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The map label for this gene is rafR [H]

Identifier: 170024716

GI number: 170024716

Start: 2722900

End: 2723916

Strand: Reverse

Name: rafR [H]

Synonym: YPK_2491

Alternate gene names: 170024716

Gene position: 2723916-2722900 (Counterclockwise)

Preceding gene: 170024720

Following gene: 170024711

Centisome position: 58.09

GC content: 48.77

Gene sequence:

>1017_bases
ATGTCATTGAAGAAAATTGCAAATGAGCTTGGGCTGTCCTCCACAACGGTAAGCCGCGCGTTAAATGGCTATGATGATGT
TGCGGCCGAAACACGTGAGCGGATTATCGATGCGGCCAAGAGATTGGGTTATCAACCGAATTCCTTAGCTCGGCGGCTTA
AAATGGGGAGAACCGATGCCATTGCTTTGGCGTATCCATCACGTCCACGAGTGTTGAATAATTCGACATTTTTGGAAATG
ATAAGTTGGATAGGTATCGAACTCGGAAAACGGGGTCTCGATCTGTTGCTCATTCCTGATGAACCTGGTGAGAAATACCA
GTCACTTATCCACTTGGTGGAAACGCGTAGAGTGGATGCATTGATCGTGGCTCATACCCAGCCTGAAGACTTTCGGTTGC
AGTATTTGCAGAAACAAAACTTTCCTTTTTTGGCATTGGGGCGTAGCCATTTACCCAAGCCATATGCATGGTTTGATTTT
GATAATCACGCTGGCGCTTCGTTGGCAGTGAAGCGGCTTCTCGAACTTGGGCACCAGAGAATTGCATTTGTGAGTACCGA
TGCAAGGATTTCATATGTCGATCAGCGTTTGCAGGGATATGTGCAGACGATGTCCGAAGCGGGCCTGATGCCGTTGGCAG
GGTATCTGCAAAAAGCGGATCCCACTCGTCCTGGCGGTTATCTTGCTGCCTCGCGTTTATTGGCGCTTGAGGTTCCTCCT
ACTGCCATTATCACCGACTGTAATATGCTGGGTGATGGCGTGGCGAGTGCGCTTGATAAAGCGGGCTTGTTGGGCGGCGA
GGGGATATCGCTTATCGCTTATGATGGGCTACCGGATGATAGTTTGTTAGATATTGCCGTGACCCCTATTGTTCAAAATA
CGCGTACCAGTGTAGGTAAACAAATTGCATCAATGATTTGTGATTTACTGGGGGGGAAGGATCCTAAAGAACTACAGGTC
CTCTGGCAGCCAGAAATAGGAGAGGGTGAAACCGACGGGGTGAATCGACGTGGATAA

Upstream 100 bases:

>100_bases
ACAACGGACGTATAACCTGATTTATGTGTAGCTTACTTGGGAACCAATACAGGTTAAATCATGCTCAATTTAAGGTCGTT
GACCTGCGGATCAAAAAATC

Downstream 100 bases:

>100_bases
CTGGCTATTTGGGTCGGGTCGGGTCGGGAAAGGGAAGGGAGAGGAAGGGTGCTGTTGAGCCGCTGAGACTAGACGTAGAT
AAGCGAGGAGAGTAACTCAG

Product: LacI family transcription regulator

Products: NA

Alternate protein names: Raffinose operon repressor [H]

Number of amino acids: Translated: 338; Mature: 337

Protein sequence:

>338_residues
MSLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDAIALAYPSRPRVLNNSTFLEM
ISWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDALIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDF
DNHAGASLAVKRLLELGHQRIAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPP
TAIITDCNMLGDGVASALDKAGLLGGEGISLIAYDGLPDDSLLDIAVTPIVQNTRTSVGKQIASMICDLLGGKDPKELQV
LWQPEIGEGETDGVNRRG

Sequences:

