Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   K08M3_RS06485 Genome accession   NZ_CP017913
Coordinates   1371180..1372601 (-) Length   473 a.a.
NCBI ID   WP_086046658.1    Uniprot ID   -
Organism   Vibrio alginolyticus strain K08M3     
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 1370750..1410642 1371180..1372601 within 0


Gene organization within MGE regions


Location: 1370750..1410642
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  K08M3_RS06480 (K08M3_12800) - 1370750..1371124 (-) 375 WP_005397786.1 CidA/LrgA family protein -
  K08M3_RS06485 (K08M3_12810) sbcB 1371180..1372601 (-) 1422 WP_086046658.1 exodeoxyribonuclease I Machinery gene
  K08M3_RS06490 (K08M3_12820) - 1372782..1373999 (+) 1218 WP_086046659.1 tyrosine-type recombinase/integrase -
  K08M3_RS06495 (K08M3_12830) - 1374122..1374649 (+) 528 WP_086046660.1 hypothetical protein -
  K08M3_RS06500 (K08M3_12840) - 1374652..1375209 (+) 558 WP_086046661.1 hypothetical protein -
  K08M3_RS06505 (K08M3_12850) - 1375357..1376112 (+) 756 WP_086046662.1 hypothetical protein -
  K08M3_RS06510 (K08M3_12860) - 1376186..1376842 (+) 657 WP_086046663.1 TauD/TfdA family dioxygenase -
  K08M3_RS06515 (K08M3_12870) - 1376853..1377824 (+) 972 WP_086046664.1 hypothetical protein -
  K08M3_RS06520 (K08M3_12880) - 1377964..1378668 (+) 705 WP_086046665.1 Abi-alpha family protein -
  K08M3_RS06525 (K08M3_12890) - 1378740..1379045 (-) 306 WP_086046666.1 helix-turn-helix transcriptional regulator -
  K08M3_RS26695 (K08M3_12900) - 1379086..1379244 (-) 159 WP_020333055.1 hypothetical protein -
  K08M3_RS06530 (K08M3_12910) - 1379342..1379584 (-) 243 WP_086046667.1 hypothetical protein -
  K08M3_RS06535 (K08M3_12920) - 1379739..1380011 (-) 273 WP_025766807.1 hypothetical protein -
  K08M3_RS06540 (K08M3_12930) - 1380211..1381407 (+) 1197 WP_157664331.1 BRCT domain-containing protein -
  K08M3_RS06545 (K08M3_12940) - 1381422..1382108 (-) 687 WP_086046669.1 LexA family protein -
  K08M3_RS06550 (K08M3_12950) - 1382214..1382468 (+) 255 WP_086046670.1 hypothetical protein -
  K08M3_RS06555 (K08M3_12960) - 1382508..1383056 (+) 549 WP_053807278.1 toxin YdaT family protein -
  K08M3_RS27115 (K08M3_12980) - 1383244..1384029 (+) 786 WP_231970820.1 hypothetical protein -
  K08M3_RS06565 (K08M3_12990) - 1384026..1384757 (+) 732 WP_086046671.1 ATP-binding protein -
  K08M3_RS06570 (K08M3_13000) - 1384758..1385339 (+) 582 WP_086046672.1 hypothetical protein -
  K08M3_RS06575 (K08M3_13010) - 1385606..1386841 (+) 1236 WP_086046673.1 AAA family ATPase -
  K08M3_RS06580 (K08M3_13020) - 1386834..1387352 (+) 519 WP_050450732.1 hypothetical protein -
  K08M3_RS06585 (K08M3_13030) - 1387583..1388347 (+) 765 WP_031812313.1 hypothetical protein -
  K08M3_RS06590 (K08M3_13040) - 1388507..1388794 (+) 288 WP_031812312.1 hypothetical protein -
  K08M3_RS06595 (K08M3_13050) - 1388760..1389218 (+) 459 WP_086046674.1 hypothetical protein -
  K08M3_RS06600 (K08M3_13060) - 1389260..1389445 (+) 186 WP_025766795.1 hypothetical protein -
  K08M3_RS06605 (K08M3_13070) - 1389773..1390987 (+) 1215 WP_086046675.1 tyrosine-type recombinase/integrase -
  K08M3_RS06610 (K08M3_13080) - 1391436..1392005 (+) 570 WP_025632836.1 terminase small subunit -
  K08M3_RS06615 (K08M3_13090) - 1392016..1393950 (+) 1935 WP_086046676.1 terminase gpA endonuclease subunit -
  K08M3_RS06620 (K08M3_13100) - 1393944..1394471 (+) 528 WP_025632833.1 hypothetical protein -
  K08M3_RS06625 (K08M3_13110) - 1394471..1396030 (+) 1560 WP_086046677.1 phage portal protein -
  K08M3_RS06630 (K08M3_13120) - 1395996..1397969 (+) 1974 WP_086046678.1 phage major capsid protein -
  K08M3_RS06635 (K08M3_13130) - 1398029..1398220 (+) 192 WP_025632827.1 hypothetical protein -
  K08M3_RS06640 (K08M3_13140) - 1398213..1398491 (+) 279 WP_025766788.1 ATP-binding sugar transporter from pro-phage family protein -
  K08M3_RS06645 (K08M3_13150) - 1398488..1399120 (+) 633 WP_086046679.1 phage tail protein -
  K08M3_RS06650 (K08M3_13160) gpU 1399110..1399556 (+) 447 WP_025766786.1 phage tail terminator protein -
  K08M3_RS06655 (K08M3_13170) - 1399559..1400056 (+) 498 WP_086046680.1 phage tail tube protein -
  K08M3_RS06660 (K08M3_13180) - 1400059..1400538 (+) 480 WP_086046681.1 phage minor tail protein G -
  K08M3_RS06665 (K08M3_13190) - 1400562..1400894 (+) 333 WP_025632816.1 phage tail assembly protein T -
  K08M3_RS06670 (K08M3_13200) - 1400875..1403106 (+) 2232 WP_086046682.1 hypothetical protein -
  K08M3_RS06675 (K08M3_13210) - 1403113..1403589 (+) 477 WP_086046683.1 hypothetical protein -
  K08M3_RS06680 (K08M3_13220) - 1403579..1405477 (+) 1899 WP_086046684.1 sialate O-acetylesterase -
  K08M3_RS06685 (K08M3_13230) - 1405480..1406163 (+) 684 WP_025766780.1 hypothetical protein -
  K08M3_RS06690 (K08M3_13240) - 1406169..1406705 (+) 537 WP_005376972.1 DUF1833 family protein -
  K08M3_RS06695 (K08M3_13250) - 1406705..1407130 (+) 426 WP_086046685.1 phage tail protein -
  K08M3_RS06700 (K08M3_13260) - 1407090..1409903 (+) 2814 WP_086046686.1 host specificity factor TipJ family phage tail protein -
  K08M3_RS06705 (K08M3_13270) - 1409929..1410642 (-) 714 WP_025766776.1 hypothetical protein -

