rpsF: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

rpsF

Gene Synonym(s)

ECK4196, b4200, JW4158, sdgH[1], sdgH

Product Desc.

30S ribosomal subunit protein S6[2][3];

Component of 30S ribosomal subunit[2][3]; ribosome[2][3]

30S ribosomal subunit protein S6; suppressor of dnaG-Ts[4]

Product Synonyms(s)

30S ribosomal subunit protein S6[1], B4200[2][1], SdgH[2][1], RpsF[2][1] , ECK4196, JW4158, sdgH, b4200

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rpsF-priB-rpsR-rplI[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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RpsF is modified posttranslationally by RimK, which adds four glutamic acid residues to the RpsF C-terminus.[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

rpsF

Mnemonic

Ribosomal protein, small

Synonyms

ECK4196, b4200, JW4158, sdgH[1], sdgH

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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

95.33 minutes, 95.33 minutes 

MG1655: 4423141..4423536
<gbrowseImage> name=NC_000913:4423141..4423536 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4403273..4403668
<gbrowseImage> name=NC_012967:4403273..4403668 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4361876..4362271
<gbrowseImage> name=NC_012759:4361876..4362271 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4429798..4430193
<gbrowseImage> name=NC_007779:4429798..4430193 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4523503..4523898
<gbrowseImage> name=NC_010473:4523503..4523898 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

Coding Start (SO:0000323)

MG1655

4423141

Edman degradation

PMID:328274
PMID:8740179
PMID:9298646
PMID:9600841
PMID:9740056
PMID:9868784

Coding Start (SO:0000323)

MG1655

4423153

Edman degradation

PMID:328274
PMID:8740179
PMID:9298646
PMID:9600841
PMID:9740056
PMID:9868784


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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

ΔrpsF (Keio:JW4158)

deletion

deletion

PMID:16738554

Shigen
CGSC10995[5]

ΔrpsF750::kan

PMID:16738554

CGSC:102798

rpsF

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484

fig 2

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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

JW4158

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGTCATTACGAAATCGTTTT

Primer 2:CCtTCTTCAGAATCCCCAGCTTC

1G10

Kohara Phage

Genobase

PMID:3038334

7E9

Kohara Phage

Genobase

PMID:3038334

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[5]

est. P1 cotransduction: 2% [6]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[5]

est. P1 cotransduction: 90% [6]

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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:EG10905

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10905

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000896

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948723

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0898

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013740

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

RpsF

Synonyms

30S ribosomal subunit protein S6[1], B4200[2][1], SdgH[2][1], RpsF[2][1] , ECK4196, JW4158, sdgH, b4200

Product description

30S ribosomal subunit protein S6[2][3];

Component of 30S ribosomal subunit[2][3]; ribosome[2][3]

30S ribosomal subunit protein S6; suppressor of dnaG-Ts[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:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000529

F

Seeded from EcoCyc (v14.0)

complete

GO:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020814

F

Seeded from EcoCyc (v14.0)

complete

GO:0022627

cytosolic small ribosomal subunit

PMID:4587209

IDA: Inferred from Direct Assay

C

complete

GO:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020815

F

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00360

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000529

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020814

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020815

P

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00360

F

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000529

F

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020814

F

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020815

F

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0699

F

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

Subunits of 30S ribosomal subunit

could be indirect

Protein

rplE

PMID:16606699

Experiment(s):EBI-1147655

Protein

mnmG

PMID:16606699

Experiment(s):EBI-1147655

Protein

thrS

PMID:16606699

Experiment(s):EBI-1147655

Protein

yeeX

PMID:16606699

Experiment(s):EBI-1147655

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1147655

Protein

yfiH

PMID:16606699

Experiment(s):EBI-1147655

Protein

ulaC

PMID:16606699

Experiment(s):EBI-1147655

Protein

Subunits of ribosome

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
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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 

MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV
LMNVEAPQEV IDELETTFRF NDAVIRSMVM RTKHAVTEAS PMVKAKDERR ERRDDFANET
ADDAEAGDSE E
Length

131

Mol. Wt

15.186 kDa

pI

5.2 (calculated)

Extinction coefficient

11,460 (calc based on 4 Y, 1 W, and 0 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

2..92

PF01250 Ribosomal protein S6

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=rpsF 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:296044035

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948723

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013740

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P02358

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10905

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10905

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948723

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000896

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0898

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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 MC4100

2.84E+04

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 EMG2

560

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: Ml41

PMID: 9298646

Protein

E. coli K-12 EMG2

1120

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: Ml42

PMID: 9298646

Protein

E. coli K-12 EMG2

940

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: Ml43

PMID: 9298646

Protein

E. coli K-12 MG1655

170065

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

26478

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

87500

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)

rpsF-priB-rpsR-rplI

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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_000913:4423121..4423161 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:b4200 (EcoliWiki Page)

NCBI GEO profiles for rpsF

microarray

GenExpDB:b4200 (EcoliWiki Page)

Summary of data for rpsF 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
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Notes

Accessions Related to rpsF Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10905

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0898

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4200

EcoGene

EcoGene:EG10905

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000896

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013740

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

Arabidopsis thaliana

  • AT3G17170 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000028791 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RPSF

From SHIGELLACYC

E. coli O157

RPSF

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)

PF01250 Ribosomal protein S6

EcoCyc

EcoCyc:EG10905

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10905

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000896

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0898

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013740

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 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 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).

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