Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   PY250_RS06235 Genome accession   NZ_CP119334
Coordinates   1355784..1357205 (-) Length   473 a.a.
NCBI ID   WP_086046658.1    Uniprot ID   -
Organism   Vibrio alginolyticus strain 2-1     
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 1355354..1393077 1355784..1357205 within 0


Gene organization within MGE regions


Location: 1355354..1393077
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PY250_RS06230 (PY250_06230) - 1355354..1355728 (-) 375 WP_005397786.1 CidA/LrgA family protein -
  PY250_RS06235 (PY250_06235) sbcB 1355784..1357205 (-) 1422 WP_086046658.1 exodeoxyribonuclease I Machinery gene
  PY250_RS06240 (PY250_06240) - 1357386..1358582 (+) 1197 WP_275593495.1 tyrosine-type recombinase/integrase -
  PY250_RS06245 (PY250_06245) - 1358725..1359360 (+) 636 WP_275593496.1 AbiV family abortive infection protein -
  PY250_RS06250 (PY250_06250) - 1359504..1360655 (+) 1152 WP_275593497.1 hypothetical protein -
  PY250_RS06255 (PY250_06255) - 1360790..1361227 (+) 438 WP_275593498.1 hypothetical protein -
  PY250_RS06265 (PY250_06265) - 1361377..1361850 (+) 474 WP_275593500.1 hypothetical protein -
  PY250_RS06270 (PY250_06270) - 1362124..1362840 (+) 717 WP_275593501.1 FRG domain-containing protein -
  PY250_RS06275 (PY250_06275) - 1362932..1363552 (+) 621 WP_275593502.1 hypothetical protein -
  PY250_RS06280 (PY250_06280) - 1363594..1363899 (-) 306 WP_275593503.1 helix-turn-helix transcriptional regulator -
  PY250_RS06285 (PY250_06285) - 1364056..1364328 (-) 273 WP_025766807.1 hypothetical protein -
  PY250_RS06290 (PY250_06290) - 1364595..1365257 (-) 663 WP_025766806.1 LexA family protein -
  PY250_RS06295 (PY250_06295) - 1365373..1365582 (+) 210 WP_025766805.1 helix-turn-helix domain-containing protein -
  PY250_RS06300 (PY250_06300) - 1365635..1366183 (+) 549 WP_275593504.1 toxin YdaT family protein -
  PY250_RS06305 (PY250_06305) - 1366371..1367156 (+) 786 WP_258671426.1 hypothetical protein -
  PY250_RS06310 (PY250_06310) - 1367153..1367884 (+) 732 WP_064368129.1 ATP-binding protein -
  PY250_RS06315 (PY250_06315) - 1367885..1368466 (+) 582 WP_275593505.1 hypothetical protein -
  PY250_RS06320 (PY250_06320) - 1368693..1369841 (+) 1149 WP_275593506.1 AAA family ATPase -
  PY250_RS06325 (PY250_06325) - 1369849..1370790 (+) 942 WP_275593507.1 DUF4435 domain-containing protein -
  PY250_RS06330 (PY250_06330) - 1370943..1371230 (+) 288 WP_275593508.1 hypothetical protein -
  PY250_RS06335 (PY250_06335) - 1371196..1371654 (+) 459 WP_275593509.1 hypothetical protein -
  PY250_RS06340 (PY250_06340) - 1371696..1371881 (+) 186 WP_275593510.1 hypothetical protein -
  PY250_RS06345 (PY250_06345) - 1372467..1373423 (+) 957 WP_275593511.1 tyrosine-type recombinase/integrase -
  PY250_RS06350 (PY250_06350) - 1373871..1374440 (+) 570 WP_275593512.1 terminase small subunit -
  PY250_RS06355 (PY250_06355) - 1374505..1376388 (+) 1884 WP_275593541.1 terminase gpA endonuclease subunit -
  PY250_RS06360 (PY250_06360) - 1376382..1376909 (+) 528 WP_275593513.1 hypothetical protein -
  PY250_RS06365 (PY250_06365) - 1376909..1378462 (+) 1554 WP_275593514.1 phage portal protein -
  PY250_RS06370 (PY250_06370) - 1378434..1380404 (+) 1971 WP_275593515.1 phage major capsid protein -
  PY250_RS06375 (PY250_06375) - 1380464..1380655 (+) 192 WP_025766789.1 hypothetical protein -
  PY250_RS06380 (PY250_06380) - 1380648..1380926 (+) 279 WP_275593516.1 sugar transporter -
  PY250_RS06385 (PY250_06385) - 1380923..1381555 (+) 633 WP_025766787.1 phage tail protein -
  PY250_RS06390 (PY250_06390) gpU 1381545..1381991 (+) 447 WP_275593517.1 phage tail terminator protein -
  PY250_RS06395 (PY250_06395) - 1381994..1382491 (+) 498 WP_086046680.1 phage tail tube protein -
  PY250_RS06400 (PY250_06400) - 1382494..1382973 (+) 480 WP_086046681.1 phage minor tail protein G -
  PY250_RS06405 (PY250_06405) - 1382997..1383329 (+) 333 WP_025632816.1 phage tail assembly protein T -
  PY250_RS06410 (PY250_06410) - 1383310..1385541 (+) 2232 WP_275593518.1 hypothetical protein -
  PY250_RS06415 (PY250_06415) - 1385548..1386024 (+) 477 WP_275593519.1 hypothetical protein -
  PY250_RS06420 (PY250_06420) - 1386014..1387912 (+) 1899 WP_275593520.1 sialate O-acetylesterase -
  PY250_RS06425 (PY250_06425) - 1387915..1388598 (+) 684 WP_275593521.1 hypothetical protein -
  PY250_RS06430 (PY250_06430) - 1388604..1389140 (+) 537 WP_275593522.1 DUF1833 family protein -
  PY250_RS06435 (PY250_06435) - 1389140..1389565 (+) 426 WP_275593523.1 phage tail protein -
  PY250_RS06440 (PY250_06440) - 1389525..1392338 (+) 2814 WP_275593524.1 host specificity factor TipJ family phage tail protein -
  PY250_RS06445 (PY250_06445) - 1392364..1393077 (-) 714 WP_025766776.1 hypothetical protein -