Sequence

Protein


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

>NTDB_id=204000 K08M3_RS06485 WP_086046658.1 1371180..1372601(-) (sbcB) [Vibrio alginolyticus strain K08M3]
MNNTEQPTFFFFDYETWGTNPAKDRPSQFAGVRTDENFNIIGEPLVMYCQPPADYLPSPEAALITGITPQKTVQEGLSEP
EFIAKIHAELARPNTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVLRACHALRPEGVEWPENEDGFT
SFKLEHLSVANGIEHSNAHDAMADVIATIEMAKKVKAAQPKLFDYFFSMRQKRKLNDLVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELHERLYTKREDLGELLPVPVKLVHLNKCPILAPAKTLTAENAES
IGIDRQQCLANLALLRQHPEIREKLISLFSVERKFDKSDDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARNFPGTLDEQEQRRWALHCREVFESQIEEYMLNLENLVHEHESDEKKIAILKSVYCYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=204000 K08M3_RS06485 WP_086046658.1 1371180..1372601(-) (sbcB) [Vibrio alginolyticus strain K08M3]
ATGAATAATACCGAACAGCCTACATTCTTCTTCTTTGATTATGAGACATGGGGAACCAACCCCGCGAAAGATCGCCCAAG
CCAGTTTGCTGGTGTTCGTACAGATGAAAACTTTAATATCATCGGCGAGCCTTTAGTCATGTACTGTCAACCACCAGCTG
ATTATCTTCCGTCTCCTGAAGCTGCGCTTATTACTGGTATTACTCCGCAAAAAACGGTTCAAGAAGGCCTTTCTGAGCCA
GAGTTTATCGCTAAGATTCACGCTGAACTCGCGAGACCAAATACCACCAGTTTAGGCTACAACAGCATTCGCTTTGATGA
CGAAGTGACCCGTTATACTTGTTATCGCAACTTTATCGATCCATACGCATGGAGTTGGCAAAACGGTAACTCGCGTTGGG
ATTTACTCGATGTACTACGCGCGTGCCATGCCCTTCGCCCAGAAGGCGTAGAATGGCCAGAAAACGAAGATGGCTTCACT
AGCTTTAAATTAGAACACTTGTCTGTGGCTAACGGCATAGAACATAGTAACGCGCACGATGCCATGGCAGATGTGATTGC
GACTATCGAAATGGCAAAGAAAGTAAAAGCAGCGCAACCAAAATTGTTTGATTACTTTTTTTCTATGCGCCAAAAGCGCA
AGCTCAATGATTTAGTCGACATCGTCAACATGACACCGTTGATGCACGTTTCAGGCATGCTAGGGCGCGAATGCCAGTAC
ACTAGCTGGATTGTGCCTGTTGCTTGGCATCCAACCAATAATAACGCCGTTATCACCATCGATTTAGCGAAAGACCCTCA
ACCTATTCTTGAGCTATCCGCAGAAGAGCTGCACGAAAGACTCTACACTAAGCGCGAAGATCTTGGTGAATTGCTACCAG
TGCCAGTTAAACTAGTTCATTTGAACAAATGCCCTATTCTCGCCCCTGCAAAAACGTTAACGGCTGAAAATGCGGAGTCT
ATTGGCATTGATCGCCAGCAATGTCTCGCTAATCTCGCTTTGTTGCGCCAACATCCTGAAATTAGAGAAAAGCTGATTAG
CCTCTTTTCAGTCGAGCGTAAATTCGATAAAAGTGATGACGTCGATACACAGCTTTACGACGGGTTCTTTTCTCCGGCTG
ATCGCGCAGCTATGGATATCATTCGAGAAACCGACCCGAATAATCTTGCTGCATTAGACATTGAATTTGATGACAAGCGC
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

Multiple sequence alignment