Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   PWW25_RS06585 Genome accession   NZ_CP118584
Coordinates   1503137..1504558 (+) Length   473 a.a.
NCBI ID   WP_005445536.1    Uniprot ID   A0A9X3ML51
Organism   Vibrio harveyi strain fish5     
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)
Genomic island 1481701..1515004 1503137..1504558 within 0


Gene organization within MGE regions


Location: 1481701..1515004
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PWW25_RS06480 - 1481701..1482144 (-) 444 WP_017818016.1 AAA family ATPase -
  PWW25_RS06485 - 1482692..1483108 (-) 417 WP_009697380.1 lysozyme inhibitor LprI family protein -
  PWW25_RS06490 - 1483272..1483628 (-) 357 WP_017190311.1 hypothetical protein -
  PWW25_RS06495 - 1483682..1484203 (-) 522 WP_045452642.1 hypothetical protein -
  PWW25_RS06500 - 1484262..1485443 (-) 1182 WP_274876969.1 hypothetical protein -
  PWW25_RS06505 btuD 1485690..1486457 (-) 768 WP_274876970.1 vitamin B12 ABC transporter ATP-binding protein BtuD -
  PWW25_RS06510 btuC 1486444..1487439 (-) 996 WP_274876971.1 vitamin B12 ABC transporter permease BtuC -
  PWW25_RS06515 - 1487542..1488570 (-) 1029 WP_274876972.1 succinylglutamate desuccinylase -
  PWW25_RS06520 - 1488809..1490608 (-) 1800 WP_274876973.1 M3 family oligoendopeptidase -
  PWW25_RS06525 cobC 1490691..1491305 (-) 615 WP_274876974.1 alpha-ribazole phosphatase -
  PWW25_RS06530 cobU 1491302..1491850 (-) 549 WP_274876975.1 bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase -
  PWW25_RS06535 - 1491847..1492653 (-) 807 WP_274876976.1 adenosylcobinamide-GDP ribazoletransferase -
  PWW25_RS06540 cobT 1492653..1493696 (-) 1044 WP_274876977.1 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase -
  PWW25_RS06545 - 1493716..1494327 (-) 612 WP_017190319.1 flavin reductase family protein -
  PWW25_RS06550 - 1495061..1495756 (+) 696 WP_274876978.1 NAD(P)H-binding protein -
  PWW25_RS06555 - 1495951..1497324 (+) 1374 WP_256902106.1 L-cystine transporter -
  PWW25_RS06560 - 1497546..1498235 (+) 690 WP_101960465.1 DUF1826 domain-containing protein -
  PWW25_RS06565 - 1499018..1499827 (-) 810 WP_042606225.1 LysR family transcriptional regulator -
  PWW25_RS06570 - 1500221..1500916 (-) 696 WP_042606224.1 aspartate/glutamate racemase family protein -
  PWW25_RS06575 - 1501510..1502145 (+) 636 WP_050921745.1 LysE family translocator -
  PWW25_RS06580 - 1502285..1502647 (+) 363 WP_050921748.1 cupin domain-containing protein -
  PWW25_RS06585 sbcB 1503137..1504558 (+) 1422 WP_005445536.1 exodeoxyribonuclease I Machinery gene
  PWW25_RS06590 - 1504617..1504991 (+) 375 WP_274876979.1 CidA/LrgA family protein -
  PWW25_RS06595 - 1504993..1505670 (+) 678 WP_005445538.1 LrgB family protein -
  PWW25_RS06600 cdd 1505926..1506813 (+) 888 WP_005445539.1 cytidine deaminase -
  PWW25_RS06605 purT 1506962..1508137 (+) 1176 WP_050903239.1 formate-dependent phosphoribosylglycinamide formyltransferase -
  PWW25_RS06610 - 1508479..1509129 (-) 651 WP_005445541.1 thiopurine S-methyltransferase -
  PWW25_RS06615 - 1509466..1510239 (+) 774 WP_005445543.1 phosphoribosylglycinamide formyltransferase -
  PWW25_RS06620 ihfA 1510383..1510679 (-) 297 WP_005445544.1 integration host factor subunit alpha -
  PWW25_RS06625 - 1511206..1512084 (+) 879 WP_274876980.1 AEC family transporter -
  PWW25_RS06630 - 1512267..1512506 (+) 240 WP_114321187.1 hypothetical protein -
  PWW25_RS06635 - 1512528..1512950 (+) 423 WP_274876981.1 hypothetical protein -
  PWW25_RS06640 - 1513103..1513363 (+) 261 WP_005445548.1 hypothetical protein -
  PWW25_RS06645 - 1513363..1513746 (+) 384 WP_017817997.1 hypothetical protein -
  PWW25_RS06650 - 1513737..1514075 (+) 339 WP_050903088.1 hypothetical protein -
  PWW25_RS06655 - 1514279..1515004 (+) 726 WP_050902615.1 metallophosphoesterase -

