Uncharacterised protein family UPF0005
Panther (EcoliWiki Page)	PTHR23291:SF20
PFAM (EcoliWiki Page)	PFAM:PF01027
EcoCyc	EcoCyc:EG11113	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11113	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001099	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1104	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003280	Escherichia coli str. K-12 substr. MG1655
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Notes

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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 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 ^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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
↑ Yamamoto, K & Ishihama, A (2005) Transcriptional response of Escherichia coli to external copper. Mol. Microbiol. 56 215-27 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yccA: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

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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 yccA Expression

Notes

Links

Evolution

Homologs in Other Organisms

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Notes

Families

Notes

Links

References

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