Click here to switch to the map view.

The map label for this gene is vacB [H]

Identifier: 21909888

GI number: 21909888

Start: 390994

End: 393249

Strand: Direct

Name: vacB [H]

Synonym: SpyM3_0352

Alternate gene names: 21909888

Gene position: 390994-393249 (Clockwise)

Preceding gene: 21909887

Following gene: 21909889

Centisome position: 20.57

GC content: 41.31

Gene sequence:

>2256_bases
ATGGCTGGAGCTAAGCGTTTTCCCAGCCTTATTAAAACCATTTCCAAAATGGAAAGTCAGAGCCTTTTACGGTTTTCAGA
TGATGGCAGTCTGGCTCTTAGAAAAGAGCGTGAAAAGAAAAAAGAACCTACTGTTCAGGGTGTTTTTCGTGCCAATAAAG
CAGGCTTTGGTTTCTTACATGTGGATGAGAATGAAGACGATATGTTTATCGGTCGTAATGATGTTGGGTATGCTATTGAT
GGTGATACTGTCGAAGTAGTGGTTAAAAAGCCAGCAGACCGTCTCAAAGGCACAGCGGCTGAAGCTAAGGTCGTTGCTAT
TGTTGACCGTTCTTTAAAAACAGCTGTTGGAACCTTTATTTTAGATGATGACAAACCAAAATATGCTGGTTATATCAGGT
CCAAAAATCAAAAGATTCAACAAAAAATCTATATCAAAAAAGAACCTGTTGTGCTTAAAGGCACTGAAATCATCAAGGTT
GATATTGATAAATACCCGACACGCGGGCACGATTATTTTGTAGCCAGTGTGCGTGATATCGTAGGCCATCAAGGAGACGT
TGGAATTGATGTCCTAGAAGTCCTTGAATCGATGGATATCGTGTCAGAGTTCCCAGCAGAAGTTTTAGTCGAGGCCAATG
CTATTTCAGAAGCACCAACTGCTAAAGATTTAATAGGCCGTGTGGATTTGCGTCAAGAAACCACCATTACTATTGATGGT
GCGGACGCCAAAGACTTAGATGATGCTATCCATATTAAGCTATTGGATAACGGTAACTATGAACTTGGGGTACATATTGC
GGATGTCTCATATTATGTGACAGAAGGATCTGCCCTTGATAAGGAAGCTATCGCCCGTGGCACTTCTGTCTATGTCACCG
ATCGTGTGGTTCCGATGTTACCAGAGCGTTTGTCAAATGGCATCTGCTCTTTGAACCCTAACGTTGATCGTTTGACCCAG
TCAGCCTTGATGGAAATTAATTCTCAAGGGCATGTGGTCAATTATCAAATCTGTCAATCAGTGATTAAGACAACTTACCG
AATGACGTATAGTACGGTCAATGACATGATTGCAGGAGATGAAGAAGCGCTCCAAGAATTCGCTAGCATTGCTGATGATG
TGACCCTCATGGTGGCTTTGCATAGGATTTTGGAAGCTATGCGGTCAAAACGAGGCGCCTTGAATTTTGATACGCAAGAA
GCTAAAGTTATTGTTAATGACAAAGGAATGCCGGTTGATGTGGTGCTTCGTCAAAGGGGAATTGCAGAGCGGATGATTGA
GTCCTTTATGCTAGCAGCCAATGAGTGTGTGGCAGAACATTTTGCAAAAGCTAAGTTACCGTTTATCTACCGTATTCACG
AAGAACCAAAGGCCGAAAAACTTCAACAATTTATTGATTACGCTAGCACCTTTGGTATTCACATTCAAGGAACAGCCAAC
AAGATTTCTCAGGAAGCCTTGCAAGCCTTTATGGCAAAAGTCGAAGGTCAACCAGGAGCAGAAGTGCTTAACATGATGCT
CTTACGCTCTATGCAACAGGCAAGATATTCTGAACATAATCATGGGCATTACGGTTTGGCCGCAGAATATTACACTCACT
TTACCAGTCCGATTCGTCGTTACCCTGACTTGTTGGTTCACCGCATGGTTCGTGAGTACAGTCAACCTAGTCAAGAAAAG
CGCGACCATTTTACTCAGATCATTCCAGAATTAGCAACATCTTCTTCACAGTTAGAGCGTCGTGCTATTGATGCTGAACG
CGTGGTTGAAGCCATGAAAAAAGCTGAGTATATGGCAGAGTATGTGGGTGAAGAATTTGACGGTATCGTGGCCAGTGTCG
TTAAATTTGGTTTTTTTGTAGAATTGCCAAATACGATTGAAGGTTTGGTTCATATTACTAGCTTACCGGAATACTATCAC
TTTAATGAAAGAACGCTAAGCCTTCAAGGTGAAAAATCAGGTAAAGTCTTTAAAGTTGGTCAACCTATTCGTGTGAAATT
GGTTAAGGCTGACAAGGAAACTGGTGACATTGACTTTGAGTATTTACCTAGCGACTTTGATGTGGTTGAAAAAATCAAGA
TGTCGGATAAAGCTAGTCGACGAGATCGCCGTAAATCCTCAAAATCATCTAAAGGGATAAAGAAAAAAGAACCTAAAGAA
GTAGCCAAGGCAAAAACCAAGGGTAAAACTAAAAAAGGGTCTAAAAAACCATTTTACAAAGAACAAGCAAAAAAGAAGAG
TCGTAAAAGGAGTTAA

