yciS:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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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

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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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<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

28.84 minutes 

MG1655: 1338267..1338575
<gbrowseImage> name=NC_000913:1338267..1338575 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1338615..1338923
<gbrowseImage> name=NC_012967:1338615..1338923 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1229116..1229424
<gbrowseImage> name=NC_012759:1229116..1229424 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1341957..1342265
<gbrowseImage> name=NC_007779:1341957..1342265 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1427663..1427971
<gbrowseImage> name=NC_010473:1427663..1427971 source=DH10B preset=GeneLocation </gbrowseImage>

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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

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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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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<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: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 Notes References Evidence

Protein

gapA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplP

PMID:19402753

LCMS(ID Probability):99.6

Protein

eno

PMID:19402753

LCMS(ID Probability):99.6

Protein

yfiD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.6

Protein

fimA

PMID:19402753

LCMS(ID Probability):99.5

Protein

rplJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753

MALDI(Z-score):22.383920

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753

MALDI(Z-score):23.392908

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

hns

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

ompA

PMID:19402753

MALDI(Z-score):23.915548

Protein

atpA

PMID:19402753

MALDI(Z-score):27.333083

Protein

pgm

PMID:19402753

LCMS(ID Probability):99.6

Protein

hemY

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):39.545073

Protein

ftsH

PMID:19402753

MALDI(Z-score):27.343825

Protein

talB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6

Protein

glpD

PMID:19402753

MALDI(Z-score):22.481683

Protein

atpG

PMID:19402753

MALDI(Z-score):25.445700

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

putA

PMID:19402753

LCMS(ID Probability):99.6

Protein

qmcA

PMID:19402753

MALDI(Z-score):20.564619

Protein

yhcB

PMID:19402753

MALDI(Z-score):22.077756

Protein

hemX

PMID:19402753

LCMS(ID Probability):99.4 MALDI(Z-score):32.931734

Protein

rplL

PMID:19402753

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) [7]


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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 

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

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<motif_map/>

tmhmm.php?gene=yciS&show=pic&.jpg
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

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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: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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Notes

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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

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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<protect>

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

Transcription unit(s)

yciS

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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_000913:1338247..1338287 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: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[8]

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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

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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

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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)

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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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ 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. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  8. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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