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Standard Name	rutR
Gene Synonym(s)	ycdC, ECK1004, b1013, JW0998^[1]^[2], JW0998
Product Desc.	predicted DNA-binding transcriptional regulator^[2]^[3] Repressor for divergent rut operon; pyrimidine nitrogen catabolism^[4]
Product Synonyms(s)	predicted DNA-binding transcriptional regulator^[1], B1013^[2]^[1], YcdC^[2]^[1], RutR^[2]^[1] , ECK1004, JW0998, ycdC, b1013
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rutR^[2], ycdC
Regulation/Activity
Quick Links
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Notes

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RutR is also the global regulator of a pyrimidine metabolism regulon (Shimada, 2007). TetR family. NtrC regulon. The rut operon is required for the utilization of thymidine, uridine and cytidine as nitrogen sources at 37C, but not at room temperature.^[4]

Gene

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Nomenclature

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Standard name	rutR
Mnemonic	PyRimidine UTilization
Synonyms	ycdC, ECK1004, b1013, JW0998^[1]^[2], JW0998
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Notes

Location(s) and DNA Sequence

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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	23.14 minutes	MG1655: 1073465..1074103 <gbrowseImage> name=NC_000913:1073465..1074103 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1090526..1091164 <gbrowseImage> name=NC_012967:1090526..1091164 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 976433..977071 <gbrowseImage> name=NC_012759:976433..977071 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1074664..1075302 <gbrowseImage> name=NC_007779:1074664..1075302 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1127393..1128031 <gbrowseImage> name=NC_010473:1127393..1128031 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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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	Reference	Availability
rutR1::FLK2(lacZ,kan)	PMID:12142427	CGSC:87250
ΔrutR2	PMID:12142427	CGSC:87253
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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

7B5

Kohara Phage

Genobase

PMID:3038334

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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:EG12301	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12301	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002180	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945075	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2207	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003422	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	YcdC
Synonyms	predicted DNA-binding transcriptional regulator^[1], B1013^[2]^[1], YcdC^[2]^[1], RutR^[2]^[1] , ECK1004, JW0998, ycdC, b1013
Product description	predicted DNA-binding transcriptional regulator^[2]^[3] Repressor for divergent rut operon; pyrimidine nitrogen catabolism^[4]
EC number (for enzymes)
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Notes

Function

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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:IPR001647	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:15944459^[5]	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACS9	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:17919280^[6]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:18515344^[7]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:15944459^[5]	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACS9	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:17919280^[6]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:18515344^[7]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015893	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:15944459^[5]	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACS9	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:17919280^[6]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:18515344^[7]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:15944459^[5]	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACS9	P	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:17919280^[6]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:18515344^[7]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:15944459^[5]	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACS9	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:17919280^[6]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:18515344^[7]	IDA: Inferred from Direct Assay		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	References	Evidence
Protein	rpsI	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	uspG	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	purR	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	rpsM	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	glpC	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	rpsG	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	rpmE	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	ynaE	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	rpmB	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	slyD	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	pqqL	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	rplQ	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	rplB	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	ompL	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	insO2	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	rplA	PMID:16606699^[8]	Experiment(s):EBI-1138623
Protein	rpsT	PMID:16606699^[8]	Experiment(s):EBI-1138623
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Notes

Localization

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Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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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 MTQGAVKTTG KRSRAVSAKK KAILSAALDT FSQFGFHGTR LEQIAELAGV SKTNLLYYFP SKEALYIAVL RQILDIWLAP LKAFREDFAP LAAIKEYIRL KLEVSRDYPQ ASRLFCMEML AGAPLLMDEL TGDLKALIDE KSALIAGWVK SGKLAPIDPQ HLIFMIWAST QHYADFAPQV EAVTGATLRD EVFFNQTVEN VQRIIIEGIR PR
Length	212
Mol. Wt	23.688 kDa
pI	9.2 (calculated)
Extinction coefficient	25,440 - 25,565 (calc based on 6 Y, 3 W, and 1 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	References
Domain	23..69	PF00440 Bacterial regulatory proteins, tetR family	PMID:19920124^[9]
Domain	70..212	PF08362 YcdC-like protein, C-terminal region	PMID:19920124^[9]
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<motif_map/>

Structure
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Structures

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

Models

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Structure figures

Notes

Gene Product Resources

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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:16128979	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945075	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003422	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACU2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12301	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12301	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945075	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002180	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2207	Escherichia coli str. K-12 substr. MG1655
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Notes

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	201	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	92	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	73^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)
rutR
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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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<gbrowseImage> name=NC_000913:1073445..1073485 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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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:b1013 (EcoliWiki Page)	NCBI GEO profiles for rutR
microarray	GenExpDB:b1013 (EcoliWiki Page)	Summary of data for rutR 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 (1073137..1073536) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ15; Well:G6^[10]
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Notes

Accessions Related to rutR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12301	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2207	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1013
EcoGene	EcoGene:EG12301	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002180	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003422	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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Organism	Homologs (Statistics)	Comments
Xenopus tropicalis	ENSXETP00000040128 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YCDC	From SHIGELLACYC
E. coli O157	YCDC	From ECOO157CYC
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Do-It-Yourself Web Tools

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)	PF00440 Bacterial regulatory proteins, tetR family
Superfamily (EcoliWiki Page)	SUPERFAMILY:46689
Superfamily (EcoliWiki Page)	SUPERFAMILY:48498
Pfam (EcoliWiki Page)	PF08362 YcdC-like protein, C-terminal region
EcoCyc	EcoCyc:EG12301	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12301	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002180	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2207	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003422	Escherichia coli str. K-12 substr. MG1655
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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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^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
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 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 ^5.3 ^5.4 Ramos, JL et al. (2005) The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 69 326-56 PubMed
↑ ^6.0 ^6.1 ^6.2 ^6.3 ^6.4 Shimada, T et al. (2007) RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. Mol. Microbiol. 66 744-57 PubMed
↑ ^7.0 ^7.1 ^7.2 ^7.3 ^7.4 Shimada, T et al. (2008) The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res. 36 3950-5 PubMed
↑ ^8.00 ^8.01 ^8.02 ^8.03 ^8.04 ^8.05 ^8.06 ^8.07 ^8.08 ^8.09 ^8.10 ^8.11 ^8.12 ^8.13 ^8.14 ^8.15 ^8.16 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^9.0 ^9.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rutR:On One Page

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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 rutR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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