RegulonDB

Gene
Name:	rutR
Synonym(s):	ECK1004, EG12301, b1013, ycdC
Genome position(nucleotides):	1074242 --> 1074880 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.33
External database links:

ASAP:	ABE-0003422
ECHOBASE:	EB2207
OU-MICROARRAY:	b1013
PortEco:	rutR
STRING:	511145.b1013
COLOMBOS:	rutR

Product

Name:

DNA-binding transcriptional dual regulator RutR

Synonym(s):

RutR, YcdC

Sequence:

Get amino acid sequence Fasta Format

Regulator Family:

TetR/AcrR

Cellular location:

cytosol

Molecular weight:

23.688

Isoelectric point:

9.311

Motif(s):

Type	Positions	Sequence
	17 -> 77	SAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIW
	70 -> 212	LRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR
	23 -> 69	ILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAV
	39 -> 58	TRLEQIAELAGVSKTNLLYY

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
		3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003677 - DNA binding GO:0005515 - protein binding GO:0003700 - DNA-binding transcription factor activity GO:0000976 - transcription regulatory region sequence-specific DNA binding
	biological_process	GO:0006355 - regulation of transcription, DNA-templated GO:0045892 - negative regulation of transcription, DNA-templated GO:0045893 - positive regulation of transcription, DNA-templated

Note(s):

Note(s): ...[more].

Evidence:

[AIFS] Automated inference of function from sequence
[APPH] Assay of protein purified to homogeneity
[HIFS] Human inference of function from sequence
[IMP] Inferred from mutant phenotype

Reference(s):

[1] Loh KD., et al., 2006
[2] Perez-Rueda E., et al., 2004
[3] Shimada T., et al., 2007

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PANTHER:

PDB:

PDB:

PDB:

PDB:

PFAM:

PFAM:

PRIDE:

PRINTS:

PRODB:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

rutR

Operon arrangement:

Transcription unit	Promoter
rutR	rutRp2
rutR	rutRp

Transcriptional Regulation
	Display Regulation
Repressed by:	RutR

RNA cis-regulatory element

Attenuation:	Transcriptional

Elements in the selected gene context region unrelated to any object in RegulonDB

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References

Reference(s)
[1] Loh KD., Gyaneshwar P., Markenscoff Papadimitriou E., Fong R., Kim KS., Parales R., Zhou Z., Inwood W., Kustu S., 2006, A previously undescribed pathway for pyrimidine catabolism., Proc Natl Acad Sci U S A 103(13):5114-9
[2] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50
[3] Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A., 2007, RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines., Mol Microbiol 66(3):744-57