Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   OCV37_RS08565 Genome accession   NZ_AP024903
Coordinates   2012780..2014204 (+) Length   474 a.a.
NCBI ID   WP_038186191.1    Uniprot ID   -
Organism   Vibrio rhizosphaerae strain LMG 23790     
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 1991611..2018910 2012780..2014204 within 0


Gene organization within MGE regions


Location: 1991611..2018910
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  OCV37_RS08425 - 1991611..1992630 (-) 1020 WP_038181574.1 phage-like tail protein -
  OCV37_RS08430 - 1992621..1992830 (-) 210 WP_038181572.1 tail protein X -
  OCV37_RS08435 - 1992827..1993207 (-) 381 WP_038181569.1 phage tail protein -
  OCV37_RS08440 - 1993204..1995666 (-) 2463 WP_038181566.1 phage tail tape measure protein -
  OCV37_RS08445 - 1995789..1996349 (-) 561 WP_038181563.1 phage tail assembly protein -
  OCV37_RS08450 tnpA 1996486..1996947 (-) 462 WP_261855926.1 IS200/IS605 family transposase -
  OCV37_RS08455 - 1997149..1997655 (-) 507 WP_038186220.1 phage major tail tube protein -
  OCV37_RS08460 - 1997655..1998824 (-) 1170 WP_038186217.1 tail protein -
  OCV37_RS08465 - 1998817..1999020 (-) 204 WP_038186215.1 hypothetical protein -
  OCV37_RS08470 - 1999100..1999375 (-) 276 WP_077335925.1 hypothetical protein -
  OCV37_RS08475 - 1999390..2000622 (-) 1233 WP_261888071.1 formylglycine-generating enzyme family protein -
  OCV37_RS08480 - 2000615..2000998 (-) 384 WP_261888072.1 hypothetical protein -
  OCV37_RS08485 - 2000946..2001221 (-) 276 WP_261888073.1 hypothetical protein -
  OCV37_RS08490 - 2001236..2002468 (-) 1233 WP_261888074.1 formylglycine-generating enzyme family protein -
  OCV37_RS08495 - 2002461..2002703 (-) 243 WP_261888075.1 hypothetical protein -
  OCV37_RS08500 - 2002849..2003124 (-) 276 WP_261888076.1 hypothetical protein -
  OCV37_RS08505 - 2003139..2004371 (-) 1233 WP_261888077.1 formylglycine-generating enzyme family protein -
  OCV37_RS08510 - 2004364..2004918 (-) 555 WP_261888078.1 phage tail protein -
  OCV37_RS08515 - 2004915..2005679 (-) 765 WP_051680914.1 phage tail protein I -
  OCV37_RS08520 - 2005639..2006640 (-) 1002 WP_038186212.1 baseplate J/gp47 family protein -
  OCV37_RS08525 - 2006612..2006971 (-) 360 WP_038186209.1 phage baseplate protein -
  OCV37_RS08530 - 2006971..2007168 (-) 198 WP_038186207.1 hypothetical protein -
  OCV37_RS08535 - 2007170..2007787 (-) 618 WP_169739391.1 phage baseplate assembly protein V -
  OCV37_RS08540 - 2007771..2008328 (-) 558 WP_038186204.1 hypothetical protein -
  OCV37_RS08545 - 2009016..2009612 (-) 597 WP_038186202.1 transposase -
  OCV37_RS08550 - 2010484..2011425 (-) 942 WP_169739390.1 restriction endonuclease -
  OCV37_RS08555 - 2011539..2012195 (-) 657 WP_261888079.1 hypothetical protein -
  OCV37_RS08560 - 2012192..2012599 (-) 408 WP_038186194.1 Arm DNA-binding domain-containing protein -
  OCV37_RS08565 sbcB 2012780..2014204 (+) 1425 WP_038186191.1 exodeoxyribonuclease I Machinery gene
  OCV37_RS08570 - 2014300..2014665 (+) 366 WP_038186233.1 CidA/LrgA family protein -
  OCV37_RS08575 - 2014678..2015367 (+) 690 WP_038186190.1 CidB/LrgB family autolysis modulator -
  OCV37_RS08580 cdd 2015515..2016402 (+) 888 WP_038186188.1 cytidine deaminase -
  OCV37_RS08585 purT 2016546..2017721 (+) 1176 WP_038186185.1 formate-dependent phosphoribosylglycinamide formyltransferase -
  OCV37_RS08590 - 2017829..2018473 (-) 645 WP_038186184.1 thiopurine S-methyltransferase -
  OCV37_RS08595 ihfA 2018611..2018910 (-) 300 WP_038186182.1 integration host factor subunit alpha -

Sequence

Protein


Download         Length: 474 a.a.        Molecular weight: 54933.21 Da        Isoelectric Point: 5.7266

