rpmD:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

rpmD

Gene Synonym(s)

ECK3289, b3302, JW3264[1], JW3264

Product Desc.

50S ribosomal subunit protein L30[2][3];

Component of 50S ribosomal subunit[3]; ribosome[2][3]

50S ribosomal subunit protein L30[4]

Product Synonyms(s)

50S ribosomal subunit protein L30[1], B3302[2][1], RpmD[2][1] , ECK3289, JW3264, b3302

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ[2], rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-prlA-rpmJ

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]





Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

rpmD

Mnemonic

Ribosomal protein, large

Synonyms

ECK3289, b3302, JW3264[1], JW3264

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

74.2 minutes 

MG1655: 3442744..3442565
<gbrowseImage> name=NC_000913:3442565..3442744 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3372627..3372448
<gbrowseImage> name=NC_012967:3372448..3372627 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3329722..3329901
<gbrowseImage> name=NC_012759:3329722..3329901 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4195694..4195873
<gbrowseImage> name=NC_007779:4195694..4195873 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3540489..3540310
<gbrowseImage> name=NC_010473:3540310..3540489 source=DH10B preset=GeneLocation </gbrowseImage>

</protect>

Notes

Sequence Features

[back to top]


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

3442568

Edman degradation

PMID:776670
PMID:10739205


<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

rpmD1

CGSC:73979

ErmDep rpmD

Loss of ribosomal protein L30

Growth Phenotype

Loss of erythromycin dependence

PMID:387748

It is unknown whether the loss of the protein caused renewed dependence for erythromycin. There were 3 mutants AM10, AM46, AM98 (see table 1.) See Figure 1.

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW3264

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCAAAGACTATTAAAATTAC

Primer 2:CCtTCCTCAACTTTAACCATGAA

E1H9

Kohara Phage

Genobase

PMID:3038334

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[5]

est. P1 cotransduction: 62% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[5]

est. P1 cotransduction: 4% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10888

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10888

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000879

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947797

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0881

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010821

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

RpmD

Synonyms

50S ribosomal subunit protein L30[1], B3302[2][1], RpmD[2][1] , ECK3289, JW3264, b3302

Product description

50S ribosomal subunit protein L30[2][3];

Component of 50S ribosomal subunit[3]; ribosome[2][3]

50S ribosomal subunit protein L30[4]

EC number (for enzymes)


<protect></protect>

Notes

Function

[back to top]


<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:IPR000517

F

Seeded from EcoCyc (v14.0)

complete

GO:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005996

F

Seeded from EcoCyc (v14.0)

complete

GO:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016082

F

Seeded from EcoCyc (v14.0)

complete

GO:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018038

F

Seeded from EcoCyc (v14.0)

complete

GO:0005840

ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000517

C

Seeded from EcoCyc (v14.0)

complete

GO:0005840

ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016082

C

Seeded from EcoCyc (v14.0)

complete

GO:0005840

ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018038

C

Seeded from EcoCyc (v14.0)

complete

GO:0005840

ribosome

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0689

C

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01371

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000517

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005996

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016082

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018038

P

Seeded from EcoCyc (v14.0)

complete

GO:0015934

large ribosomal subunit

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005996

C

Seeded from EcoCyc (v14.0)

complete

GO:0030529

ribonucleoprotein complex

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0687

C

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 50S ribosomal subunit

could be indirect

Protein

Subunits of ribosome

could be indirect


</protect>

Notes

Localization

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

Compartment Description Evidence Reference/Source Notes

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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

MAKTIKITQT RSAIGRLPKH KATLLGLGLR RIGHTVERED TPAIRGMINA VSFMVKVEE
Length

59

Mol. Wt

6.541 kDa

pI

11.4 (calculated)

Extinction coefficient

0 (calc based on 0 Y, 0 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

Initiator Methionine

1

Removed

UniProt:P0AG51

Domain

4..55

PF00327 Ribosomal protein L30p/L7e

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=rpmD taxon=562,83333 </beststructure>

Models

View models at:

</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16131181

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947797

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010821

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AG51

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10888

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10888

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947797

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000879

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0881

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

1.73E+06

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

110113

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

18522

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

68938

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

[back to top]


<protect>

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

Transcription unit(s)

rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ

Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:3442724..3442764 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

[back to top]


<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:b3302 (EcoliWiki Page)

NCBI GEO profiles for rpmD

microarray

GenExpDB:b3302 (EcoliWiki Page)

Summary of data for rpmD 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

<protect></protect>

Notes

Accessions Related to rpmD Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10888

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0881

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3302

EcoGene

EcoGene:EG10888

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000879

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010821

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Shigella flexneri

RPMD

From SHIGELLACYC

E. coli O157

RPMD

From ECOO157CYC


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Superfamily (EcoliWiki Page)

SUPERFAMILY:55129

Pfam (EcoliWiki Page)

PF00327 Ribosomal protein L30p/L7e

EcoCyc

EcoCyc:EG10888

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10888

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000879

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0881

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010821

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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 2.7 2.8 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).

Categories

[back to top]