ykgM: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

ykgM

Gene Synonym(s)

ECK0296, b0296, JW5035[1], JW5035

Product Desc.

predicted ribosomal protein[2][3]

RpmE paralog, function unknown[4]

Product Synonyms(s)

predicted ribosomal protein[1], B0296[2][1], YkgM[2][1] , ECK0296, JW5035, b0296

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ykgO[2]

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

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YkgM is homologous to ribosomal protein L31.[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

ykgM

Mnemonic

Systematic nomenclature

Synonyms

ECK0296, b0296, JW5035[1], JW5035

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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

6.72 minutes 

MG1655: 312001..311738
<gbrowseImage> name=NC_000913:311738..312001 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 282957..282694
<gbrowseImage> name=NC_012967:282694..282957 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 312001..311738
<gbrowseImage> name=NC_007779:311738..312001 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 287551..287288
<gbrowseImage> name=NC_010473:287288..287551 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

ykgM(del) (Keio:JW5034)

deletion

deletion

PMID:16738554

Shigen

CGSC11141[5]

ykgM::Tn5KAN-I-SceI (FB20133)

Insertion at nt 51 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20133

does not contain pKD46

ykgM::Tn5KAN-I-SceI (FB20134)

Insertion at nt 51 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20134

contains pKD46

ykgM(del) (Keio:JW5035)

deletion

deletion

PMID:16738554

Shigen

CGSC11141[5]

ykgM741(del)::kan

PMID:16738554

CGSC:105682

ykgM742(del)::kan

PMID:16738554

CGSC:105684


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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

JW5034

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAGTTCTTAACTCTCTGCG

Primer 2:CCACGTTTTTTCTTACGACCCTG

3E3

Kohara Phage

Genobase

PMID:3038334

9G4

Kohara Phage

Genobase

PMID:3038334

JW5035

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAGCCCAATATCCATCCTGA

Primer 2:CCtGCCCCCTTTTTCGTGCTAAC

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[5]

est. P1 cotransduction: 9% [6]

lacI3042::Tn10

Linked marker

CAG18439 = CGSC7334[5]

est. P1 cotransduction: 7% [6]
Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).

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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:G6167

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14326

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944960

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002787

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4072

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001021

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

YkgM

Synonyms

predicted ribosomal protein[1], B0296[2][1], YkgM[2][1] , ECK0296, JW5035, b0296

Product description

predicted ribosomal protein[2][3]

RpmE paralog, 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:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002150

F

Seeded from EcoCyc (v14.0)

complete

GO:0005840

ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002150

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_00502

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002150

P

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

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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

MKPNIHPEYR TVVFHDTSVD EYFKIGSTIK TDREIELDGV TYPYVTIDVS SKSHPFYTGK
LRTVASEGNV ARFTQRFGRF VSTKKGA
Length

87

Mol. Wt

9.919 kDa

pI

9.7 (calculated)

Extinction coefficient

7,450 (calc based on 5 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

Domain

1..80

PF01197 Ribosomal protein L31

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=ykgM 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:16128281

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944960

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001021

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A7N1

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6167

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14326

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944960

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002787

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4072

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 MG1655

487

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

2318

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

85458

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

Transcription unit(s)

ykgO

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_000913:311981..312021 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:b0296 (EcoliWiki Page)

NCBI GEO profiles for ykgM

microarray

GenExpDB:b0296 (EcoliWiki Page)

Summary of data for ykgM 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 (311908..313645) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ05; Well:E8[7]

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Notes

Accessions Related to ykgM Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6167

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4072

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0296

EcoGene

EcoGene:EG14326

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002787

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001021

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

Apis mellifera

  • ENSAPMP00000032980 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000024186 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

E. coli O157

YKGM

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:143800

Pfam (EcoliWiki Page)

PF01197 Ribosomal protein L31

EcoCyc

EcoCyc:G6167

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14326

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002787

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4072

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001021

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 5.3 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

Categories

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