Sequence

Protein


Download         Length: 473 a.a.        Molecular weight: 54341.54 Da        Isoelectric Point: 4.7710

>NTDB_id=798541 PY250_RS06235 WP_086046658.1 1355784..1357205(-) (sbcB) [Vibrio alginolyticus strain 2-1]
MNNTEQPTFFFFDYETWGTNPAKDRPSQFAGVRTDENFNIIGEPLVMYCQPPADYLPSPEAALITGITPQKTVQEGLSEP
EFIAKIHAELARPNTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVLRACHALRPEGVEWPENEDGFT
SFKLEHLSVANGIEHSNAHDAMADVIATIEMAKKVKAAQPKLFDYFFSMRQKRKLNDLVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELHERLYTKREDLGELLPVPVKLVHLNKCPILAPAKTLTAENAES
IGIDRQQCLANLALLRQHPEIREKLISLFSVERKFDKSDDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARNFPGTLDEQEQRRWALHCREVFESQIEEYMLNLENLVHEHESDEKKIAILKSVYCYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=798541 PY250_RS06235 WP_086046658.1 1355784..1357205(-) (sbcB) [Vibrio alginolyticus strain 2-1]
ATGAATAATACCGAACAGCCCACATTCTTCTTCTTTGATTATGAGACATGGGGAACCAACCCCGCGAAAGATCGCCCAAG
CCAGTTTGCTGGTGTTCGTACAGATGAAAACTTTAATATCATCGGCGAGCCTTTAGTCATGTACTGCCAGCCACCTGCTG
ATTATCTTCCGTCTCCTGAAGCTGCGCTTATTACTGGTATTACTCCGCAAAAAACGGTTCAAGAAGGCCTTTCTGAGCCA
GAGTTTATCGCTAAGATTCACGCTGAACTCGCGAGACCAAATACCACCAGTTTAGGCTACAACAGCATTCGCTTTGATGA
CGAAGTGACCCGTTATACTTGTTATCGCAACTTTATCGATCCATACGCATGGAGTTGGCAAAACGGTAACTCGCGTTGGG
ATTTACTCGATGTACTACGCGCGTGCCATGCCCTTCGCCCAGAAGGCGTAGAATGGCCAGAAAACGAAGATGGCTTCACT
AGCTTTAAATTAGAACACTTGTCTGTGGCTAACGGCATAGAACATAGTAACGCGCACGATGCCATGGCAGATGTGATTGC
GACTATCGAAATGGCAAAGAAAGTAAAAGCAGCGCAACCAAAATTGTTTGATTACTTTTTTTCTATGCGCCAAAAGCGCA
AGCTCAATGATTTAGTCGACATCGTCAACATGACACCGTTGATGCACGTTTCAGGCATGTTAGGGCGCGAATGCCAGTAC
ACTAGCTGGATTGTGCCTGTTGCTTGGCATCCAACCAATAATAATGCCGTTATCACCATCGATTTAGCGAAAGACCCTCA
ACCTATTCTTGAGCTATCCGCAGAAGAGCTGCACGAAAGACTCTACACTAAGCGCGAAGATCTTGGTGAATTGCTACCAG
TGCCAGTTAAACTAGTTCATTTGAACAAATGCCCTATTCTCGCCCCTGCAAAAACGTTAACGGCTGAAAATGCAGAGTCT
ATTGGCATTGATCGCCAGCAATGTCTCGCTAATCTCGCTTTGTTGCGCCAACATCCTGAAATTAGAGAAAAGCTGATTAG
CCTCTTTTCAGTCGAGCGTAAATTCGATAAAAGTGATGACGTCGATACACAGCTTTACGACGGGTTCTTTTCTCCGGCTG
ATCGCGCAGCTATGGATATCATTCGAGAAACCGACCCGAATAATCTTGCTGCATTAGACATTGAATTTGATGACAAGCGT
ATTAAACCTCTATTGTTCCGCTATCGTGCGCGTAACTTCCCAGGCACATTAGACGAGCAAGAACAAAGACGCTGGGCACT
ACACTGTCGAGAAGTGTTTGAAAGCCAAATTGAAGAGTACATGCTGAATTTAGAAAACTTAGTTCACGAACATGAAAGTG
ACGAAAAGAAGATTGCGATATTAAAATCCGTGTACTGTTATGTAGAGAGCTTAGCTTCCTAA

Domains

Predicted by InterproScan.

Exonuclease (RNase_T)

(11-190)

Exonuclease C-terminal (Exonuc_X-T_C)

(210-469)


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

79.493

100

0.795