Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   JV59_RS08270 Genome accession   NZ_CP009264
Coordinates   1749191..1750615 (+) Length   474 a.a.
NCBI ID   WP_038511920.1    Uniprot ID   -
Organism   Vibrio coralliilyticus strain OCN014     
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 1711746..1749122 1749191..1750615 flank 69


Gene organization within MGE regions


Location: 1711746..1750615
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JV59_RS08035 (JV59_32190) - 1711746..1712984 (-) 1239 WP_038511792.1 site-specific integrase -
  JV59_RS08040 (JV59_32195) - 1712985..1713956 (-) 972 WP_038511795.1 hypothetical protein -
  JV59_RS08045 (JV59_32200) - 1713956..1714159 (-) 204 WP_038511798.1 hypothetical protein -
  JV59_RS08050 (JV59_32205) - 1714143..1714523 (-) 381 WP_038511801.1 phage tail protein -
  JV59_RS08055 (JV59_32210) - 1714548..1717271 (-) 2724 WP_038511804.1 phage tail tape measure protein -
  JV59_RS08060 (JV59_32215) - 1717428..1718099 (-) 672 WP_235284676.1 phage tail assembly protein -
  JV59_RS08065 (JV59_32220) - 1718167..1718658 (-) 492 WP_038511807.1 hypothetical protein -
  JV59_RS08070 (JV59_32225) - 1718782..1719270 (-) 489 WP_038511810.1 phage major tail tube protein -
  JV59_RS08075 (JV59_32230) - 1719270..1720448 (-) 1179 WP_038511828.1 tail protein -
  JV59_RS08080 (JV59_32235) - 1720448..1720654 (-) 207 WP_038511831.1 hypothetical protein -
  JV59_RS26300 - 1720759..1721250 (-) 492 WP_052131695.1 hypothetical protein -
  JV59_RS08090 (JV59_32245) - 1721247..1721720 (-) 474 WP_038511834.1 hypothetical protein -
  JV59_RS26305 - 1721687..1722784 (-) 1098 WP_052131696.1 phage tail protein -
  JV59_RS08100 (JV59_32255) - 1722781..1723404 (-) 624 WP_038511837.1 phage tail protein -
  JV59_RS08105 (JV59_32260) - 1723388..1724368 (-) 981 WP_038511840.1 baseplate J/gp47 family protein -
  JV59_RS08110 (JV59_32265) - 1724365..1724697 (-) 333 WP_038511842.1 phage baseplate protein -
  JV59_RS08115 (JV59_32270) - 1724694..1725392 (-) 699 WP_052131697.1 phage baseplate assembly protein V -
  JV59_RS08120 (JV59_32275) - 1725361..1725858 (-) 498 WP_235284677.1 hypothetical protein -
  JV59_RS08125 (JV59_32280) - 1725824..1726351 (-) 528 WP_038511845.1 hypothetical protein -
  JV59_RS08130 (JV59_32285) - 1726329..1726661 (-) 333 WP_038511847.1 hypothetical protein -
  JV59_RS08135 (JV59_32290) - 1726663..1726995 (-) 333 WP_038511850.1 hypothetical protein -
  JV59_RS08140 (JV59_32295) - 1727073..1729244 (-) 2172 WP_038511852.1 head maturation protease, ClpP-related -
  JV59_RS08145 (JV59_32300) - 1729237..1730724 (-) 1488 WP_038511854.1 phage portal protein -
  JV59_RS08150 (JV59_32305) - 1730717..1730923 (-) 207 WP_038511857.1 hypothetical protein -
  JV59_RS08155 (JV59_32310) - 1730920..1733013 (-) 2094 WP_038511860.1 terminase gpA endonuclease subunit -
  JV59_RS08160 (JV59_32315) - 1732994..1733464 (-) 471 WP_038511863.1 DUF1441 family protein -
  JV59_RS27045 (JV59_32320) - 1733935..1734123 (-) 189 WP_038511866.1 hypothetical protein -
  JV59_RS08170 (JV59_32325) - 1734124..1734393 (-) 270 WP_038511868.1 hypothetical protein -
  JV59_RS08175 (JV59_32330) - 1734448..1734876 (-) 429 WP_038511871.1 M15 family metallopeptidase -
  JV59_RS08180 (JV59_32335) - 1734873..1735157 (-) 285 WP_038511874.1 hypothetical protein -
  JV59_RS26310 - 1735340..1736023 (-) 684 WP_052131698.1 hypothetical protein -
  JV59_RS08190 (JV59_32345) - 1736028..1737320 (-) 1293 WP_038511877.1 AAA family ATPase -
  JV59_RS08195 (JV59_32350) - 1737557..1738135 (-) 579 WP_038511880.1 hypothetical protein -
  JV59_RS08200 (JV59_32355) - 1738176..1738589 (-) 414 WP_038511883.1 hypothetical protein -
  JV59_RS08205 (JV59_32360) - 1738555..1739484 (-) 930 WP_038511886.1 hypothetical protein -
  JV59_RS08210 (JV59_32365) - 1739666..1740214 (-) 549 WP_038511889.1 toxin YdaT family protein -
  JV59_RS08215 (JV59_32370) - 1740248..1740496 (-) 249 WP_038511892.1 helix-turn-helix domain-containing protein -
  JV59_RS08220 (JV59_32375) - 1740587..1741255 (+) 669 WP_038511895.1 LexA family protein -
  JV59_RS08225 (JV59_32380) - 1741489..1741758 (+) 270 WP_038511898.1 hypothetical protein -
  JV59_RS08230 (JV59_32385) - 1741921..1742169 (+) 249 WP_080749081.1 hypothetical protein -
  JV59_RS08235 (JV59_32390) - 1742166..1742537 (+) 372 WP_038511901.1 hypothetical protein -
  JV59_RS08240 (JV59_32395) - 1742611..1742850 (+) 240 WP_038511904.1 hypothetical protein -
  JV59_RS08245 (JV59_32400) - 1742884..1743186 (+) 303 WP_038511907.1 helix-turn-helix transcriptional regulator -
  JV59_RS08250 (JV59_32405) - 1743576..1744970 (+) 1395 WP_038511910.1 hypothetical protein -
  JV59_RS26315 - 1744963..1745589 (+) 627 WP_052131699.1 hypothetical protein -
  JV59_RS08260 (JV59_32415) - 1745589..1747565 (+) 1977 WP_038511914.1 hypothetical protein -
  JV59_RS08265 (JV59_32420) - 1747818..1749008 (-) 1191 WP_038511917.1 tyrosine-type recombinase/integrase -
  JV59_RS08270 (JV59_32425) sbcB 1749191..1750615 (+) 1425 WP_038511920.1 exodeoxyribonuclease I Machinery gene

