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Standard Name	yciS
Gene Synonym(s)	ECK1274, b1279, JW1271^[1], JW1271
Product Desc.	conserved inner membrane protein^[2]^[3] Inner membrane protein, function unknown^[4]
Product Synonyms(s)	conserved inner membrane protein^[1], B1279^[2]^[1], YciS^[2]^[1] , ECK1274, JW1271, b1279
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yciS^[2]
Regulation/Activity
Quick Links
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Notes

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YciS is predicted to have two TM segments; the first segment may be erroneously predicted to be a type II signal peptide prediction.^[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	yciS
Mnemonic	Systematic nomenclature
Synonyms	ECK1274, b1279, JW1271^[1], JW1271
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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	28.84 minutes	MG1655: 1338267..1338575 <gbrowseImage> name=NC_000913:1338267..1338575 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1338615..1338923 <gbrowseImage> name=NC_012967:1338615..1338923 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1229116..1229424 <gbrowseImage> name=NC_012759:1229116..1229424 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1341957..1342265 <gbrowseImage> name=NC_007779:1341957..1342265 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1427663..1427971 <gbrowseImage> name=NC_010473:1427663..1427971 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)	Reference	Availability
ΔyciS (Keio:JW1271)	deletion	deletion	PMID:16738554	Shigen CGSC9143^[5]
ΔyciS787::kan			PMID:16738554	CGSC:104074
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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
JW1271	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAATATTTACTCATTTTCTT Primer 2:CCTTCCTTCGCCGCTGACGAGTG
18B6	Kohara Phage	Genobase	PMID:3038334
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[5]	est. P1 cotransduction: 47% ^[6] Synonyms:trpB83::Tn10
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[5]	est. P1 cotransduction: 30% ^[6] Synonyms:zci-233::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:G6637	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13904	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003232	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944936	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3663	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004298	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	YciS
Synonyms	conserved inner membrane protein^[1], B1279^[2]^[1], YciS^[2]^[1] , ECK1274, JW1271, b1279
Product description	conserved inner membrane protein^[2]^[3] Inner membrane protein, function unknown^[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: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:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	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
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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	References	Evidence
Protein	gapA	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpsR	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpsP	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rplP	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	eno	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	yfiD	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpsJ	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rplE	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	fimA	PMID:19402753^[7]	LCMS(ID Probability):99.5
Protein	rplJ	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpmB	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpmG	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpmC	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpsC	PMID:19402753^[7]	MALDI(Z-score):22.383920
Protein	rpsN	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	tufB	PMID:19402753^[7]	MALDI(Z-score):23.392908
Protein	hupA	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	hns	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rplI	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rplA	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rplX	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	ompA	PMID:19402753^[7]	MALDI(Z-score):23.915548
Protein	atpA	PMID:19402753^[7]	MALDI(Z-score):27.333083
Protein	pgm	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	hemY	PMID:19402753^[7]	LCMS(ID Probability):99.6 MALDI(Z-score):39.545073
Protein	ftsH	PMID:19402753^[7]	MALDI(Z-score):27.343825
Protein	talB	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rplD	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	glpD	PMID:19402753^[7]	MALDI(Z-score):22.481683
Protein	atpG	PMID:19402753^[7]	MALDI(Z-score):25.445700
Protein	rplW	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	putA	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	qmcA	PMID:19402753^[7]	MALDI(Z-score):20.564619
Protein	yhcB	PMID:19402753^[7]	MALDI(Z-score):22.077756
Protein	hemX	PMID:19402753^[7]	LCMS(ID Probability):99.4 MALDI(Z-score):32.931734
Protein	rplL	PMID:19402753^[7]	LCMS(ID Probability):99.6
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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	C-terminus localized in the cytoplasm with 2 predicted transmembrane domains	Daley et al. (2005) ^[8]
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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 MKYLLIFLLV LAIFVISVTL GAQNDQQVTF NYLLAQGEYR ISTLLAVLFA AGFAIGWLIC GLFWLRVRVS LARAERKIKR LENQLSPATD VAVVPHSSAA KE
Length	102
Mol. Wt	11.351 kDa
pI	10.0 (calculated)
Extinction coefficient	15,470 - 15,595 (calc based on 3 Y, 2 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	10..89	PF06305 Protein of unknown function (DUF1049)		PMID:19920124^[9]
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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=yciS taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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:16129240	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944936	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004298	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACV4	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6637	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13904	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944936	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003232	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3663	Escherichia coli str. K-12 substr. MG1655
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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	702	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	351	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	370	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)
yciS
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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_000913:1338247..1338287 source=MG1655 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

</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

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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:b1279 (EcoliWiki Page)	NCBI GEO profiles for yciS
microarray	GenExpDB:b1279 (EcoliWiki Page)	Summary of data for yciS 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 (1338045..1338311) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ14; Well:F6^[10]
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Notes

Accessions Related to yciS Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6637	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3663	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1279
EcoGene	EcoGene:EG13904	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003232	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004298	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
Shigella flexneri	YCIS	From SHIGELLACYC
E. coli O157	YCIS	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)	PF06305 Protein of unknown function (DUF1049)
EcoCyc	EcoCyc:G6637	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13904	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003232	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3663	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004298	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 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).
↑ ^7.00 ^7.01 ^7.02 ^7.03 ^7.04 ^7.05 ^7.06 ^7.07 ^7.08 ^7.09 ^7.10 ^7.11 ^7.12 ^7.13 ^7.14 ^7.15 ^7.16 ^7.17 ^7.18 ^7.19 ^7.20 ^7.21 ^7.22 ^7.23 ^7.24 ^7.25 ^7.26 ^7.27 ^7.28 ^7.29 ^7.30 ^7.31 ^7.32 ^7.33 ^7.34 ^7.35 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yciS: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 yciS Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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