rhaS: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

rhaS

Gene Synonym(s)

ECK3898, b3905, JW3876, rhaC, rhaC2[1], rhaC2

Product Desc.

RhaS[2][3];

Component of RhaS transcriptional activator[2][3]; RhaS-L-rhamnose transcriptional activator[2][3]

Transcriptional activator for rhaBAD and rhaT, AraC family[4]

Product Synonyms(s)

DNA-binding transcriptional activator, L-rhamnose-binding[1], B3905[2][1], RhaS[2][1], positive regulator for rhaBAD operon[2][1] , ECK3898, JW3876, rhaC2, b3905

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rhaSR[2], OP00087, rha

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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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

rhaS

Mnemonic

Rhamnose

Synonyms

ECK3898, b3905, JW3876, rhaC, rhaC2[1], rhaC2

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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

88.28 minutes 

MG1655: 4095759..4096595
<gbrowseImage> name=NC_000913:4095759..4096595 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4077218..4078054
<gbrowseImage> name=NC_012967:4077218..4078054 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3985428..3986264
<gbrowseImage> name=NC_012759:3985428..3986264 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3538945..3538109
<gbrowseImage> name=NC_007779:3538109..3538945 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4195456..4196292
<gbrowseImage> name=NC_010473:4195456..4196292 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

ΔrhaS (Keio:JW3876)

deletion

deletion

PMID:16738554

Shigen

rhaSR202A

R202A

4% of wild-type activity

seeded from UniProt:P09377

rhaSS255A

S255A

80% of wild-type activity

seeded from UniProt:P09377

rhaST256A

T256A

61% of wild-type activity

seeded from UniProt:P09377

rhaSS249G

S249G

93% of wild-type activity

seeded from UniProt:P09377

rhaSD250A

D250A

8.3% of wild-type activity

seeded from UniProt:P09377

rhaSS251G

S251G

87% of wild-type activity

seeded from UniProt:P09377

rhaSF248V

F248V

3.3% of wild-type activity

seeded from UniProt:P09377

rhaSF254A

F254A

1.2% of wild-type activity

seeded from UniProt:P09377

rhaSL201A

L201A

48% of wild-type activity

seeded from UniProt:P09377

rhaSF248A

F248A

0.9% of wild-type activity

seeded from UniProt:P09377

rhaSN252H

N252H

0.4% of wild-type activity

seeded from UniProt:P09377

rhaSN252I

N252I

0.3% of wild-type activity

seeded from UniProt:P09377

rhaSN252S

N252S

37% of wild-type activity

seeded from UniProt:P09377

rhaSH253A

H253A

48% of wild-type activity

seeded from UniProt:P09377

rhaSH253Q

H253Q

32% of wild-type activity

seeded from UniProt:P09377

rhaSN252A

N252A

31% of wild-type activity

seeded from UniProt:P09377

rhaSH205A

H205A

28% of wild-type activity

seeded from UniProt:P09377

rhaSR206A

R206A

0.1% of wild-type activity

seeded from UniProt:P09377

rhaSC246A

C246A

66% of wild-type activity

seeded from UniProt:P09377

rhaSG247A

G247A

6.2% of wild-type activity

seeded from UniProt:P09377

rhaSG247R

G247R

0.9% of wild-type activity

seeded from UniProt:P09377

xx

xx

xx

Growth Phenotype

xx


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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

JW3876

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACCGTATTACATAGTGTGGA

Primer 2:CCTTGCAGAAAGCCATCCCGTCC

4B6

Kohara Phage

Genobase

PMID:3038334

7G8

Kohara Phage

Genobase

PMID:3038334

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[5]

est. P1 cotransduction: 29% [6]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[5]

est. P1 cotransduction: 12% [6]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

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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:EG10843

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10843

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000834

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948397

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0836

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012745

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

RhaS

Synonyms

DNA-binding transcriptional activator, L-rhamnose-binding[1], B3905[2][1], RhaS[2][1], positive regulator for rhaBAD operon[2][1] , ECK3898, JW3876, rhaC2, b3905

Product description

RhaS[2][3];

Component of RhaS transcriptional activator[2][3]; RhaS-L-rhamnose transcriptional activator[2][3]

Transcriptional activator for rhaBAD and rhaT, AraC family[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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012287

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:0003700

transcription factor activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01534

