rpsP:On One Page

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

Quickview

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Standard Name

rpsP

Gene Synonym(s)

ECK2606, b2609, JW2590[1], JW2590

Product Desc.

30S ribosomal subunit protein S16[2][3];

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

30S ribosomal subunit protein S16; endonuclease[4]

Product Synonyms(s)

30S ribosomal subunit protein S16[1], B2609[2][1], RpsP[2][1] , ECK2606, JW2590, b2609

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rpsP-rimM-trmD-rplS[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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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

rpsP

Mnemonic

Ribosomal protein, small

Synonyms

ECK2606, b2609, JW2590[1], JW2590

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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

59.14 minutes 

MG1655: 2744207..2743959
<gbrowseImage> name=NC_000913:2743959..2744207 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2667592..2667344
<gbrowseImage> name=NC_012967:2667344..2667592 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2629771..2630019
<gbrowseImage> name=NC_012759:2629771..2630019 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2744841..2744593
<gbrowseImage> name=NC_007779:2744593..2744841 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2835972..2835724
<gbrowseImage> name=NC_010473:2835724..2835972 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

2743959

Edman degradation

PMID:336510
PMID:8730873
PMID:9298646


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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

JW2590

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGTAACTATTCGTTTAGCACG

Primer 2:CCAGCTGCTTTGTTTACTTCTTT

E8F2

Kohara Phage

Genobase

PMID:3038334

22D7

Kohara Phage

Genobase

PMID:3038334

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: 80% [6]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: % [6]
Synonyms:zfh-3131::Tn10, zfi-3131::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:EG10915

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10915

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000906

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947103

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0908

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008583

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

RpsP

Synonyms

30S ribosomal subunit protein S16[1], B2609[2][1], RpsP[2][1] , ECK2606, JW2590, b2609

Product description

30S ribosomal subunit protein S16[2][3];

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

30S ribosomal subunit protein S16; endonuclease[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:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000307

F

Seeded from EcoCyc (v14.0)

complete

GO:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020592

F

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00385

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000307

P

Seeded from EcoCyc (v14.0)

complete

GO:0022627

cytosolic small ribosomal subunit

IDA: Inferred from Direct Assay

C

Missing: reference

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020592

P

Seeded from EcoCyc (v14.0)

complete

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

rplQ

PMID:16606699

Experiment(s):EBI-1143455

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1143455

Protein

rplD

PMID:16606699

Experiment(s):EBI-1143455

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1143455

Protein

nadE

PMID:16606699

Experiment(s):EBI-1143455

Protein

rplA

PMID:16606699

Experiment(s):EBI-1143455

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1143455

Protein

btuD

PMID:16606699

Experiment(s):EBI-1143455

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1143455

Protein

rplB

PMID:16606699

Experiment(s):EBI-1143455

Protein

rpsG

PMID:16606699

Experiment(s):EBI-1143455

Protein

matC

PMID:16606699

Experiment(s):EBI-1143455

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

MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW
VGQGATISDR VAALIKEVNK AA
Length

82

Mol. Wt

9.19 kDa

pI

11.0 (calculated)

Extinction coefficient

6,990 (calc based on 1 Y, 1 W, and 0 C residues)


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

8..68

PF00886 Ribosomal protein S16

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=rpsP 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:16130530

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947103

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008583

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A7T3

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10915

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10915

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947103

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000906

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0908

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

6.10E+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 MG1655

162221

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

25778

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

73106

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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)

rpsP-rimM-trmD-rplS

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_000913:2744187..2744227 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


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b2609 (EcoliWiki Page)

NCBI GEO profiles for rpsP

microarray

GenExpDB:b2609 (EcoliWiki Page)

Summary of data for rpsP from multiple microarray studies


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 (2744133..2744473) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ19; Well:C4[7]

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Notes

Accessions Related to rpsP Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10915

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0908

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2609

EcoGene

EcoGene:EG10915

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000906

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008583

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

  • ENSANGP00000016416 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000001406 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G34620 (score: 1.000; bootstrap: 100%)
  • AT5G56940 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000001255 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000021607 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-041010-123 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-041010-123 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0033907 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA21001-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000000702 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000014788 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000000194 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1913492 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000009207 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YPL013C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC3546 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000147402 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00012888001 (score: 1.000; bootstrap: 100%)
  • GSTENP00027573001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000002965 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RPSP

From SHIGELLACYC

E. coli O157

RPSP

From ECOO157CYC


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

Panther (EcoliWiki Page)

PTHR12919:SF12

Superfamily (EcoliWiki Page)

SUPERFAMILY:54565

Pfam (EcoliWiki Page)

PF00886 Ribosomal protein S16

EcoCyc

EcoCyc:EG10915

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10915

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000906

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0908

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008583

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. 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 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 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 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. Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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