>Translated_338_residues
MSLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDAIALAYPSRPRVLNNSTFLEM
ISWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDALIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDF
DNHAGASLAVKRLLELGHQRIAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPP
TAIITDCNMLGDGVASALDKAGLLGGEGISLIAYDGLPDDSLLDIAVTPIVQNTRTSVGKQIASMICDLLGGKDPKELQV
LWQPEIGEGETDGVNRRG
>Mature_337_residues
SLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDAIALAYPSRPRVLNNSTFLEMI
SWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDALIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDFD
NHAGASLAVKRLLELGHQRIAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPPT
AIITDCNMLGDGVASALDKAGLLGGEGISLIAYDGLPDDSLLDIAVTPIVQNTRTSVGKQIASMICDLLGGKDPKELQVL
WQPEIGEGETDGVNRRG

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=316, Percent_Identity=28.1645569620253, Blast_Score=124, Evalue=9e-30,
Organism=Escherichia coli, GI1787948, Length=324, Percent_Identity=26.5432098765432, Blast_Score=105, Evalue=5e-24,
Organism=Escherichia coli, GI1788474, Length=282, Percent_Identity=26.9503546099291, Blast_Score=97, Evalue=2e-21,
Organism=Escherichia coli, GI1790194, Length=301, Percent_Identity=28.2392026578073, Blast_Score=92, Evalue=5e-20,
Organism=Escherichia coli, GI1787580, Length=326, Percent_Identity=23.0061349693252, Blast_Score=86, Evalue=2e-18,
Organism=Escherichia coli, GI1789068, Length=327, Percent_Identity=25.6880733944954, Blast_Score=84, Evalue=1e-17,
Organism=Escherichia coli, GI1786540, Length=316, Percent_Identity=26.8987341772152, Blast_Score=84, Evalue=2e-17,
Organism=Escherichia coli, GI1789202, Length=308, Percent_Identity=27.2727272727273, Blast_Score=83, Evalue=2e-17,
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,
Organism=Escherichia coli, GI1787906, Length=300, Percent_Identity=24.3333333333333, Blast_Score=64, Evalue=2e-11,

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: 36978; Mature: 36847

Theoretical pI: Translated: 6.38; Mature: 6.38

Prosite motif: PS50932 HTH_LACI_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.6 %Cys     (Translated Protein)
2.1 %Met     (Translated Protein)
2.7 %Cys+Met (Translated Protein)
0.6 %Cys     (Mature Protein)
1.8 %Met     (Mature Protein)
2.4 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MSLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDA
CCHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCE
IALAYPSRPRVLNNSTFLEMISWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDA
EEEECCCCCCEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCE
LIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDFDNHAGASLAVKRLLELGHQR
EEEEECCCHHHHHHHHHHCCCCEEEECHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCCE
IAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPP
EEEEECCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCHHHHHCEEEEECCC
TAIITDCNMLGDGVASALDKAGLLGGEGISLIAYDGLPDDSLLDIAVTPIVQNTRTSVGK
CEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCEEEEEECCHHHHHHHHHHH
QIASMICDLLGGKDPKELQVLWQPEIGEGETDGVNRRG
HHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCCCCCCC
>Mature Secondary Structure 
SLKKIANELGLSSTTVSRALNGYDDVAAETRERIIDAAKRLGYQPNSLARRLKMGRTDA
CHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCE
IALAYPSRPRVLNNSTFLEMISWIGIELGKRGLDLLLIPDEPGEKYQSLIHLVETRRVDA
EEEECCCCCCEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCE
LIVAHTQPEDFRLQYLQKQNFPFLALGRSHLPKPYAWFDFDNHAGASLAVKRLLELGHQR
EEEEECCCHHHHHHHHHHCCCCEEEECHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCCE
IAFVSTDARISYVDQRLQGYVQTMSEAGLMPLAGYLQKADPTRPGGYLAASRLLALEVPP
EEEEECCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCHHHHHCEEEEECCC
TAIITDCNMLGDGVASALDKAGLLGGEGISLIAYDGLPDDSLLDIAVTPIVQNTRTSVGK
CEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCEEEEEECCHHHHHHHHHHH
QIASMICDLLGGKDPKELQVLWQPEIGEGETDGVNRRG
HHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCCCCCCC

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]