matP: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

matP

Gene Synonym(s)

ycbG, ECK0947, b0956, JW0939[1], JW0939

Product Desc.

conserved protein[2]; putative dehydrogenase[3]

Function unknown[4]

Product Synonyms(s)

conserved protein[1], B0956[2][1], YcbG[2][1]

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ycbG[2]

Regulation/Activity
Quick Links

porteco.png

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

matP

Mnemonic

Systematic nomenclature

Synonyms

ycbG, ECK0947, b0956, JW0939[1], JW0939

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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

21.93 minutes 

MG1655: 1017708..1018160
<gbrowseImage> name=NC_000913:1017708..1018160 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1035576..1036028
<gbrowseImage> name=NC_012967:1035576..1036028 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 920676..921128
<gbrowseImage> name=NC_012759:920676..921128 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1018907..1019359
<gbrowseImage> name=NC_007779:1018907..1019359 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1071636..1072088
<gbrowseImage> name=NC_010473:1071636..1072088 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

ΔycbG (Keio:JW0939)

deletion

deletion

PMID:16738554

Shigen


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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

JW0939

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAATATCAACAACTTGAAAA

Primer 2:CCTTCCTTACCCAGCAATGCCTG

E2E5

Kohara Phage

Genobase

PMID:3038334

9B10

Kohara Phage

Genobase

PMID:3038334

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[5]

est. P1 cotransduction: 58% [6]

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[5]

est. P1 cotransduction: 14% [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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0956

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1092

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YCBG

EcoCyc (EcoliWiki Page)

ECOCYC:EG12855

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945570

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

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

MatP

Synonyms

conserved protein[1], B0956[2][1], YcbG[2][1]

Product description

conserved protein[2]; putative dehydrogenase[3]

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(s) Evidence Code with/from Aspect Notes Status

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

rplB

PMID:16606699

Experiment(s):EBI-1138481

Protein

pflA

PMID:16606699

Experiment(s):EBI-1138481

Protein

rplA

PMID:16606699

Experiment(s):EBI-1138481

Protein

rpsE

PMID:16606699

Experiment(s):EBI-1138481

Protein

ycgE

PMID:16606699

Experiment(s):EBI-1138481

Protein

ulaF

PMID:16606699

Experiment(s):EBI-1138481

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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 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.

Sequence

at EcoCyc

MKYQQLENLE SGWKWKYLVK KHREGELITR YIEASAAQEA VDVLLSLENE PVLVNGWIDK
HMNPELVNRM KQTIRARRKR HFNAEHQHTR KKSIDLEFIV WQRLAGLAQR RGKTLSETIV
QLIEDAENKE KYANKMSSLK QDLQALLGKE
Length

150

Mol. Wt

17.693 kDa

pI

9.9 (calculated)

Extinction coefficient

27,960 (calc based on 4 Y, 4 W, and 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..148

PF06303 Organiser of macrodomain of Terminus of chromosome

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=ycbG 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

UniProt (EcoliWiki Page)

UniProt:P0A8N0

PFAM (EcoliWiki Page)

Pfam:P0A8N0

RefSeq (EcoliWiki Page)

RefSeq:NP_415476

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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

601

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

360

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

347

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)

ycbG

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_000913:1017688..1017728 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


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

Type Reference Notes

microarray

GEO Profiles:b0956 (EcoliWiki Page)

NCBI GEO profiles for ycbG

microarray

GenExpDB:b0956 (EcoliWiki Page)

Summary of data for ycbG 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

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Notes

Accessions Related to matP Expression

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

Database Accession Notes

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0956

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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

Shigella flexneri

YCBG

From SHIGELLACYC

E. coli O157

YCBG

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

Pfam (EcoliWiki Page)

PF05362 Lon protease (S16) C-terminal proteolytic domain

Pfam (EcoliWiki Page)

PF06303 Organiser of macrodomain of Terminus of chromosome

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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 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

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