ypaA: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

ypaA

Gene Synonym(s)

ECK2237, b4543, JW5964[1], JW5964

Product Desc.
Product Synonyms(s)

, ECK2237, JW5964, b4543

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression
Regulation/Activity
Quick Links



     

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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

ypaA

Mnemonic

Systematic nomenclature

Synonyms

ECK2237, b4543, JW5964[1], JW5964

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Notes

Location(s) and DNA Sequence

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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

50.78 minutes 

MG1655: 2355838..2356023
<gbrowseImage> name=NC_000913:2355838..2356023 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2241643..2241828
<gbrowseImage> name=NC_012759:2241643..2241828 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2362486..2362671
<gbrowseImage> name=NC_007779:2362486..2362671 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2446826..2447011
<gbrowseImage> name=NC_010473:2446826..2447011 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

ΔypaA (Keio:JW5964)

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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

2E8

Kohara Phage

Genobase

PMID:3038334

22C4

Kohara Phage

Genobase

PMID:3038334

4B4

Kohara Phage

Genobase

PMID:3038334

zfa-723::Tn10

Linked marker

CAG12178 gyrA+ = CGSC7526[2]

est. P1 cotransduction: 64% [3]
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[2]

est. P1 cotransduction: 26% [3]
Synonyms:zej-223::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:

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:1450280

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120026452

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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Product(s)

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Nomenclature

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

Standard name
Synonyms

, ECK2237, JW5964, b4543

Product description
EC number (for enzymes)


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

Notes

Function

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Gene Ontology <protect> 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
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See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

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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See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki. </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
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See Help:Product_localization for how to add or edit information in this section of EcoliWiki.


Notes

Structure and Physical Properties

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Physical Properties <protect> See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence
Length
Mol. Wt
pI
Extinction coefficient
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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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

<motif_map/>

Structure

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

Structures

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

Models

View models at:

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

</protect>

Structure figures

Notes

Gene Product Resources


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

Notes

Accessions in Other Databases


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:145698287

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:1450280

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:1450280

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120026452

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

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

Notes

Links



See Help:Links_table for how to enter or edit information in this section of EcoliWiki.



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


See Help:Cellular levels

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

Protein

E. coli K-12 MG1655

188

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

96

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

45a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation


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

Transcription unit(s)

yfaD

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Figure courtesy of RegulonDB


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


<gbrowseImage> name=NC_000913:2355818..2355858 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.


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


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
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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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<protect>

Notes

Accessions Related to ypaA Expression


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

Database Accession Notes

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120026452

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



Evolution


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Homologs in Other Organisms


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

Do-It-Yourself Web Tools


Notes

{{{HOMOLOGY_NOTES}}}

Families


{{{EVOLUTION_FAMILIES_TABLE}}} See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Notes

{{{FAMILIES_NOTES}}}

Links


{{{LINKS}}} See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

References


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 CGSC: The Coli Genetics Stock Center
  3. ↑ 3.0 3.1 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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