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Expression|

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Standard Name	rbsR
Gene Synonym(s)	ECK3747, b3753, JW3732^[1], JW3732
Product Desc.	RbsR transcriptional repressor^[2]^[3] Regulatory gene for rbs operon^[4]
Product Synonyms(s)	DNA-binding transcriptional repressor of ribose metabolism^[1], B3753^[2]^[1], RbsR^[2]^[1], regulator for rbs operon^[2]^[1] , ECK3747, JW3732, b3753
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rbsDACBKR^[2], OP00289
Regulation/Activity
Quick Links
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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	rbsR
Mnemonic	Ribose
Synonyms	ECK3747, b3753, JW3732^[1], JW3732
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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	84.84 minutes, 84.84 minutes	MG1655: 3936250..3937242 <gbrowseImage> name=NC_000913:3936250..3937242 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3900034..3901026 <gbrowseImage> name=NC_012967:3900034..3901026 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3824592..3825131 <gbrowseImage> name=NC_012759:3824592..3825131 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
BW2952		NC_012759: 3826423..3826911 <gbrowseImage> name=NC_012759:3826423..3826911 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3698454..3697462 <gbrowseImage> name=NC_007779:3697462..3698454 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
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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
Coding Start (SO:0000323)	MG1655	3936253	Edman degradation	PMID:1304369
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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)	Reference	Availability	Comments
ΔrbsR (Keio:JW3732)	deletion	deletion	PMID:16738554 PMID:1304369	Shigen CGSC10725^[5]
rbsR::Tn5KAN-I-SceI (FB21438)	Insertion at nt 366 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21438	does not contain pKD46
rbsR::Tn5KAN-I-SceI (FB21439)	Insertion at nt 366 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21439	contains pKD46
rbsR782(del)::kan	insertion	insertion
rbsR22				CGSC:8887
ΔrbsR782::kan			PMID:16738554	CGSC:102608
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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
JW3732	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTACAATGAAAGATGTTGC Primer 2:CCAGCCGAACCGCGTTCCATCAG
15D10	Kohara Phage	Genobase	PMID:3038334
4F4	Kohara Phage	Genobase	PMID:3038334
rbsD296::Tn10	Linked marker	CAG18501 = CGSC7460^[5]	est. P1 cotransduction: 81% ^[6] Synonyms:zie-296::Tn10
ilvD500::Tn10	Linked marker	CAG18431 = CGSC7462^[5]	est. P1 cotransduction: 55% ^[6] Synonyms:ilv500::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:EG10819	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10819	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000810	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948266	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0812	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012271	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	RbsR
Synonyms	DNA-binding transcriptional repressor of ribose metabolism^[1], B3753^[2]^[1], RbsR^[2]^[1], regulator for rbs operon^[2]^[1] , ECK3747, JW3732, b3753
Product description	RbsR transcriptional repressor^[2]^[3] Regulatory gene for rbs operon^[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:IPR010982	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:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000843	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000843	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:IPR000843	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	groL		PMID:16606699	Experiment(s):EBI-1146648
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Notes

Repressor protein for rbs operon. rbsR is distal to the rbs operon, and it appears to have its own transcription control. ^[7]

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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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 MATMKDVARL AGVSTSTVSH VINKDRFVSE AITAKVEAAI KELNYAPSAL ARSLKLNQTH TIGMLITAST NPFYSELVRG VERSCFERGY SLVLCNTEGD EQRMNRNLET LMQKRVDGLL LLCTETHQPS REIMQRYPTV PTVMMDWAPF DGDSDLIQDN SLLGGDLATQ YLIDKGHTRI ACITGPLDKT PARLRLEGYR AAMKRAGLNI PDGYEVTGDF EFNGGFDAMR QLLSHPLRPQ AVFTGNDAMA VGVYQALYQA ELQVPQDIAV IGYDDIELAS FMTPPLTTIH QPKDELGELA IDVLIHRITQ PTLQQQRLQL TPILMERGSA
Length	330
Mol. Wt	36.612 kDa
pI	5.3 (calculated)
Extinction coefficient	20,400 - 20,900 (calc based on 10 Y, 1 W, and 4 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
Initiator Methionine	1	Removed	UniProt:P0ACQ0
Domain	3..48	PF00356 Bacterial regulatory proteins, lacI family		PMID:19920124
Domain	59..327	PF00532 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=rbsR 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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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:16131621	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948266	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012271	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACQ0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10819	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10819	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948266	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000810	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0812	Escherichia coli str. K-12 substr. MG1655
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Links

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Name	URL	Comments
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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	93	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	30	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	43^a	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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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
rbsDACBKR
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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_000913:3936230..3936270 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:b3753 (EcoliWiki Page)	NCBI GEO profiles for rbsR
microarray	GenExpDB:b3753 (EcoliWiki Page)	Summary of data for rbsR 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 rbsR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10819	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0812	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3753
EcoGene	EcoGene:EG10819	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000810	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012271	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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
Apis mellifera	ENSAPMP00000034998 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000047522 (score: 1.000; bootstrap: 89%)	From Inparanoid:20070104
Shigella flexneri	RBSR	From SHIGELLACYC
E. coli O157	RBSR	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)	PF00356 Bacterial regulatory proteins, lacI family
Pfam (EcoliWiki Page)	PF00532 family
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^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)
↑ ^2.0 ^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
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ Lopilato, JE et al. (1984) D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport. J. Bacteriol. 158 665-73 PubMed

rbsR:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to rbsR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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