Sequence

Protein


Download         Length: 473 a.a.        Molecular weight: 54569.91 Da        Isoelectric Point: 4.9808

>NTDB_id=793649 PWW25_RS06585 WP_005445536.1 1503137..1504558(+) (sbcB) [Vibrio harveyi strain fish5]
MHQDNQPTFFFFDYETWGTSPAKDRPSQFAGVRTDENFNIIGEPLVMYCRPPADYLPSPEAALITGITPQKAMQEGLPEP
EFIAKIHAELSKPKTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVMRACHALRPEGVEWPENDEGFT
SFKLEHLSVANGIEHSNAHDAMADVIATIEMAKKVKAAQPKLFDYFFSMRNKRKLNELVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELKERLYTKRDELGDLLPVPVKLVHLNKCPILAPAKTLTAENAEV
IGIDRQQCLNNLALLRQHPEIREKLISLFSIEREFEKSNDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARHYAGTLDEQEQRRWAQHCREVFESQIEEYMMNLENLVHEHESDEKKIAILKSVYRYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=793649 PWW25_RS06585 WP_005445536.1 1503137..1504558(+) (sbcB) [Vibrio harveyi strain fish5]
ATGCACCAAGACAATCAGCCCACTTTTTTCTTTTTCGATTACGAGACTTGGGGAACAAGTCCAGCCAAAGACCGCCCAAG
CCAGTTTGCTGGCGTTCGCACTGATGAAAACTTCAATATCATTGGTGAACCTTTGGTGATGTACTGTCGTCCACCTGCTG
ATTACCTTCCTTCGCCAGAAGCAGCTTTGATCACTGGTATTACACCACAAAAAGCAATGCAAGAAGGCTTACCTGAACCT
GAGTTTATTGCCAAAATTCATGCCGAATTGTCTAAACCAAAGACGACTAGCCTTGGCTACAACAGCATACGTTTTGATGA
TGAAGTCACTCGTTACACTTGCTACCGAAACTTCATCGACCCATACGCATGGAGCTGGCAAAACGGCAACTCACGATGGG
ATTTGCTTGACGTGATGCGAGCATGTCATGCCCTGCGTCCTGAAGGCGTAGAATGGCCAGAGAACGATGAAGGCTTTACA
AGCTTCAAGCTAGAGCATTTATCCGTAGCGAATGGCATTGAACACAGCAATGCTCACGATGCGATGGCCGACGTGATTGC
CACGATTGAAATGGCGAAGAAAGTTAAAGCCGCCCAACCTAAGCTATTTGACTACTTTTTCTCGATGCGTAACAAGCGCA
AACTCAATGAGCTGGTTGATATTGTCAATATGACTCCGTTGATGCATGTATCAGGCATGCTTGGGCGTGAATGCCAATAC
ACAAGCTGGATTGTGCCTGTGGCTTGGCATCCAACCAACAATAACGCTGTTATCACGATTGATTTAGCCAAAGATCCTCA
GCCGATCCTTGAACTTTCAGCGGAAGAACTGAAAGAACGCTTGTACACCAAGCGTGACGAATTGGGCGACTTACTGCCTG
TACCAGTGAAGCTAGTGCATCTGAACAAGTGCCCTATTCTCGCTCCAGCAAAAACATTAACCGCGGAAAATGCGGAAGTC
ATTGGTATTGACCGCCAACAATGTTTAAACAATTTAGCGTTGTTGCGCCAACACCCAGAGATCCGAGAGAAGCTGATTAG
TCTATTCTCTATAGAACGTGAATTCGAAAAGAGTAATGACGTTGATACGCAGCTTTACGATGGTTTTTTCTCGCCTGCTG
ATCGCGCTGCTATGGACATCATTCGTGAAACCGATCCGAATAACTTAGCCGCACTGGACATTGAATTCGATGATAAACGA
ATCAAGCCATTGCTTTTCCGTTACCGTGCTCGCCATTATGCAGGCACATTAGATGAACAAGAACAAAGACGCTGGGCACA
ACATTGTCGTGAAGTTTTCGAAAGTCAGATTGAAGAGTACATGATGAATTTGGAAAACTTAGTTCACGAACATGAAAGTG
ACGAAAAGAAGATAGCAATATTAAAATCCGTCTATCGTTATGTAGAGAGCCTAGCCTCCTAA

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