hcaR: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

hcaR

Gene Synonym(s)

ECK2534, b2537, JW2521, yfhT, phdR[1], phdR

Product Desc.

HcaR transcriptional dual regulator[2][3]

Transcriptional activator of the hca operon; inducd by 3-phenylpropionate and cinnamic acid; autoregulatory[4]

Product Synonyms(s)

DNA-binding transcriptional activator of 3-phenylpropionic acid catabolism[1], B2537[2][1], PhdR[2][1], HcaR[2][1], YfhT[2][1] , ECK2534, JW2521, phdR, yfhT, b2537

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hcaR[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]


Hydrocinnamic acid is a synonym for 3-phenylpropionic acid. LysR family.[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

hcaR

Mnemonic

Hydrocinnamic acid

Synonyms

ECK2534, b2537, JW2521, yfhT, phdR[1], phdR

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

57.46 minutes, 57.46 minutes 

MG1655: 2666918..2666028
<gbrowseImage> name=NC_000913:2666028..2666918 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2589595..2588705
<gbrowseImage> name=NC_012967:2588705..2589595 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2551833..2552723
<gbrowseImage> name=NC_012759:2551833..2552723 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2667552..2666662
<gbrowseImage> name=NC_007779:2666662..2667552 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2758683..2757793
<gbrowseImage> name=NC_010473:2757793..2758683 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
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

ΔhcaR (Keio:JW2521)

deletion

deletion

PMID:16738554

Shigen
CGSC10007[5]

ΔhcaR782::kan

PMID:16738554

CGSC:101316


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

JW2521

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGAACTACGGCATTTACGCTA

Primer 2:CCTGCCGTTACGCTTGCCAAACG

5E10

Kohara Phage

Genobase

PMID:3038334

6F10

Kohara Phage

Genobase

PMID:3038334

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 91% [6]
Synonyms:zff-208::Tn10

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[5]

est. P1 cotransduction: 15% [6]

hcaR::cat

Strain

FB85

PMID: 15808934

hcaR::lacZ

Strain

FB82

PMID: 15808934

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:G7331

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13455

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003903

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947000

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3228

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008351

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

HcaR

Synonyms

DNA-binding transcriptional activator of 3-phenylpropionic acid catabolism[1], B2537[2][1], PhdR[2][1], HcaR[2][1], YfhT[2][1] , ECK2534, JW2521, phdR, yfhT, b2537

Product description

HcaR transcriptional dual regulator[2][3]

Transcriptional activator of the hca operon; inducd by 3-phenylpropionate and cinnamic acid; autoregulatory[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:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000847

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:11200225

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:9603882

ISS: Inferred from Sequence or Structural Similarity

GB:M33817
GB:M76991
GB:L04470
GB:D90801
GB:D38633
GB:M98445
GB:M80212
GB:L06464
GB:AE16782
GB:U32867
GB:J04233

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:11200225

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:9603882

ISS: Inferred from Sequence or Structural Similarity

GB:M33817
GB:M76991
GB:L04470
GB:D90801
GB:D38633
GB:M98445
GB:M80212
GB:L06464
GB:AE16782
GB:U32867
GB:J04233

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:11200225

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

PMID: 15808934

IDA: Inferred from Direct Assay

F

complete

GO:0016566

specific transcriptional repressor activity

PMID:9603882

ISS: Inferred from Sequence or Structural Similarity

GB:M33817
GB:M76991
GB:L04470
GB:D90801
GB:D38633
GB:M98445
GB:M80212
GB:L06464
GB:AE16782
GB:U32867
GB:J04233

F

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:11200225

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:9603882

ISS: Inferred from Sequence or Structural Similarity

GB:M33817
GB:M76991
GB:L04470
GB:D90801
GB:D38633
GB:M98445
GB:M80212
GB:L06464
GB:AE16782
GB:U32867
GB:J04233

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:11200225

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:9603882

ISS: Inferred from Sequence or Structural Similarity

GB:M33817
GB:M76991
GB:L04470
GB:D90801
GB:D38633
GB:M98445
GB:M80212
GB:L06464
GB:AE16782
GB:U32867
GB:J04233

P

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

groL

PMID:16606699

Experiment(s):EBI-1143188

Protein

rfaC

PMID:16606699

Experiment(s):EBI-1143188
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 

MELRHLRYFV AVAQALNFTR AAEKLHTSQP SLSSQIRDLE NCVGVPLLVR DKRKVALTAA
GECFLQDALA ILEQAENAKL RARKIVQEDR QLTIGFVPSA EVNLLPKVLP MFRLRQPDTL
IELVSLITTQ QEEKIRRGEL DVGLMRHPVY SPEIDYLELF DEPLVVVLPV DHPLAHEKEI
TAAQLDGVNF VSTDPVYSGS LAPIVKAWFA QENSQPNIVQ VATNILVTMN LVGMGLGVTL
IPGYMNNFNT GQVVFRPIAG NVPSIALLMA WKKGEMKPAL RDFIAIVQER LASVTA
Length

296

Mol. Wt

32.838 kDa

pI

6.4 (calculated)

Extinction coefficient

18,450 - 18,700 (calc based on 5 Y, 2 W, and 2 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

86..292

PF03466 LysR substrate binding domain

PMID:19920124

Domain

3..62

PF00126 Bacterial regulatory helix-turn-helix protein, lysR family

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=hcaR 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:16130462

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947000

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008351

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:Q47141

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7331

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13455

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947000

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003903

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3228

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 MG1655

33

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

61

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

22a

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

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)

hcaR

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_000913:2666898..2666938 source=MG1655 flip=1 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:b2537 (EcoliWiki Page)

NCBI GEO profiles for hcaR

microarray

GenExpDB:b2537 (EcoliWiki Page)

Summary of data for hcaR 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 (2666838..2667091) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ03; Well:E2[7]

edit table

<protect></protect>

Notes

Accessions Related to hcaR Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G7331

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3228

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2537

EcoGene

EcoGene:EG13455

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003903

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008351

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

Shigella flexneri

HCAR

From SHIGELLACYC

E. coli O157

HCAR

From ECOO157CYC

edit table

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF03466 LysR substrate binding domain

Pfam (EcoliWiki Page)

PF00126 Bacterial regulatory helix-turn-helix protein, lysR family


edit table

</protect> <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. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 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=hcaR:On_One_Page&oldid=220932"