rtcR: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

rtcR

Gene Synonym(s)

ECK3408, b3422, JW3385, yhgB[1], yhgB

Product Desc.

RtcR transcriptional regulator[2]; RtcR transcriptional activator[3]

Transcriptional regulator for rtcAB[4]

Product Synonyms(s)

sigma 54-dependent transcriptional regulator of rtcBA expression[1], B3422[2][1], YhgB[2][1], RtcR[2][1] , ECK3408, JW3385, yhgB, b3422

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rtcR[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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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

rtcR

Mnemonic

RNA terminal phosphate cyclase

Synonyms

ECK3408, b3422, JW3385, yhgB[1], yhgB

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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

76.65 minutes 

MG1655: 3556290..3557888
<gbrowseImage> name=NC_000913:3556290..3557888 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3486868..3488466
<gbrowseImage> name=NC_012967:3486868..3488466 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3444784..3446382
<gbrowseImage> name=NC_012759:3444784..3446382 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4082148..4080550
<gbrowseImage> name=NC_007779:4080550..4082148 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3654035..3655633
<gbrowseImage> name=NC_010473:3654035..3655633 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

ΔrtcR (Keio:JW3385)

deletion

deletion

PMID:16738554

Shigen
CGSC10520[5]

rtcR::Tn5KAN-I-SceI (FB21192)

Insertion at nt 1417 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21192

does not contain pKD46

rtcR::Tn5KAN-I-SceI (FB21193)

Insertion at nt 1417 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21193

contains pKD46

ΔrtcR755::kan

PMID:16738554

CGSC:102846


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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

JW3385

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGTAAAACAGTGGCTTTTGG

Primer 2:CCACTGGAGCTGTGCTGATCCTG

E5B4

Kohara Phage

Genobase

PMID:3038334

E4E4

Kohara Phage

Genobase

PMID:3038334

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[5]

est. P1 cotransduction: 8% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[5]

est. P1 cotransduction: 79% [6]
Synonyms:zhg-3086::Tn10, zhh-21::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:EG12356

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12356

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002224

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947928

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2259

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011174

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

RtcR

Synonyms

sigma 54-dependent transcriptional regulator of rtcBA expression[1], B3422[2][1], YhgB[2][1], RtcR[2][1] , ECK3408, JW3385, yhgB, b3422

Product description

RtcR transcriptional regulator[2]; RtcR transcriptional activator[3]

Transcriptional regulator for rtcAB[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:0000160

two-component signal transduction system (phosphorelay)

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0902

P

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

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:0003700

transcription factor activity

PMID:9738023

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:9738023

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:P07604
UniProtKB:P45512
UniProtKB:P38022
UniProtKB:P37930
UniProtKB:P28614
UniProtKB:P12627
UniProtKB:P12626
UniProtKB:P09133
UniProtKB:P06519
UniProtKB:P37344
UniProtKB:P10046
UniProtKB:P06184
UniProtKB:Q04849
UniProtKB:P0AFB8
UniProtKB:P26408
UniProtKB:P31908
UniProtKB:P23747
UniProtKB:Q00934
UniProtKB:Q06065
UniProtKB:P14375
UniProtKB:P19323

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

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:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

C

Seeded from EcoCyc (v14.0)

complete

GO:0008134

transcription factor binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:9738023

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:9738023

ISS: Inferred from Sequence or Structural Similarity

UniProtKB:P07604
UniProtKB:P45512
UniProtKB:P38022
UniProtKB:P37930
UniProtKB:P28614
UniProtKB:P12627
UniProtKB:P12626
UniProtKB:P09133
UniProtKB:P06519
UniProtKB:P37344
UniProtKB:P10046
UniProtKB:P06184
UniProtKB:Q04849
UniProtKB:P0AFB8
UniProtKB:P26408
UniProtKB:P31908
UniProtKB:P23747
UniProtKB:Q00934
UniProtKB:Q06065
UniProtKB:P14375
UniProtKB:P19323

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:9738023

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:9738023

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P07604
Swiss-Prot:P45512
Swiss-Prot:P38022
Swiss-Prot:P37930
Swiss-Prot:P28614
Swiss-Prot:P12627
Swiss-Prot:P12626
Swiss-Prot:P09133
Swiss-Prot:P06519
Swiss-Prot:P37344
Swiss-Prot:P10046
Swiss-Prot:P06184
Swiss-Prot:Q04849
Swiss-Prot:P0AFB8
Swiss-Prot:P26408
Swiss-Prot:P31908
Swiss-Prot:P23747
Swiss-Prot:Q00934
Swiss-Prot:Q06065
Swiss-Prot:P14375
Swiss-Prot:P19323