>NTDB_id=89313 OCV37_RS08565 WP_038186191.1 2012780..2014204(+) (sbcB) [Vibrio rhizosphaerae strain LMG 23790]
MNNQEQPTFFFFDYETWGTHPAKDRPCQFAGVRTDMDFNIIGEPLVIFCKPPADYLPAPEAALITGITPQQASAKGLSEP
EFIQRIHQELSHPHTTCLGYNNIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVARACHALRPEGVVWPENEDGNT
SFKLEHLSVANGIEHTNAHDAMADVYATIELAKVIKNAQPKLFDYFYSMRHKRKLNALIDIVSMTPLMHVSGMLGSHCQY
TSWVVPLAWHPQNKNAVIMVDLAKDPQPLFDLNADEIRQRLYTKRDDLQEDELPIPVKLVHLNKCPILAPAKTLTAENAQ
TIGIDRDKCLHHLSLIKQSQDIREKLVQVFGEEKEYPTDTDVDTMLYHDFFNPADKAAMEIIRQTSPEALPDLSISFQDA
RIKPLLFRYRARNWPETLTLHEQQQWQSHCQDYFSQYLDDYILRLENLAHEHEQDPHKMQILKSIYHYVLNLTS

Nucleotide


Download         Length: 1425 bp        

>NTDB_id=89313 OCV37_RS08565 WP_038186191.1 2012780..2014204(+) (sbcB) [Vibrio rhizosphaerae strain LMG 23790]
ATGAACAACCAAGAACAACCGACATTCTTCTTCTTCGATTATGAGACATGGGGCACTCACCCCGCGAAAGATCGTCCCTG
TCAGTTTGCCGGGGTCAGAACAGATATGGACTTCAATATCATTGGTGAACCACTGGTGATCTTTTGTAAACCGCCAGCCG
ATTATCTGCCGGCACCGGAAGCGGCACTCATCACCGGTATTACACCTCAACAAGCCAGTGCCAAAGGTTTGTCAGAGCCC
GAGTTTATTCAGCGGATTCATCAGGAACTGTCTCATCCCCATACCACCTGTCTGGGTTATAACAACATCCGCTTTGACGA
TGAAGTGACACGCTACACCTGTTATCGCAATTTCATTGATCCTTATGCATGGAGCTGGCAAAACGGCAATTCGCGTTGGG
ATCTGCTCGACGTCGCGCGCGCCTGTCATGCATTACGTCCCGAAGGGGTTGTATGGCCAGAAAACGAAGACGGTAATACC
AGCTTTAAACTCGAACATCTTTCCGTTGCCAATGGGATTGAACATACCAATGCCCATGATGCGATGGCCGATGTCTATGC
CACCATTGAGTTGGCAAAAGTGATCAAAAATGCCCAGCCGAAACTCTTCGATTATTTCTACTCAATGCGCCATAAGCGTA
AACTGAATGCACTGATCGATATTGTCAGTATGACGCCATTGATGCACGTTTCCGGTATGCTCGGCAGCCACTGCCAATAT
ACCAGCTGGGTTGTGCCGCTGGCTTGGCATCCGCAGAACAAAAATGCCGTGATTATGGTCGACTTGGCGAAAGATCCTCA
GCCACTGTTTGATCTCAATGCTGACGAAATTCGGCAACGGCTCTACACAAAACGTGATGATTTACAAGAAGATGAGTTAC
CGATTCCGGTAAAATTGGTTCATCTCAATAAATGCCCGATCCTCGCTCCCGCGAAGACGTTGACAGCAGAAAATGCCCAG
ACAATCGGCATCGACAGAGACAAATGTTTACATCATTTGTCTCTCATCAAGCAATCTCAGGATATCAGAGAGAAACTGGT
ACAAGTATTTGGTGAAGAGAAAGAATATCCGACAGATACGGATGTCGATACGATGTTATACCATGACTTTTTCAATCCGG
CTGACAAAGCTGCGATGGAAATTATCCGGCAAACATCACCCGAAGCTTTACCGGATTTATCAATCTCTTTCCAAGACGCT
CGGATCAAACCCTTGTTGTTTCGCTACCGAGCCAGAAACTGGCCTGAAACCCTTACCCTGCATGAACAACAACAATGGCA
GTCCCACTGTCAGGATTATTTTTCCCAGTATCTGGATGATTATATTCTTCGTCTGGAAAATCTGGCGCACGAACATGAGC
AGGATCCACATAAAATGCAGATCCTGAAATCAATCTACCATTATGTGCTGAACCTGACATCATAG

Domains

Predicted by InterproScan.

Exonuclease (RNase_T)

(11-191)

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

73.362

99.789

0.732

Multiple sequence alignment