Sequence

Protein


Download         Length: 474 a.a.        Molecular weight: 54740.94 Da        Isoelectric Point: 4.9057

>NTDB_id=127856 JV59_RS08270 WP_038511920.1 1749191..1750615(+) (sbcB) [Vibrio coralliilyticus strain OCN014]
MNNTEQPTFFFFDYETWGTNPAKDRPSQFAGVRTDMDFNIIGEPLVIYCQPPSDYLPSPEAALITGITPQTAASKGLPEP
EFITKIHEQFSTPNTINLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVMRACHALRPEGINWPENEEGFI
SFKLEHLSVANGIEHENAHDAMADVIATIEMAKKVKAAQPKLFDYFLSMRHKRKLNELVDIVNMTPLMHVSGMLGRECNY
TSWVVPVAWHPTNQNAVIVVDLAKDPQPLLDLDVEQLNERLYTKHSELGPDELPVPIKLVHLNKCPILAPAKTLTAENAA
NIGIDREKCLQNLERLRQHPEIREKLNSLYSIEREYEKSDDVDTMLYDGFFSPAAKQSMDIIRETEPKNLSALDISFSDD
RIAPLLFRYRARHFPWTLDESEQQKWAAHSREYFESRIEDYMLNLENLVHEHESDEKKIAILKSVYQYVQKLVS

