Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   BA890_RS06260 Genome accession   NZ_CP016345
Coordinates   1375899..1377320 (-) Length   473 a.a.
NCBI ID   WP_020333046.1    Uniprot ID   A0AAN1CW98
Organism   Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 strain ATCC 14048     
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 1375466..1412517 1375899..1377320 within 0


Gene organization within MGE regions


Location: 1375466..1412517
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  BA890_RS06255 (BA890_06255) - 1375466..1375840 (-) 375 WP_020333045.1 CidA/LrgA family protein -
  BA890_RS06260 (BA890_06260) sbcB 1375899..1377320 (-) 1422 WP_020333046.1 exodeoxyribonuclease I Machinery gene
  BA890_RS06265 (BA890_06265) - 1377503..1378699 (+) 1197 WP_020333047.1 tyrosine-type recombinase/integrase -
  BA890_RS06270 (BA890_06270) - 1378846..1379691 (+) 846 WP_020333048.1 hypothetical protein -
  BA890_RS06275 (BA890_06275) - 1379804..1380847 (+) 1044 WP_020333049.1 hypothetical protein -
  BA890_RS06280 (BA890_06280) - 1380937..1381260 (+) 324 WP_020333050.1 hypothetical protein -
  BA890_RS06285 (BA890_06285) - 1381617..1382126 (+) 510 WP_061778632.1 hypothetical protein -
  BA890_RS06290 (BA890_06290) - 1382366..1382671 (-) 306 WP_020333054.1 helix-turn-helix transcriptional regulator -
  BA890_RS23875 - 1382712..1382870 (-) 159 WP_020333055.1 hypothetical protein -
  BA890_RS06295 (BA890_06295) - 1382845..1383246 (-) 402 WP_020333056.1 hypothetical protein -
  BA890_RS06300 (BA890_06300) - 1383243..1383485 (-) 243 WP_020333057.1 hypothetical protein -
  BA890_RS06305 (BA890_06305) - 1383647..1383919 (-) 273 WP_020333058.1 hypothetical protein -
  BA890_RS06310 (BA890_06310) - 1384245..1384673 (-) 429 WP_020333059.1 hypothetical protein -
  BA890_RS06315 (BA890_06315) - 1384894..1385562 (-) 669 WP_020333060.1 LexA family protein -
  BA890_RS23330 - 1385653..1385886 (+) 234 WP_020333061.1 helix-turn-helix transcriptional regulator -
  BA890_RS06320 (BA890_06320) - 1385933..1386481 (+) 549 WP_020333062.1 toxin YdaT family protein -
  BA890_RS24285 - 1386551..1386682 (+) 132 WP_255201246.1 hypothetical protein -
  BA890_RS06325 (BA890_06325) - 1386679..1387467 (+) 789 WP_236614642.1 helix-turn-helix domain-containing protein -
  BA890_RS06330 (BA890_06330) - 1387464..1388195 (+) 732 WP_020333064.1 ATP-binding protein -
  BA890_RS06335 (BA890_06335) - 1388196..1388777 (+) 582 WP_020333065.1 hypothetical protein -
  BA890_RS06340 (BA890_06340) - 1388953..1389573 (+) 621 WP_020333066.1 hypothetical protein -
  BA890_RS06345 (BA890_06345) - 1389705..1390388 (+) 684 WP_020333068.1 GIY-YIG nuclease family protein -
  BA890_RS06350 (BA890_06350) - 1390746..1391183 (+) 438 WP_020333069.1 hypothetical protein -
  BA890_RS06355 (BA890_06355) - 1391237..1391914 (+) 678 WP_020333071.1 hypothetical protein -
  BA890_RS06360 (BA890_06360) - 1392044..1392325 (+) 282 WP_020333072.1 hypothetical protein -
  BA890_RS06365 (BA890_06365) - 1392291..1392749 (+) 459 WP_020333073.1 hypothetical protein -
  BA890_RS06370 (BA890_06370) - 1392791..1392976 (+) 186 WP_020333074.1 hypothetical protein -
  BA890_RS06375 (BA890_06375) - 1393096..1394310 (+) 1215 WP_020333075.1 tyrosine-type recombinase/integrase -
  BA890_RS06380 (BA890_06380) - 1394749..1395318 (+) 570 WP_020333076.1 terminase small subunit -
  BA890_RS06385 (BA890_06385) - 1395272..1397266 (+) 1995 WP_231113042.1 terminase gpA endonuclease subunit -
  BA890_RS06390 (BA890_06390) - 1397260..1397787 (+) 528 WP_020333078.1 hypothetical protein -
  BA890_RS06395 (BA890_06395) - 1397787..1399340 (+) 1554 WP_020333079.1 phage portal protein -
  BA890_RS06400 (BA890_06400) - 1399312..1401282 (+) 1971 WP_020333080.1 phage major capsid protein -
  BA890_RS06405 (BA890_06405) - 1401343..1401534 (+) 192 WP_020333081.1 hypothetical protein -
  BA890_RS06410 (BA890_06410) - 1401527..1401805 (+) 279 WP_020333082.1 hypothetical protein -
  BA890_RS06415 (BA890_06415) - 1401802..1402434 (+) 633 WP_020333083.1 phage tail protein -
  BA890_RS06420 (BA890_06420) gpU 1402424..1402870 (+) 447 WP_020333084.1 phage tail terminator protein -
  BA890_RS06425 (BA890_06425) - 1402873..1403373 (+) 501 WP_020333085.1 phage tail tube protein -
  BA890_RS06430 (BA890_06430) - 1403379..1403819 (+) 441 WP_020333086.1 phage minor tail protein domain-containing protein -
  BA890_RS06435 (BA890_06435) - 1403885..1404169 (+) 285 WP_020333088.1 phage tail assembly protein T -
  BA890_RS06440 (BA890_06440) - 1404150..1406381 (+) 2232 WP_020333090.1 hypothetical protein -
  BA890_RS06445 (BA890_06445) - 1406381..1406977 (+) 597 WP_020333091.1 hypothetical protein -
  BA890_RS06450 (BA890_06450) - 1406974..1407525 (+) 552 WP_020333092.1 DUF2163 domain-containing protein -
  BA890_RS06455 (BA890_06455) - 1407529..1412517 (+) 4989 WP_020333093.1 phage tail tip protein -