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

dld

PMID:16606699

Experiment(s):EBI-1145849

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1145849

Protein

groL

PMID:16606699

Experiment(s):EBI-1145849

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1145849

Protein

rpsB

PMID:16606699

Experiment(s):EBI-1145849
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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 

MRKTVAFGFV GTVLDYAGRG SQRWSKWRPT LCLCQQESLV IDRLELLHDA RSRSLFETLK
RDIASVSPET EVVSVEIELH NPWDFEEVYA CLHDFARGYE FQPEKEDYLI HITTGTHVAQ
ICWFLLAEAR YLPARLIQSS PPRKKEQPRG PGEVTIIDLD LSRYNAIASR FAEERQQTLD
FLKSGIATRN PHFNRMIEQI EKVAIKSRAP ILLNGPTGAG KSFLARRILE LKQARHQFSG
AFVEVNCATL RGDTAMSTLF GHVKGAFTGA RESREGLLRS ANGGMLFLDE IGELGADEQA
MLLKAIEEKT FYPFGSDRQV SSDFQLIAGT VRDLRQLVAE GKFREDLYAR INLWTFTLPG
LRQRQEDIEP NLDYEVERHA SLTGDSVRFN TEARRAWLAF ATSPQATWRG NFRELSASVT
RMATFATSGR ITLDVVEDEI NRLRYNWQES RPSALTALLG AEAENIDLFD RMQLEHVIAI
CRQAKSLSAA GRQLFDVSRQ GKASVNDADR LRKYLARFGL TWEAVQDQHS SS
Length

532

Mol. Wt

60.3 kDa

pI

7.1 (calculated)

Extinction coefficient

65,890 - 66,640 (calc based on 11 Y, 9 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

Domain

186..357

PF00158 Sigma-54 interaction domain

PMID:19920124

Domain

1..185

PF06956 Regulator of RNA terminal phosphate cyclase

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=rtcR 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:16131296

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947928

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011174

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P38035

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12356

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12356

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947928

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002224

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2259

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

8a

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

6

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)

rtcR

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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_000913:3556270..3556310 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

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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:b3422 (EcoliWiki Page)

NCBI GEO profiles for rtcR

microarray

GenExpDB:b3422 (EcoliWiki Page)

Summary of data for rtcR 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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Notes

Accessions Related to rtcR Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12356

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2259

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3422

EcoGene

EcoGene:EG12356

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002224

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011174

Escherichia coli str. K-12 substr. MG1655

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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

  • AT1G19050 (score: 1.000; bootstrap: 100%)
  • AT1G74890 (score: 0.581)
  • AT5G24470 (score: 0.061)
  • AT5G02810 (score: 0.052)

From Inparanoid:20070104

Oryza gramene

  • Q4GZL0 (score: 1.000; bootstrap: 100%)
  • Q9FRY8 (score: 0.455)
  • Q6YVX7 (score: 0.448)
  • Q4GZK9 (score: 0.448)
  • Q7XRI1 (score: 0.361)
  • Q6H468 (score: 0.164)
  • Q9FRZ0 (score: 0.159)
  • Q9FXQ7 (score: 0.157)
  • Q7XKF6 (score: 0.157)
  • Q4GZK6 (score: 0.152)
  • Q942A1 (score: 0.152)
  • Q4GZK7 (score: 0.152)
  • Q9FRZ1 (score: 0.147)
  • Q6K9T0 (score: 0.144)
  • Q4GZK8 (score: 0.144)
  • Q4GZK2 (score: 0.137)
  • Q9FRY9 (score: 0.134)
  • Q9S7U8 (score: 0.134)
  • Q7XQA6 (score: 0.134)
  • Q4JF20 (score: 0.134)
  • Q4GZK5 (score: 0.134)
  • Q8H5N4 (score: 0.122)
  • Q4GZK4 (score: 0.122)
  • Q9ZQW0 (score: 0.117)
  • Q8GVV6 (score: 0.092)
  • Q4GZK3 (score: 0.092)
  • Q8GVV1 (score: 0.055)
  • Q6YZK8 (score: 0.055)

From Inparanoid:20070104

Shigella flexneri

RTCR

From SHIGELLACYC

E. coli O157

RTCR

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Pfam (EcoliWiki Page)

PF00158 Sigma-54 interaction domain

Pfam (EcoliWiki Page)

PF06956 Regulator of RNA terminal phosphate cyclase

EcoCyc

EcoCyc:EG12356

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12356

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002224

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2259

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011174

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. ↑ 2.0 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 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).

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