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The map label for this gene is rafR [H]

Identifier: 108812556

GI number: 108812556

Start: 2675293

End: 2676180

Strand: Reverse

Name: rafR [H]

Synonym: YPN_2395

Alternate gene names: 108812556

Gene position: 2676180-2675293 (Counterclockwise)

Preceding gene: 108812557

Following gene: 108812555

Centisome position: 59.02

GC content: 49.55

Gene sequence:

>888_bases
ATGTCATTGAAGAAAATTGCAAATGAGCTTGGGCTGTCCTCCACAACGGTAAGCCGCGCGTTAAATGGCTATGATGATGT
TGCGGCCGAAACACGTGAGCGGATTATCGATGCGGCCAAGAGATTGGGTTATCAACCGAATTCCTTAGCTCGGCGGCTTA
AAATGGGGAGAACCGATGCCATTGCTTTGGCGTATCCATCACGTCCACGAGTGTTGAATAATTCGACATTTTTGGAAATG
ATAAGTTGGATAGGTATCGAACTCGGAAAACGGGGTCTCGATCTGTTGCTCATTCCTGATGAACCTGGTGAGAAATACCA
GTCACTTATCCACTTGGTGGAAACGCGTAGAGTGGATGCATTGATCGTGGCTCATACCCAGCCTGAAGACTTTCGGTTGC
AGTATTTGCAGAAACAAAACTTTCCTTTTTTGGCATTGGGGCGTAGCCATTTACCCAAGCCATATGCATGGTTTGATTTT
GATAATCACGCTGGCGCTTCGTTGGCAGTGAAGCGGCTTCTCGAACTTGGGCACCAGAGAATTGCATTTGTGAGTACCGA
TGCAAGGATTTCATATGTCGATCAGCGTTTGCAGGGATATGTGCAGACGATGTCCGAAGCGGGCCTGATGCCGTTGGCAG
GGTATCTGCAAAAAGCGGATCCCACTCGTCCTGGCGGTTATCTTGCTGCCTCGCGTTTATTGGCGCTTGAGGTTCCTCCT
ACTGCCATTATCACCGACTGTAATATGCTGGGTGATGGCGTGGCGAGTGCGCTTGATAAAGCGGGCTTGTTGGGCGGCGA
GGGGATATCGCTTATTGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGGGGGTAATCTGC
TCTCCTGA

Upstream 100 bases:

>100_bases
ACAACGGACGTATAACCTGATTTATGTGTAGCTTACTTGGGAACCAATACAGGTTAAATCATGCTCAATTTAAGGTCGTT
GACCTGCGGATCAAAAAATC

Downstream 100 bases:

>100_bases
TTCAGGAGAGTTTATGGTCACTTTTGAGACAGTTATGGAAATTAAAATCCTGCACAAGCAGGGAATGAGTAGCCGGGCGA
TTGCCAGAGAACTGGGGATC

Product: hypothetical protein

Products: NA

Alternate protein names: Raffinose operon repressor [H]

Number of amino acids: Translated: 295; Mature: 294

Protein sequence:

>295_residues
MSLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDAIALAYPSRPRVLNNSTFLEM
ISWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDALIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDF
DNHAGASLAVKRLLELGHQRIAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPP
TAIITDCNMLGDGVASALDKAGLLGGEGISLIVTNGAIVIHTQRLKSDPGGNLLS

Sequences:

>Translated_295_residues
MSLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDAIALAYPSRPRVLNNSTFLEM
ISWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDALIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDF
DNHAGASLAVKRLLELGHQRIAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPP
TAIITDCNMLGDGVASALDKAGLLGGEGISLIVTNGAIVIHTQRLKSDPGGNLLS
>Mature_294_residues
SLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDAIALAYPSRPRVLNNSTFLEMI
SWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDALIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDFD
NHAGASLAVKRLLELGHQRIAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPPT
AIITDCNMLGDGVASALDKAGLLGGEGISLIVTNGAIVIHTQRLKSDPGGNLLS

Specific function: The raffinose (raf) operon is negatively controlled by the specific binding of raf repressor to raf operator (rafO) DNA. Binds raffinose as an inducer [H]