Nucleotide


Download         Length: 1425 bp        

>NTDB_id=127856 JV59_RS08270 WP_038511920.1 1749191..1750615(+) (sbcB) [Vibrio coralliilyticus strain OCN014]
ATGAACAATACCGAACAACCGACATTCTTCTTTTTTGATTATGAAACGTGGGGAACCAACCCAGCAAAAGACAGACCGTC
CCAATTTGCTGGTGTACGCACCGACATGGATTTCAATATCATCGGTGAGCCTCTTGTTATCTACTGCCAACCGCCTTCAG
ATTATCTTCCATCCCCCGAAGCTGCGCTTATCACAGGTATCACACCTCAGACGGCAGCTAGTAAAGGGTTACCAGAACCG
GAATTTATTACCAAAATTCATGAGCAGTTTTCCACGCCAAACACCATCAACTTGGGTTACAATAGCATTCGATTTGATGA
CGAAGTGACGCGATATACCTGTTACCGAAATTTCATCGATCCGTATGCGTGGAGCTGGCAAAACGGCAACTCTCGCTGGG
ACTTACTCGATGTCATGCGCGCCTGTCACGCCCTTCGCCCAGAAGGTATTAATTGGCCAGAGAATGAAGAAGGTTTTATC
AGCTTTAAGCTAGAGCACTTATCCGTTGCCAATGGCATTGAGCACGAGAATGCACACGATGCCATGGCTGACGTTATAGC
AACGATTGAAATGGCTAAAAAGGTAAAAGCCGCTCAGCCTAAGCTCTTTGATTATTTCCTTAGCATGCGCCACAAGCGCA
AACTGAACGAACTCGTCGATATCGTGAATATGACACCGCTTATGCACGTATCGGGTATGTTGGGACGCGAATGCAATTAC
ACTAGCTGGGTGGTTCCGGTCGCTTGGCATCCAACCAACCAGAATGCGGTGATCGTGGTCGATTTGGCGAAAGATCCTCA
GCCGTTGTTGGATTTAGATGTAGAACAGCTTAATGAGCGTCTCTACACCAAACATTCTGAACTTGGCCCAGACGAACTGC
CTGTACCAATCAAACTTGTCCATCTCAACAAGTGCCCTATTTTGGCTCCAGCCAAAACATTAACTGCTGAGAATGCAGCT
AACATAGGCATTGACAGAGAAAAATGCTTACAAAACCTTGAGCGACTAAGACAGCACCCTGAGATTAGAGAAAAACTCAA
TTCGCTATACAGTATCGAGAGAGAATACGAAAAGAGCGATGATGTTGATACTATGCTTTACGATGGCTTCTTCTCTCCTG
CGGCAAAGCAATCAATGGATATCATACGAGAAACTGAACCAAAGAATCTTTCCGCCCTTGATATCTCATTCAGTGACGAC
AGAATTGCTCCGCTTCTATTCCGCTATCGCGCCAGACATTTTCCGTGGACATTGGATGAGAGTGAACAACAAAAATGGGC
AGCACACAGCCGCGAATACTTCGAAAGTCGAATAGAAGACTACATGTTGAATTTGGAAAACTTAGTTCACGAGCATGAGA
GTGACGAAAAAAAGATAGCTATCTTAAAATCTGTTTACCAATACGTTCAAAAGCTAGTATCTTAA

Domains

Predicted by InterproScan.

Exonuclease (RNase_T)

(11-190)

Exonuclease C-terminal (Exonuc_X-T_C)

(210-470)


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

78.224

99.789

0.781

Multiple sequence alignment