Upstream 100 bases:

>100_bases
AAAACAGAAATAGAAATTAGGTATGATGAAAGAAAGAATAATGACTTACCTCAAGGAGCATGGCAAGTCCAATGTGAACG
ACTTGGCTGCGGCCTTGGAG

Downstream 100 bases:

>100_bases
CTATGGCAAAAGGTGAAGGTCATATACTGGCGCAAAATAAAAAGGCTAGACATGATTATCACATTGTTGAAACCGTTGAA
GCAGGGATTGTCTTAACGGG

Product: putative exoribonuclease R

Products: NA

Alternate protein names: RNase R 1; VacB protein homolog 1 [H]

Number of amino acids: Translated: 751; Mature: 750

Protein sequence:

>751_residues
MAGAKRFPSLIKTISKMESQSLLRFSDDGSLALRKEREKKKEPTVQGVFRANKAGFGFLHVDENEDDMFIGRNDVGYAID
GDTVEVVVKKPADRLKGTAAEAKVVAIVDRSLKTAVGTFILDDDKPKYAGYIRSKNQKIQQKIYIKKEPVVLKGTEIIKV
DIDKYPTRGHDYFVASVRDIVGHQGDVGIDVLEVLESMDIVSEFPAEVLVEANAISEAPTAKDLIGRVDLRQETTITIDG
ADAKDLDDAIHIKLLDNGNYELGVHIADVSYYVTEGSALDKEAIARGTSVYVTDRVVPMLPERLSNGICSLNPNVDRLTQ
SALMEINSQGHVVNYQICQSVIKTTYRMTYSTVNDMIAGDEEALQEFASIADDVTLMVALHRILEAMRSKRGALNFDTQE
AKVIVNDKGMPVDVVLRQRGIAERMIESFMLAANECVAEHFAKAKLPFIYRIHEEPKAEKLQQFIDYASTFGIHIQGTAN
KISQEALQAFMAKVEGQPGAEVLNMMLLRSMQQARYSEHNHGHYGLAAEYYTHFTSPIRRYPDLLVHRMVREYSQPSQEK
RDHFTQIIPELATSSSQLERRAIDAERVVEAMKKAEYMAEYVGEEFDGIVASVVKFGFFVELPNTIEGLVHITSLPEYYH
FNERTLSLQGEKSGKVFKVGQPIRVKLVKADKETGDIDFEYLPSDFDVVEKIKMSDKASRRDRRKSSKSSKGIKKKEPKE
VAKAKTKGKTKKGSKKPFYKEQAKKKSRKRS

Sequences:

