Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   K6748_RS08975 Genome accession   NZ_CP082307
Coordinates   1901108..1902529 (+) Length   473 a.a.
NCBI ID   WP_064368108.1    Uniprot ID   -
Organism   Vibrio alginolyticus strain HNV2     
Function   promote homologous recombination (predicted from homology)   
Homologous recombination

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
Prophage 1864394..1908511 1901108..1902529 within 0


Gene organization within MGE regions


Location: 1864394..1908511
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  K6748_RS23925 - 1864394..1865002 (+) 609 WP_074191204.1 acyltransferase -
  K6748_RS08780 (K6748_08710) - 1865216..1865359 (-) 144 WP_176310930.1 hypothetical protein -
  K6748_RS08785 (K6748_08715) - 1865361..1867538 (-) 2178 WP_229628088.1 hypothetical protein -
  K6748_RS08790 (K6748_08720) - 1867593..1870352 (-) 2760 WP_176310928.1 host specificity factor TipJ family phage tail protein -
  K6748_RS08795 (K6748_08725) - 1870309..1870731 (-) 423 WP_238958875.1 hypothetical protein -
  K6748_RS08800 (K6748_08730) - 1870728..1871180 (-) 453 WP_225472820.1 DUF1833 family protein -
  K6748_RS08805 (K6748_08735) - 1871191..1871742 (-) 552 WP_238958876.1 hypothetical protein -
  K6748_RS08810 (K6748_08740) - 1871742..1873994 (-) 2253 WP_176310926.1 hypothetical protein -
  K6748_RS08815 (K6748_08745) - 1873975..1874259 (-) 285 WP_025500496.1 phage tail protein -
  K6748_RS08820 (K6748_08750) - 1874325..1874795 (-) 471 WP_176310925.1 phage minor tail protein G -
  K6748_RS08825 (K6748_08755) - 1874799..1875302 (-) 504 WP_176310924.1 phage tail tube protein -
  K6748_RS08830 (K6748_08760) gpU 1875305..1875751 (-) 447 WP_176310923.1 phage tail terminator protein -
  K6748_RS08835 (K6748_08765) - 1875741..1876373 (-) 633 WP_025632824.1 phage tail protein -
  K6748_RS08840 (K6748_08770) - 1876370..1876648 (-) 279 WP_176310922.1 sugar transporter -
  K6748_RS08845 (K6748_08775) - 1876641..1876832 (-) 192 WP_025632827.1 hypothetical protein -
  K6748_RS08850 (K6748_08780) - 1876893..1878866 (-) 1974 WP_086046678.1 phage major capsid protein -
  K6748_RS08855 (K6748_08785) - 1878832..1880391 (-) 1560 WP_086046677.1 phage portal protein -
  K6748_RS08860 (K6748_08790) - 1880391..1880918 (-) 528 WP_238958877.1 hypothetical protein -
  K6748_RS08865 (K6748_08795) - 1880912..1882846 (-) 1935 WP_140390462.1 terminase gpA endonuclease subunit -
  K6748_RS08870 (K6748_08800) - 1882857..1883426 (-) 570 WP_025632836.1 terminase small subunit -
  K6748_RS08875 (K6748_08805) - 1883875..1884831 (-) 957 WP_238958878.1 tyrosine-type recombinase/integrase -
  K6748_RS08880 (K6748_08810) - 1885417..1885602 (-) 186 WP_238958879.1 hypothetical protein -