Sequence

Protein


Download         Length: 473 a.a.        Molecular weight: 54415.60 Da        Isoelectric Point: 4.7761

>NTDB_id=187114 BA890_RS06260 WP_020333046.1 1375899..1377320(-) (sbcB) [Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 strain ATCC 14048]
MNNSEQPTFFFFDYETWGTNPAKDRPSQFAGVRTDENFNIIGEPLVMYCQPPADYLPSPEAALITGIIPQKAVQEGLPEP
EFIAKIHAELSKPNTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVLRACHALRPEGVEWPENEEGFP
SFKLEHLSVANGIEHSNAHDAMADVIATIEMAKKVKAAQPKLFDYFFSMRQKRKLNELVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELHERLYTKREDLGDLLPVPVKLVHLNKCPILAPAKTLTAENAES
IGIDRQQCLNNLALLRQHPEIREKLISLFSVERTFEKSDDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARNFPGTLDEQEQRRWAQHCREVFESQIEEYMLNLENLVHEHESDEKKIALLKSVYRYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=187114 BA890_RS06260 WP_020333046.1 1375899..1377320(-) (sbcB) [Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759 strain ATCC 14048]
ATGAATAACTCAGAACAGCCGACATTCTTCTTCTTTGACTACGAAACTTGGGGAACAAACCCTGCAAAAGATCGTCCGAG
TCAATTTGCTGGTGTTCGCACAGATGAAAATTTCAATATCATCGGCGAGCCTTTAGTTATGTATTGCCAGCCACCTGCTG
ATTACCTTCCTTCTCCTGAAGCTGCTTTAATTACTGGGATTATCCCACAAAAGGCGGTGCAGGAAGGTCTGCCTGAGCCT
GAGTTCATTGCTAAAATTCATGCCGAGTTATCCAAACCCAATACCACCAGTTTGGGTTACAACAGTATTCGTTTTGATGA
TGAAGTGACGCGTTACACCTGTTACCGCAACTTTATTGACCCGTATGCGTGGAGTTGGCAGAACGGCAATTCGCGCTGGG
ATTTACTTGATGTGCTGCGCGCTTGTCATGCCCTTCGACCAGAAGGCGTTGAATGGCCAGAAAATGAAGAAGGCTTTCCT
AGCTTCAAACTTGAGCATTTGTCTGTTGCCAACGGTATTGAACACAGCAATGCACACGATGCCATGGCTGACGTTATCGC
AACGATCGAGATGGCGAAGAAAGTTAAAGCCGCTCAGCCTAAGTTGTTCGATTACTTCTTCTCCATGCGTCAAAAGCGTA
AGCTGAATGAATTGGTTGATATCGTTAATATGACGCCTCTGATGCACGTTTCTGGCATGTTAGGACGCGAGTGTCAGTAC
ACAAGCTGGATTGTGCCTGTTGCATGGCATCCGACGAACAACAACGCGGTTATCACGATTGATTTAGCCAAAGATCCGCA
ACCTATCCTAGAGCTGTCTGCGGAAGAGCTGCACGAAAGGTTGTACACCAAGCGAGAAGATCTCGGTGATTTGCTGCCTG
TGCCAGTTAAACTTGTTCACTTGAATAAGTGCCCTATTCTGGCACCAGCGAAAACACTGACGGCTGAAAACGCGGAGTCT
ATCGGCATTGACCGTCAACAATGCTTGAACAATCTGGCTCTGTTGCGTCAGCACCCAGAGATTCGAGAAAAGCTGATCAG
CCTGTTTTCTGTTGAGCGCACATTTGAAAAAAGTGATGATGTGGATACTCAACTGTACGATGGCTTCTTCTCTCCGGCGG
ATCGCGCAGCGATGGATATTATTCGCGAGACCGACCCGAATAATCTGGCCGCTCTGGATATTGAGTTCGATGACAAGCGC
ATTAAACCACTGTTGTTCCGTTACCGTGCTCGAAACTTCCCTGGCACGTTAGACGAACAGGAACAAAGACGTTGGGCACA
GCACTGCCGTGAAGTGTTTGAAAGCCAAATCGAAGAGTATATGCTGAATTTAGAAAACTTAGTTCACGAACATGAAAGTG
ACGAAAAGAAAATAGCACTATTAAAATCCGTTTATCGTTACGTAGAGAGCCTAGCCTCTTAA

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

Multiple sequence alignment