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01534

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003313

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

P

Seeded from EcoCyc (v14.0)

complete

GO:0019299

rhamnose metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01534

P

Seeded from EcoCyc (v14.0)

complete

GO:0019299

rhamnose metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0684

P

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

F

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

F

Seeded from EcoCyc (v14.0)

complete

GO:0045449

regulation of transcription

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012287

P

Seeded from EcoCyc (v14.0)

complete

GO:0045449

regulation of transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0805

P

Seeded from EcoCyc (v14.0)

complete

GO:0045893

positive regulation of transcription, DNA-dependent

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01534

P

Seeded from EcoCyc (v14.0)

complete

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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

Subunits of RhaS transcriptional activator

could be indirect

Protein

ygiF

PMID:16606699

Experiment(s):EBI-1146962

Protein

rhlE

PMID:16606699

Experiment(s):EBI-1146962

Protein

yedJ

PMID:16606699

Experiment(s):EBI-1146962

Protein

cutC

PMID:16606699

Experiment(s):EBI-1146962

Protein

ybeM

PMID:16606699

Experiment(s):EBI-1146962

Protein

amiA

PMID:16606699

Experiment(s):EBI-1146962

Protein

smtA

PMID:16606699

Experiment(s):EBI-1146962

Protein

rplD

PMID:16606699

Experiment(s):EBI-1146962

Protein

yfgC

PMID:16606699

Experiment(s):EBI-1146962

Protein

rpsB

PMID:16606699

Experiment(s):EBI-1146962

Protein

rplJ

PMID:16606699

Experiment(s):EBI-1146962

Protein

rplE

PMID:16606699

Experiment(s):EBI-1146962

Protein

recT

PMID:16606699

Experiment(s):EBI-1146962

Protein

groL

PMID:16606699

Experiment(s):EBI-1146962

Protein

rdoA

PMID:16606699

Experiment(s):EBI-1146962

Protein

Subunits of RhaS-L-rhamnose transcriptional activator

could be indirect


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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 

MTVLHSVDFF PSGNASVAIE PRLPQADFPE HHHDFHEIVI VEHGTGIHVF NGQPYTITGG
TVCFVRDHDR HLYEHTDNLC LTNVLYRSPD RFQFLAGLNQ LLPQELDGQY PSHWRVNHSV
LQQVRQLVAQ MEQQEGENDL PSTASREILF MQLLLLLRKS SLQENLENSA SRLNLLLAWL
EDHFADEVNW DAVADQFSLS LRTLHRQLKQ QTGLTPQRYL NRLRLMKARH LLRHSEASVT
DIAYRCGFSD SNHFSTLFRR EFNWSPRDIR QGRDGFLQ
Length

278

Mol. Wt

32.315 kDa

pI

6.7 (calculated)

Extinction coefficient

30,940 - 31,315 (calc based on 6 Y, 4 W, and 3 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

14..154

PF02311 AraC-like ligand binding domain

PMID:19920124

Domain

180..221

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

PMID:19920124

Domain

232..271

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

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=rhaS 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:16131745

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948397

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012745

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P09377

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10843

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10843

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948397

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000834

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0836

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

E. coli K-12 MG1655

4a

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

9

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

0a

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

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<protect>

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

Transcription unit(s)

rhaSR

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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_000913:4095739..4095779 source=MG1655 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

</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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<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:b3905 (EcoliWiki Page)

NCBI GEO profiles for rhaS

microarray

GenExpDB:b3905 (EcoliWiki Page)

Summary of data for rhaS 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 (4094950..4095360) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:C8[7]

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Notes

Accessions Related to rhaS Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10843

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0836

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3905

EcoGene

EcoGene:EG10843

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000834

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012745

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

Xenopus tropicalis

  • ENSXETP00000020771 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000051238 (score: 0.204)

From Inparanoid:20070104

Shigella flexneri

RHAS

From SHIGELLACYC

E. coli O157

RHAS

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

Pfam (EcoliWiki Page)

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

Pfam (EcoliWiki Page)

PF02311 AraC-like ligand binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:46689

Superfamily (EcoliWiki Page)

SUPERFAMILY:46689

Superfamily (EcoliWiki Page)

SUPERFAMILY:51215

EcoCyc

EcoCyc:EG10843

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10843

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000834

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0836

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012745

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 1.8 1.9 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 2.11 2.12 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 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. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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