COG id: COG1609

COG function: function code K; Transcriptional regulators

Gene ontology:

Cell location: Cytoplasmic

Metaboloic importance: Non_Essential [C]

Operon status: Not Known

Operon components: None

Similarity: Contains 1 HTH lacI-type DNA-binding domain [H]

Homologues:

Organism=Escherichia coli, GI1790369, Length=275, Percent_Identity=29.0909090909091, Blast_Score=112, Evalue=3e-26,
Organism=Escherichia coli, GI1788474, Length=267, Percent_Identity=26.9662921348315, Blast_Score=92, Evalue=6e-20,
Organism=Escherichia coli, GI1787948, Length=274, Percent_Identity=26.6423357664234, Blast_Score=91, Evalue=8e-20,
Organism=Escherichia coli, GI1787580, Length=246, Percent_Identity=25.609756097561, Blast_Score=85, Evalue=6e-18,
Organism=Escherichia coli, GI1790194, Length=281, Percent_Identity=28.1138790035587, Blast_Score=85, Evalue=6e-18,
Organism=Escherichia coli, GI1789202, Length=275, Percent_Identity=27.6363636363636, Blast_Score=79, Evalue=4e-16,
Organism=Escherichia coli, GI1786540, Length=293, Percent_Identity=26.2798634812287, Blast_Score=74, Evalue=1e-14,
Organism=Escherichia coli, GI1789068, Length=288, Percent_Identity=25.6944444444444, Blast_Score=72, Evalue=6e-14,
Organism=Escherichia coli, GI1786268, Length=155, Percent_Identity=31.6129032258064, Blast_Score=69, Evalue=3e-13,
Organism=Escherichia coli, GI48994940, Length=230, Percent_Identity=26.0869565217391, Blast_Score=66, Evalue=3e-12,

Paralogues:

None

Copy number: NA

Swissprot (AC and ID): NA

Other databases:

- InterPro:   IPR000843
- InterPro:   IPR010982
- InterPro:   IPR001761 [H]

Pfam domain/function: PF00356 LacI; PF00532 Peripla_BP_1 [H]

EC number: NA

Molecular weight: Translated: 32274; Mature: 32142

Theoretical pI: Translated: 9.19; Mature: 9.19

Prosite motif: PS50932 HTH_LACI_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.3 %Cys     (Translated Protein)
2.0 %Met     (Translated Protein)
2.4 %Cys+Met (Translated Protein)
0.3 %Cys     (Mature Protein)
1.7 %Met     (Mature Protein)
2.0 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MSLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDA
CCHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCE
IALAYPSRPRVLNNSTFLEMISWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDA
EEEECCCCCCEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCE
LIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDFDNHAGASLAVKRLLELGHQR
EEEEECCCHHHHHHHHHHCCCCEEEECHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCCE
IAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPP
EEEEECCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCHHHHHCEEEEECCC
TAIITDCNMLGDGVASALDKAGLLGGEGISLIVTNGAIVIHTQRLKSDPGGNLLS
CEEEECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCEEEEEEHHHCCCCCCCCCC
>Mature Secondary Structure 
SLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDA
CHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCE
IALAYPSRPRVLNNSTFLEMISWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDA
EEEECCCCCCEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCE
LIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDFDNHAGASLAVKRLLELGHQR
EEEEECCCHHHHHHHHHHCCCCEEEECHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCCE
IAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPP
EEEEECCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCHHHHHCEEEEECCC
TAIITDCNMLGDGVASALDKAGLLGGEGISLIVTNGAIVIHTQRLKSDPGGNLLS
CEEEECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCEEEEEEHHHCCCCCCCCCC

PDB accession: NA

Resolution: NA

Structure class: Alpha Beta

Cofactors: NA

Metal ions: NA

Kcat value (1/min): NA

Specific activity: NA

Km value (mM): NA

Substrates: DNA [C]

Specific reaction: Protein + DNA = Protein-DNA [C]

General reaction: NA

Inhibitor: NA

Structure determination priority: 10.0

TargetDB status: NA

Availability: NA

References: 2180920 [H]