>Translated_751_residues
MAGAKRFPSLIKTISKMESQSLLRFSDDGSLALRKEREKKKEPTVQGVFRANKAGFGFLHVDENEDDMFIGRNDVGYAID
GDTVEVVVKKPADRLKGTAAEAKVVAIVDRSLKTAVGTFILDDDKPKYAGYIRSKNQKIQQKIYIKKEPVVLKGTEIIKV
DIDKYPTRGHDYFVASVRDIVGHQGDVGIDVLEVLESMDIVSEFPAEVLVEANAISEAPTAKDLIGRVDLRQETTITIDG
ADAKDLDDAIHIKLLDNGNYELGVHIADVSYYVTEGSALDKEAIARGTSVYVTDRVVPMLPERLSNGICSLNPNVDRLTQ
SALMEINSQGHVVNYQICQSVIKTTYRMTYSTVNDMIAGDEEALQEFASIADDVTLMVALHRILEAMRSKRGALNFDTQE
AKVIVNDKGMPVDVVLRQRGIAERMIESFMLAANECVAEHFAKAKLPFIYRIHEEPKAEKLQQFIDYASTFGIHIQGTAN
KISQEALQAFMAKVEGQPGAEVLNMMLLRSMQQARYSEHNHGHYGLAAEYYTHFTSPIRRYPDLLVHRMVREYSQPSQEK
RDHFTQIIPELATSSSQLERRAIDAERVVEAMKKAEYMAEYVGEEFDGIVASVVKFGFFVELPNTIEGLVHITSLPEYYH
FNERTLSLQGEKSGKVFKVGQPIRVKLVKADKETGDIDFEYLPSDFDVVEKIKMSDKASRRDRRKSSKSSKGIKKKEPKE
VAKAKTKGKTKKGSKKPFYKEQAKKKSRKRS
>Mature_750_residues
AGAKRFPSLIKTISKMESQSLLRFSDDGSLALRKEREKKKEPTVQGVFRANKAGFGFLHVDENEDDMFIGRNDVGYAIDG
DTVEVVVKKPADRLKGTAAEAKVVAIVDRSLKTAVGTFILDDDKPKYAGYIRSKNQKIQQKIYIKKEPVVLKGTEIIKVD
IDKYPTRGHDYFVASVRDIVGHQGDVGIDVLEVLESMDIVSEFPAEVLVEANAISEAPTAKDLIGRVDLRQETTITIDGA
DAKDLDDAIHIKLLDNGNYELGVHIADVSYYVTEGSALDKEAIARGTSVYVTDRVVPMLPERLSNGICSLNPNVDRLTQS
ALMEINSQGHVVNYQICQSVIKTTYRMTYSTVNDMIAGDEEALQEFASIADDVTLMVALHRILEAMRSKRGALNFDTQEA
KVIVNDKGMPVDVVLRQRGIAERMIESFMLAANECVAEHFAKAKLPFIYRIHEEPKAEKLQQFIDYASTFGIHIQGTANK
ISQEALQAFMAKVEGQPGAEVLNMMLLRSMQQARYSEHNHGHYGLAAEYYTHFTSPIRRYPDLLVHRMVREYSQPSQEKR
DHFTQIIPELATSSSQLERRAIDAERVVEAMKKAEYMAEYVGEEFDGIVASVVKFGFFVELPNTIEGLVHITSLPEYYHF
NERTLSLQGEKSGKVFKVGQPIRVKLVKADKETGDIDFEYLPSDFDVVEKIKMSDKASRRDRRKSSKSSKGIKKKEPKEV
AKAKTKGKTKKGSKKPFYKEQAKKKSRKRS

Specific function: 3'-5'exoribonuclease that participates in an essential cell function. Acts nonspecifically on poly(A), poly(U) and ribosomal RNAs [H]

COG id: COG0557

COG function: function code K; Exoribonuclease R

Gene ontology:

Cell location: Cytoplasm [C]

Metaboloic importance: Unknown [C]

Operon status: Not Known

Operon components: None

Similarity: Contains 1 S1 motif domain [H]

Homologues:

