yrdA: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

yrdA

Gene Synonym(s)

ECK3266, b3279, JW5710[1], JW5710

Product Desc.

putative transferase[2]; conserved protein[3]

Function unknown, low abundance protein[4]

Product Synonyms(s)

conserved protein[1], B3279[2][1], YrdA[2][1] , ECK3266, JW5710, b3279

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yrdA[2]

Regulation/Activity
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Notes

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The observed MW of YrdA is 19 kDa, consistent with the ALT_INIT. YrdA is related to gamma class carbonic anhydrases. YrdA is a member of the hexapeptide repeat acetyltransferase superfamily. yrdA is paralogous to paaY and caiE.[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

yrdA

Mnemonic

Systematic nomenclature

Synonyms

ECK3266, b3279, JW5710[1], JW5710

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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

73.87 minutes 

MG1655: 3427258..3427812
<gbrowseImage> name=NC_000913:3427258..3427812 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3357141..3357695
<gbrowseImage> name=NC_012967:3357141..3357695 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3314415..3314969
<gbrowseImage> name=NC_012759:3314415..3314969 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4211180..4210626
<gbrowseImage> name=NC_007779:4210626..4211180 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3525003..3525557
<gbrowseImage> name=NC_010473:3525003..3525557 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

ΔyrdA (Keio:JW5710)

deletion

deletion

PMID:16738554

Shigen

yrdA::Tn5KAN-I-SceI (FB21094)

Insertion at nt 548 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21094

does not contain pKD46

yrdA::Tn5KAN-I-SceI (FB21095)

Insertion at nt 548 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21095

contains pKD46

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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

JW5710

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTGATGTTTTACGCCCATA

Primer 2:CCAGGCTGGGTCTGGTTACCCTG

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[5]

est. P1 cotransduction: 65% [6]
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[5]

est. P1 cotransduction: 95% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::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:G7696

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12838

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004242

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947775

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2687

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010759

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

YrdA

Synonyms

conserved protein[1], B3279[2][1], YrdA[2][1] , ECK3266, JW5710, b3279

Product description

putative transferase[2]; conserved protein[3]

Function unknown, low abundance protein[4]

EC number (for enzymes)


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Notes

Function

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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:0016740

transferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011004

F

Seeded from EcoCyc (v14.0)

complete

GO:0003674

molecular function

n/a

ND: No biological Data available

F

Missing: reference

GO:0005575

cellular component

n/a

ND: No biological Data available

C

Missing: reference

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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

slyD

PMID:19402753[7]

LCMS(ID Probability):99.6

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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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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 

MKCFTLSSQR RRIIGIPIFC TSIFLIFFSV CCFFTLFAAI AHKTVLFCIL KDLHKANNAP
KVISKSFIAE VSMSDVLRPY RDLFPQIGQR VMIDDSSVVI GDVRLADDVG IWPLVVIRGD
VHYVQIGART NIQDGSMLHV THKSSYNPDG NPLTIGEDVT VGHKVMLHGC TIGNRVLVGM
GSILLDGAIV EDDVMIGAGS LVPQNKRLES GYLYLGSPVK QIRPLSDEEK AGLRYSANNY
VKWKDEYLDQ GNQTQP
Length

256

Mol. Wt

28.374 kDa

pI

7.8 (calculated)

Extinction coefficient

22,920 - 23,670 (calc based on 8 Y, 2 W, and 6 C residues)

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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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<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

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:90111568

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947775

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010759

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9W9

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7696

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12838

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947775

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004242

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2687

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

Ecoli K-12

98.71+/-0.47

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.388+/-0.08385

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.200361011

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

1051

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

804

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

1166

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

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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)

yrdA

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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

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<gbrowseImage> name=NC_000913:3427238..3427278 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

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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

microarray

GEO Profiles:b3279 (EcoliWiki Page)

NCBI GEO profiles for yrdA

microarray

GenExpDB:b3279 (EcoliWiki Page)

Summary of data for yrdA from multiple microarray studies

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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 yrdA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7696

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2687

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3279

EcoGene

EcoGene:EG12838

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004242

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010759

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

Arabidopsis thaliana

  • AT1G47260 (score: 1.000; bootstrap: 98%)
  • AT1G19580 (score: 1.000; bootstrap: 97%)
  • AT5G66510 (score: 0.647)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0218053 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q5N7E8 (score: 1.000; bootstrap: 100%)
  • Q9ARZ0 (score: 0.920)
  • Q8GRK1 (score: 0.595)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000040170 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YRDA

From SHIGELLACYC

E. coli O157

Z4650

From ECOO157CYC

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Do-It-Yourself Web Tools


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:51161

Panther (EcoliWiki Page)

PTHR13061:SF0

EcoCyc

EcoCyc:G7696

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12838

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004242

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2687

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010759

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 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. ↑ Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed

Categories

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