helD:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

helD

Gene Synonym(s)

ECK0953, b0962, JW0945, srjB[1], srjB

Product Desc.

DNA helicase IV[2][3]

ATP-dependent DNA Helicase IV[4]

Product Synonyms(s)

DNA helicase IV[1], B0962[2][1], SrjB[2][1], HelD[2][1] , ECK0953, JW0945, srjB, b0962

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): helD[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]


Overexpression causes filamentous biofilm formation.[4]



Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

helD

Mnemonic

Helicase

Synonyms

ECK0953, b0962, JW0945, srjB[1], srjB

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

22.06 minutes 

MG1655: 1023694..1025748
<gbrowseImage> name=NC_000913:1023694..1025748 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1041562..1043616
<gbrowseImage> name=NC_012967:1041562..1043616 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 926662..928716
<gbrowseImage> name=NC_012759:926662..928716 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1024893..1026947
<gbrowseImage> name=NC_007779:1024893..1026947 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1077622..1079676
<gbrowseImage> name=NC_010473:1077622..1079676 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

1023694

Edman degradation

PMID:2542273


edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔhelD (Keio:JW0945)

deletion

deletion

PMID:16738554

Shigen
CGSC8946[5]

ΔhelD::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

ΔhelD::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938

ΔhelD777::kan

PMID:16738554

CGSC:101336


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0945

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGAACTGAAAGCGACAACGCT

Primer 2:CCCGGTTTTCTCGCCACCGGCAC

E2E5

Kohara Phage

Genobase

PMID:3038334

9B10

Kohara Phage

Genobase

PMID:3038334

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[5]

est. P1 cotransduction: 45% [6]

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[5]

est. P1 cotransduction: 20% [6]

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10426

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10426

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000419

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946227

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0421

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003257

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

HelD

Synonyms

DNA helicase IV[1], B0962[2][1], SrjB[2][1], HelD[2][1] , ECK0953, JW0945, srjB, b0962

Product description

DNA helicase IV[2][3]

ATP-dependent DNA Helicase IV[4]

EC number (for enzymes)
edit table

<protect></protect>

Notes

Function

[back to top]


<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:0000155

two-component sensor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003661

F

Seeded from EcoCyc (v14.0)

complete

GO:0006261

DNA-dependent DNA replication

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000212

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:IPR000212

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:IPR000212

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014016

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:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000212

P

Seeded from EcoCyc (v14.0)