Organism=Homo sapiens, GI190014625, Length=471, Percent_Identity=30.9978768577495, Blast_Score=205, Evalue=1e-52,
Organism=Homo sapiens, GI190014623, Length=471, Percent_Identity=30.9978768577495, Blast_Score=205, Evalue=1e-52,
Organism=Homo sapiens, GI134288890, Length=394, Percent_Identity=32.48730964467, Blast_Score=202, Evalue=9e-52,
Organism=Homo sapiens, GI219521928, Length=407, Percent_Identity=29.2383292383292, Blast_Score=154, Evalue=2e-37,
Organism=Homo sapiens, GI19115966, Length=422, Percent_Identity=29.6208530805687, Blast_Score=154, Evalue=2e-37,
Organism=Homo sapiens, GI156105695, Length=560, Percent_Identity=23.75, Blast_Score=90, Evalue=7e-18,
Organism=Homo sapiens, GI156105693, Length=366, Percent_Identity=23.224043715847, Blast_Score=81, Evalue=5e-15,
Organism=Escherichia coli, GI87082383, Length=695, Percent_Identity=32.5179856115108, Blast_Score=377, Evalue=1e-105,
Organism=Escherichia coli, GI1787542, Length=681, Percent_Identity=25.8443465491924, Blast_Score=170, Evalue=3e-43,
Organism=Caenorhabditis elegans, GI17553506, Length=354, Percent_Identity=33.0508474576271, Blast_Score=194, Evalue=2e-49,
Organism=Caenorhabditis elegans, GI212645896, Length=472, Percent_Identity=29.8728813559322, Blast_Score=179, Evalue=5e-45,
Organism=Saccharomyces cerevisiae, GI6324552, Length=607, Percent_Identity=30.3130148270181, Blast_Score=187, Evalue=5e-48,
Organism=Saccharomyces cerevisiae, GI6320499, Length=319, Percent_Identity=26.6457680250784, Blast_Score=99, Evalue=3e-21,
Organism=Saccharomyces cerevisiae, GI6323943, Length=429, Percent_Identity=23.3100233100233, Blast_Score=70, Evalue=1e-12,
Organism=Drosophila melanogaster, GI24649634, Length=564, Percent_Identity=30.3191489361702, Blast_Score=210, Evalue=2e-54,
Organism=Drosophila melanogaster, GI24654592, Length=548, Percent_Identity=28.6496350364964, Blast_Score=171, Evalue=2e-42,
Organism=Drosophila melanogaster, GI19922976, Length=548, Percent_Identity=28.6496350364964, Blast_Score=171, Evalue=2e-42,
Organism=Drosophila melanogaster, GI24654597, Length=548, Percent_Identity=28.6496350364964, Blast_Score=171, Evalue=2e-42,

Paralogues:

None

Copy number: NA

Swissprot (AC and ID): NA

Other databases:

- InterPro:   IPR012340
- InterPro:   IPR016027
- InterPro:   IPR003029
- InterPro:   IPR022967
- InterPro:   IPR013223
- InterPro:   IPR001900
- InterPro:   IPR022966
- InterPro:   IPR004476
- InterPro:   IPR011805 [H]

Pfam domain/function: PF08206 OB_RNB; PF00773 RNB; PF00575 S1 [H]

EC number: 3.1.-.- [C]