  K6748_RS08885 (K6748_08815) - 1885644..1886102 (-) 459 WP_140139306.1 hypothetical protein -
  K6748_RS08890 (K6748_08820) - 1886068..1886355 (-) 288 WP_053807284.1 hypothetical protein -
  K6748_RS08895 - 1886490..1887140 (-) 651 WP_238958880.1 hypothetical protein -
  K6748_RS08900 (K6748_08830) - 1887154..1888152 (-) 999 WP_206928582.1 DUF4747 family protein -
  K6748_RS08905 (K6748_08835) - 1888327..1888968 (-) 642 WP_238958881.1 hypothetical protein -
  K6748_RS08910 (K6748_08840) - 1889139..1889720 (-) 582 WP_238958882.1 hypothetical protein -
  K6748_RS08915 (K6748_08845) - 1889721..1890452 (-) 732 WP_064368129.1 ATP-binding protein -
  K6748_RS08920 - 1890449..1891234 (-) 786 WP_238958883.1 hypothetical protein -
  K6748_RS23930 - 1891231..1891362 (-) 132 WP_255201246.1 hypothetical protein -
  K6748_RS08925 (K6748_08855) - 1891422..1891970 (-) 549 WP_053807278.1 toxin YdaT family protein -
  K6748_RS08930 (K6748_08860) - 1892040..1892234 (-) 195 WP_029823469.1 YdaS family helix-turn-helix protein -
  K6748_RS08935 (K6748_08865) - 1892345..1893046 (+) 702 WP_029823468.1 S24 family peptidase -
  K6748_RS08940 (K6748_08870) - 1893272..1893544 (+) 273 WP_025766807.1 hypothetical protein -
  K6748_RS08945 (K6748_08875) - 1893701..1894009 (+) 309 WP_238958884.1 hypothetical protein -
  K6748_RS08950 (K6748_08880) - 1894108..1894965 (+) 858 WP_238958885.1 DNA adenine methylase -
  K6748_RS08955 (K6748_08885) - 1894976..1896364 (-) 1389 WP_238958886.1 hypothetical protein -
  K6748_RS08960 (K6748_08890) - 1896366..1898447 (-) 2082 WP_238958887.1 DUF87 domain-containing protein -
  K6748_RS08965 (K6748_08895) - 1898887..1899582 (-) 696 WP_238958888.1 hypothetical protein -
  K6748_RS08970 (K6748_08900) - 1899731..1900927 (-) 1197 WP_238958889.1 site-specific integrase -
  K6748_RS08975 (K6748_08905) sbcB 1901108..1902529 (+) 1422 WP_064368108.1 exodeoxyribonuclease I Machinery gene
  K6748_RS08980 (K6748_08910) - 1902585..1902959 (+) 375 WP_005397786.1 CidA/LrgA family protein -
  K6748_RS08985 (K6748_08915) - 1902961..1903638 (+) 678 WP_005377888.1 LrgB family protein -
  K6748_RS08990 (K6748_08920) cdd 1904069..1904956 (+) 888 WP_005377892.1 cytidine deaminase -
  K6748_RS08995 (K6748_08925) purT 1905100..1906275 (+) 1176 WP_054866055.1 formate-dependent phosphoribosylglycinamide formyltransferase -
  K6748_RS09000 (K6748_08930) - 1906348..1906998 (-) 651 WP_021707633.1 thiopurine S-methyltransferase -
  K6748_RS09005 (K6748_08935) - 1907314..1908093 (+) 780 WP_205460916.1 phosphoribosylglycinamide formyltransferase -
  K6748_RS09010 (K6748_08940) ihfA 1908215..1908511 (-) 297 WP_005377899.1 integration host factor subunit alpha -