complete

GO:0007165

signal transduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003661

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003661

C

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014016

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

edit table

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

tufA

PMID:15690043

Experiment(s):EBI-880994, EBI-887624

Protein

accB

PMID:15690043

Experiment(s):EBI-887624

Protein

atpD

PMID:15690043

Experiment(s):EBI-887624

Protein

csrA

PMID:15690043

Experiment(s):EBI-887624

Protein

dnaK

PMID:15690043

Experiment(s):EBI-887624

Protein

gadB

PMID:15690043

Experiment(s):EBI-887624

Protein

gcvP

PMID:15690043

Experiment(s):EBI-887624

Protein

infB

PMID:15690043

Experiment(s):EBI-887624

Protein

lipA

PMID:15690043

Experiment(s):EBI-887624

Protein

groL

PMID:15690043

Experiment(s):EBI-887624

Protein

pflB

PMID:15690043

Experiment(s):EBI-887624

Protein

pgk

PMID:15690043

Experiment(s):EBI-887624

Protein

ptsI

PMID:15690043

Experiment(s):EBI-887624

Protein

rplC

PMID:15690043

Experiment(s):EBI-887624

Protein

rplD

PMID:15690043

Experiment(s):EBI-887624

Protein

rplL

PMID:15690043

Experiment(s):EBI-887624

Protein

rplU

PMID:15690043

Experiment(s):EBI-887624

Protein

rpsA

PMID:15690043

Experiment(s):EBI-887624

Protein

rpsG

PMID:15690043

Experiment(s):EBI-887624

Protein

tpiA

PMID:15690043

Experiment(s):EBI-887624

Protein

gapA

PMID:15690043

Experiment(s):EBI-887624

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1138489

Protein

groL

PMID:16606699

Experiment(s):EBI-1138489

Protein

gapA

PMID:19402753

LCMS(ID Probability):99.6

Protein

gadB

PMID:19402753

LCMS(ID Probability):99.6

Protein

pgk

PMID:19402753

LCMS(ID Probability):99.6

Protein

infB

PMID:19402753

LCMS(ID Probability):99.6

Protein

atpD

PMID:19402753

LCMS(ID Probability):99.6

Protein

groL

PMID:19402753

LCMS(ID Probability):99.6

Protein

gcvP

PMID:19402753

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753

MALDI(Z-score):19.099796

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

groS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6

Protein

accB

PMID:19402753

LCMS(ID Probability):99.3

Protein

pflB

PMID:19402753

LCMS(ID Probability):99.6

Protein

tpiA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6

Protein

csrA

PMID:19402753

LCMS(ID Probability):99.6

Protein

lipA

PMID:19402753

LCMS(ID Probability):99.3

Protein

ptsI

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

edit table

</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
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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 

MELKATTLGK RLAQHPYDRA VILNAGIKVS GDRHEYLIPF NQLLAIHCKR GLVWGELEFV
LPDEKVVRLH GTEWGETQRF YHHLDAHWRR WSGEMSEIAS GVLRQQLDLI ATRTGENKWL
TREQTSGVQQ QIRQALSALP LPVNRLEEFD NCREAWRKCQ AWLKDIESAR LQHNQAYTEA
MLTEYADFFR QVESSPLNPA QARAVVNGEH SLLVLAGAGS GKTSVLVARA GWLLARGEAS
PEQILLLAFG RKAAEEMDER IRERLHTEDI TARTFHALAL HIIQQGSKKV PIVSKLENDT
AARHELFIAE WRKQCSEKKA QAKGWRQWLT EEMQWSVPEG NFWDDEKLQR RLASRLDRWV
SLMRMHGGAQ AEMIASAPEE IRDLFSKRIK LMAPLLKAWK GALKAENAVD FSGLIHQAIV
ILEKGRFISP WKHILVDEFQ DISPQRAALL AALRKQNSQT TLFAVGDDWQ AIYRFSGAQM
SLTTAFHENF GEGERCDLDT TYRFNSRIGE VANRFIQQNP GQLKKPLNSL TNGDKKAVTL
LDESQLDALL DKLSGYAKPE ERILILARYH HMRPASLEKA ATRWPKLQID FMTIHASKGQ
QADYVIIVGL QEGSDGFPAA ARESIMEEAL LPPVEDFPDA EERRLMYVAL TRARHRVWAL
FNKENPSPFV EILKNLDVPV ARKP
Length

684

Mol. Wt

77.977 kDa

pI

8.5 (calculated)

Extinction coefficient

120,890 - 121,515 (calc based on 11 Y, 19 W, and 5 C residues)

edit table


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

197..600

PF00580 UvrD/REP helicase

PMID:19920124

Domain

1..165

PF12462 DNA helicase IV / RNA helicase N terminal

PMID:19920124

edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128929

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946227

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003257

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P15038

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10426

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10426

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946227

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000419

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0421

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

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

Protein

E. coli K-12 MC4100

8.66E+01

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

251

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

165

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

166

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

helD

edit table
Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:1023674..1023714 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
edit table


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

Type Reference Notes

microarray

GEO Profiles:b0962 (EcoliWiki Page)

NCBI GEO profiles for helD

microarray

GenExpDB:b0962 (EcoliWiki Page)

Summary of data for helD from multiple microarray studies

edit table


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 (1023492..1023758) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ10; Well:A3[7]

edit table

<protect></protect>

Notes

Accessions Related to helD Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10426

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0421

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0962

EcoGene

EcoGene:EG10426

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000419

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003257

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Mus musculus

  • MGI:1354699 (score: 1.000; bootstrap: 100%)
  • YP_026251 (score: 0.063)

From Inparanoid:20070104

Shigella flexneri

HELD

From SHIGELLACYC

E. coli O157

HELD

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Pfam (EcoliWiki Page)

PF00580 UvrD/REP helicase

Pfam (EcoliWiki Page)

PF12462 DNA helicase IV / RNA helicase N terminal

EcoCyc

EcoCyc:EG10426

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10426

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000419

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0421

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003257

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 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 2.7 2.8 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

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=helD:On_One_Page&oldid=219353"