Molecular weight: Translated: 84360; Mature: 84228

Theoretical pI: Translated: 8.33; Mature: 8.33

Prosite motif: PS50126 S1 ; PS01175 RIBONUCLEASE_II

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.4 %Cys     (Translated Protein)
2.8 %Met     (Translated Protein)
3.2 %Cys+Met (Translated Protein)
0.4 %Cys     (Mature Protein)
2.7 %Met     (Mature Protein)
3.1 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MAGAKRFPSLIKTISKMESQSLLRFSDDGSLALRKEREKKKEPTVQGVFRANKAGFGFLH
CCCHHHHHHHHHHHHHHHHHHHEEECCCCCEEHHHHHHHHCCCCHHHHHHCCCCCEEEEE
VDENEDDMFIGRNDVGYAIDGDTVEVVVKKPADRLKGTAAEAKVVAIVDRSLKTAVGTFI
ECCCCCCEEECCCCCCEEECCCEEEEEEECCHHHHCCCHHHCEEEEEHHHHHHHHHCEEE
LDDDKPKYAGYIRSKNQKIQQKIYIKKEPVVLKGTEIIKVDIDKYPTRGHDYFVASVRDI
ECCCCCCHHHHHHCCCHHHHHHHEEECCCEEEECCEEEEEECCCCCCCCCHHHHHHHHHH
VGHQGDVGIDVLEVLESMDIVSEFPAEVLVEANAISEAPTAKDLIGRVDLRQETTITIDG
HCCCCCCCHHHHHHHHHHHHHHHCCHHHEEECHHCCCCCCHHHHHHHCCCCCCCEEEECC
ADAKDLDDAIHIKLLDNGNYELGVHIADVSYYVTEGSALDKEAIARGTSVYVTDRVVPML
CCCCCCCCEEEEEEEECCCEEEEEEEEEEEEEEECCCCCCHHHHHCCCEEEEECCHHHHH
PERLSNGICSLNPNVDRLTQSALMEINSQGHVVNYQICQSVIKTTYRMTYSTVNDMIAGD
HHHHCCCCEECCCCHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHCCC
EEALQEFASIADDVTLMVALHRILEAMRSKRGALNFDTQEAKVIVNDKGMPVDVVLRQRG
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCHHHHHHHCC
IAERMIESFMLAANECVAEHFAKAKLPFIYRIHEEPKAEKLQQFIDYASTFGIHIQGTAN
HHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCEEEECCHH
KISQEALQAFMAKVEGQPGAEVLNMMLLRSMQQARYSEHNHGHYGLAAEYYTHFTSPIRR
HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHH
YPDLLVHRMVREYSQPSQEKRDHFTQIIPELATSSSQLERRAIDAERVVEAMKKAEYMAE
HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCHHHHHHHHCCHHHHHHHHHHHHHHHH
YVGEEFDGIVASVVKFGFFVELPNTIEGLVHITSLPEYYHFNERTLSLQGEKSGKVFKVG
HHCCHHHHHHHHHHHHHHEEECCHHHHHHEEHHCCCHHHCCCCEEEEECCCCCCCEEECC
QPIRVKLVKADKETGDIDFEYLPSDFDVVEKIKMSDKASRRDRRKSSKSSKGIKKKEPKE
CCEEEEEEECCCCCCCCCEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH
VAKAKTKGKTKKGSKKPFYKEQAKKKSRKRS
HHHHHHCCCCCCCCCCCCHHHHHHHHHCCCC
>Mature Secondary Structure 
AGAKRFPSLIKTISKMESQSLLRFSDDGSLALRKEREKKKEPTVQGVFRANKAGFGFLH
CCHHHHHHHHHHHHHHHHHHHEEECCCCCEEHHHHHHHHCCCCHHHHHHCCCCCEEEEE
VDENEDDMFIGRNDVGYAIDGDTVEVVVKKPADRLKGTAAEAKVVAIVDRSLKTAVGTFI
ECCCCCCEEECCCCCCEEECCCEEEEEEECCHHHHCCCHHHCEEEEEHHHHHHHHHCEEE
LDDDKPKYAGYIRSKNQKIQQKIYIKKEPVVLKGTEIIKVDIDKYPTRGHDYFVASVRDI
ECCCCCCHHHHHHCCCHHHHHHHEEECCCEEEECCEEEEEECCCCCCCCCHHHHHHHHHH
VGHQGDVGIDVLEVLESMDIVSEFPAEVLVEANAISEAPTAKDLIGRVDLRQETTITIDG
HCCCCCCCHHHHHHHHHHHHHHHCCHHHEEECHHCCCCCCHHHHHHHCCCCCCCEEEECC
ADAKDLDDAIHIKLLDNGNYELGVHIADVSYYVTEGSALDKEAIARGTSVYVTDRVVPML
CCCCCCCCEEEEEEEECCCEEEEEEEEEEEEEEECCCCCCHHHHHCCCEEEEECCHHHHH
PERLSNGICSLNPNVDRLTQSALMEINSQGHVVNYQICQSVIKTTYRMTYSTVNDMIAGD
HHHHCCCCEECCCCHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHCCC
EEALQEFASIADDVTLMVALHRILEAMRSKRGALNFDTQEAKVIVNDKGMPVDVVLRQRG
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCHHHHHHHCC
IAERMIESFMLAANECVAEHFAKAKLPFIYRIHEEPKAEKLQQFIDYASTFGIHIQGTAN
HHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCEEEECCHH
KISQEALQAFMAKVEGQPGAEVLNMMLLRSMQQARYSEHNHGHYGLAAEYYTHFTSPIRR
HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHH
YPDLLVHRMVREYSQPSQEKRDHFTQIIPELATSSSQLERRAIDAERVVEAMKKAEYMAE
HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCHHHHHHHHCCHHHHHHHHHHHHHHHH
YVGEEFDGIVASVVKFGFFVELPNTIEGLVHITSLPEYYHFNERTLSLQGEKSGKVFKVG
HHCCHHHHHHHHHHHHHHEEECCHHHHHHEEHHCCCHHHCCCCEEEEECCCCCCCEEECC
QPIRVKLVKADKETGDIDFEYLPSDFDVVEKIKMSDKASRRDRRKSSKSSKGIKKKEPKE
CCEEEEEEECCCCCCCCCEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH
VAKAKTKGKTKKGSKKPFYKEQAKKKSRKRS
HHHHHHCCCCCCCCCCCCHHHHHHHHHCCCC

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: 9.0

TargetDB status: NA

Availability: NA

References: 11337471 [H]