Sequence

Protein


Download         Length: 473 a.a.        Molecular weight: 54352.54 Da        Isoelectric Point: 4.8172

>NTDB_id=601193 K6748_RS08975 WP_064368108.1 1901108..1902529(+) (sbcB) [Vibrio alginolyticus strain HNV2]
MNNTEQPTFFFFDYETWGTNPAKDRPSQFAGVRTDENFNIIGEPLVMYCQPPADYLPSPEAALITGITPQKTVQEGLSEP
EFIAKIHAELAKPNTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVLRACHALRPEGVEWPENEDGFT
SFKLEHLSVANGIEHSNAHDAMADVVATIEMAKKVKAAQPKLFDYFFSMRQKRKLNDLVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELHERLYTKREDLGELLPVPVKLVHLNKCPILAPAKTLTAENAES
IGIDRQQCLANLALLRQHPEIREKLISLFSVERKFDKSDDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARNFPGTLDEQEQRRWALHCREVFESQIEEYMLNLENLVHEHESDEKKIAILKSVYRYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=601193 K6748_RS08975 WP_064368108.1 1901108..1902529(+) (sbcB) [Vibrio alginolyticus strain HNV2]
ATGAATAATACCGAACAGCCTACATTCTTCTTCTTTGATTATGAGACATGGGGAACCAACCCCGCGAAAGATCGCCCAAG
CCAGTTCGCTGGTGTTCGTACAGATGAAAACTTTAATATCATCGGCGAGCCTTTAGTCATGTACTGCCAGCCACCTGCTG
ATTATCTTCCGTCTCCTGAAGCTGCACTTATTACTGGTATTACTCCGCAAAAAACGGTTCAAGAAGGCCTTTCTGAGCCA
GAGTTTATCGCTAAGATTCACGCTGAACTCGCGAAACCCAATACTACCAGTTTAGGCTACAACAGCATTCGCTTTGATGA
CGAAGTGACCCGTTATACTTGTTATCGCAACTTTATCGATCCATACGCATGGAGTTGGCAAAACGGTAACTCACGTTGGG
ATTTACTCGATGTACTACGCGCGTGCCATGCCCTTCGCCCAGAAGGCGTAGAATGGCCAGAAAACGAAGATGGCTTCACT
AGCTTTAAATTAGAACACTTGTCTGTGGCTAACGGCATAGAACATAGTAACGCGCACGATGCCATGGCAGATGTGGTTGC
GACTATCGAAATGGCAAAGAAAGTAAAAGCAGCGCAACCAAAATTGTTTGATTACTTTTTTTCTATGCGCCAAAAGCGCA
AGCTCAATGATTTAGTCGACATCGTCAACATGACACCGTTGATGCACGTTTCAGGCATGCTAGGGCGCGAATGCCAGTAC
ACTAGCTGGATTGTGCCTGTTGCTTGGCATCCAACCAATAATAACGCCGTTATCACCATCGATTTAGCGAAAGACCCTCA
ACCTATTCTTGAGCTATCCGCAGAAGAGCTGCACGAAAGACTCTACACGAAGCGCGAAGATCTTGGTGAATTGCTACCAG
TGCCAGTTAAACTAGTTCATTTGAACAAATGCCCTATTCTCGCCCCTGCAAAAACGTTAACGGCTGAAAATGCAGAGTCT
ATTGGCATTGATCGCCAACAATGTCTCGCCAATCTCGCTTTGTTGCGCCAACATCCTGAAATTAGAGAAAAGCTGATTAG
CCTCTTTTCAGTCGAGCGCAAATTCGATAAAAGTGATGACGTCGATACACAACTTTACGACGGGTTCTTTTCTCCAGCCG
ATCGCGCAGCTATGGATATCATTCGCGAAACCGATCCGAATAATCTTGCTGCATTAGACATTGAATTTGATGACAAGCGC
ATTAAACCTCTATTGTTCCGCTATCGTGCGCGTAACTTCCCAGGCACATTAGACGAGCAAGAACAAAGACGCTGGGCACT
ACACTGTCGAGAAGTGTTTGAAAGCCAAATTGAAGAGTACATGCTGAATTTAGAAAACTTAGTTCACGAACATGAAAGTG
ACGAAAAGAAGATTGCGATATTAAAATCCGTGTACCGTTATGTAGAGAGCTTAGCTTCCTAA

Domains

Predicted by InterproScan.

Exonuclease C-terminal (Exonuc_X-T_C)

(210-469)

Exonuclease (RNase_T)

(11-190)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  sbcB Vibrio cholerae O1 biovar El Tor strain E7946

79.281

100

0.793