yoaA: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

yoaA

Gene Synonym(s)

ECK1806, b1808, JW1797[1], JW1797

Product Desc.

conserved protein[2][3]

Function unknown[4]

Product Synonyms(s)

conserved protein with nucleoside triphosphate hydrolase domain[1], B1808[2][1], YoaA[2][1] , ECK1806, JW1797, b1808

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yoaA[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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Notes

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AFMB Structural Genomics target No. 37 (http://afmb.cnrs-mrs.fr/article171.html).[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

yoaA

Mnemonic

Systematic nomenclature

Synonyms

ECK1806, b1808, JW1797[1], JW1797

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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

40.72 minutes 

MG1655: 1891259..1889349
<gbrowseImage> name=NC_000913:1889349..1891259 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1871813..1869903
<gbrowseImage> name=NC_012967:1869903..1871813 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1781408..1783318
<gbrowseImage> name=NC_012759:1781408..1783318 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1894949..1893039
<gbrowseImage> name=NC_007779:1893039..1894949 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1981830..1979920
<gbrowseImage> name=NC_010473:1979920..1981830 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

ΔyoaA (Keio:JW1797)

deletion

deletion

PMID:16738554

Shigen
CGSC9505[5]

ΔyoaA::kan

deletion

Biolog:respiration

unable to respire D-Mannose

PMID:16095938

ΔyoaA732::kan

PMID:16738554

CGSC:105852


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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

JW1797

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACGGACGATTTTGCACCAGA

Primer 2:CCtCTGGAGGATGGTATCGCAAG

6D1

Kohara Phage

Genobase

PMID:3038334

12B3

Kohara Phage

Genobase

PMID:3038334

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[5]

est. P1 cotransduction: 49% [6]
Synonyms:zdj-225::Tn10

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[5]

est. P1 cotransduction: 18% [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

EcoCyc

EcoCyc:G6992

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13513

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003579

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946305

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3286

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006016

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

YoaA

Synonyms

conserved protein with nucleoside triphosphate hydrolase domain[1], B1808[2][1], YoaA[2][1] , ECK1806, JW1797, b1808

Product description

conserved protein[2][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 Evidence Code with/from Aspect Notes Status

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006555

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006935

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010614

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0004003

ATP-dependent DNA helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010614

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0347

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006555

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006935

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010614

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0006139

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006555

P

Seeded from EcoCyc (v14.0)

complete

GO:0008026

ATP-dependent helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006555

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006935

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

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

GO:0008150

biological process

n/a

ND: No biological Data available

P

n/a

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

aceE

PMID:15690043

Experiment(s):EBI-879036

Protein

tufA

PMID:15690043

Experiment(s):EBI-879036

Protein

htpG

PMID:16606699

Experiment(s):EBI-1140891

Protein

macB

PMID:16606699

Experiment(s):EBI-1140891

Protein

edd

PMID:16606699

Experiment(s):EBI-1140891

Protein

groL

PMID:16606699

Experiment(s):EBI-1140891
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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 

MTDDFAPDGQ LAKAIPGFKP REPQRQMAVA VTQAIEKGQP LVVEAGTGTG KTYAYLAPAL
RAKKKVIIST GSKALQDQLY SRDLPTVSKA LKYTGNVALL KGRSNYLCLE RLEQQALAGG
DLPVQILSDV ILLRSWSNQT VDGDISTCVS VAEDSQAWPL VTSTNDNCLG SDCPMYKDCF
VVKARKKAMD ADVVVVNHHL FLADMVVKES GFGELIPEAD VMIFDEAHQL PDIASQYFGQ
SLSSRQLLDL AKDITIAYRT ELKDTQQLQK CADRLAQSAQ DFRLQLGEPG YRGNLRELLA
NPQIQRAFLL LDDTLELCYD VAKLSLGRSA LLDAAFERAT LYRTRLKRLK EINQPGYSYW
YECTSRHFTL ALTPLSVADK FKELMAQKPG SWIFTSATLS VNDDLHHFTS RLGIEQAESL
LLPSPFDYSR QALLCVLRNL PQTNQPGSAR QLAAMLRPII EANNGRCFML CTSHAMMRDL
AEQFRATMTL PVLLQGETSK GQLLQQFVSA GNALLVATSS FWEGVDVRGD TLSLVIIDKL
PFTSPDDPLL KARMEDCRLR GGDPFDEVQL PDAVITLKQG VGRLIRDADD RGVLVICDNR
LVMRPYGATF LASLPPAPRT RDIARAVRFL AIPSSR
Length

636

Mol. Wt

70.379 kDa

pI

7.1 (calculated)

Extinction coefficient

51,340 - 52,965 (calc based on 16 Y, 5 W, and 13 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

Domain

17..106

PF04851 Type III restriction enzyme, res subunit

PMID:19920124

Domain

169..247

PF06733 DEAD_2

PMID:19920124

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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=yoaA 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:16129762

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946305

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006016

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76257

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6992

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13513

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946305

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003579

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3286

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

53

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

31

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

26

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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<protect>

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

Transcription unit(s)

yoaA

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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_000913:1891239..1891279 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
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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:b1808 (EcoliWiki Page)

NCBI GEO profiles for yoaA

microarray

GenExpDB:b1808 (EcoliWiki Page)

Summary of data for yoaA 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

GFP Fusion

Intergenic region (1891177..1891353) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ04; Well:F9[7]

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Notes

Accessions Related to yoaA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6992

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3286

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1808

EcoGene

EcoGene:EG13513

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003579

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006016

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Bos taurus

  • ENSBTAP00000002680 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000028108 (score: 0.092)
  • ENSBTAP00000016008 (score: 0.082)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000221481 (score: 1.000; bootstrap: 100%)
  • ENSP00000259008 (score: 0.107)
  • ENSP00000347362 (score: 0.085)
  • ENSP00000228264 (score: 0.079)
  • ENSP00000339557 (score: 0.070)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000021212 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000022909 (score: 0.082)

From Inparanoid:20070104

Mus musculus

  • MGI:95413 (score: 1.000; bootstrap: 100%)
  • MGI:2139369 (score: 0.109)
  • MGI:2442836 (score: 0.107)
  • MGI:2443590 (score: 0.088)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000019135 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000024247 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000036908 (score: 0.105)
  • ENSRNOP00000036941 (score: 0.094)
  • ENSRNOP00000016588 (score: 0.061)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YER171W (score: 1.000; bootstrap: 100%)
  • YPL008W (score: 0.069)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000180374 (score: 1.000; bootstrap: 100%)
  • NEWSINFRUP00000139789 (score: 0.235)
  • NEWSINFRUP00000129998 (score: 0.167)
  • NEWSINFRUP00000150294 (score: 0.086)

From Inparanoid:20070104

Shigella flexneri

S1535

From SHIGELLACYC

E. coli O157

Z2851

From ECOO157CYC

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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database Accession Notes

Pfam (EcoliWiki Page)

PF04851 Type III restriction enzyme, res subunit

Pfam (EcoliWiki Page)

PF06733 DEAD_2


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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 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

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