Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   Vspart_RS09765 Genome accession   NZ_CP046268
Coordinates   2272691..2274115 (+) Length   474 a.a.
NCBI ID   WP_182287461.1    Uniprot ID   -
Organism   Vibrio spartinae strain 3.6     
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 2253543..2278857 2272691..2274115 within 0


Gene organization within MGE regions


Location: 2253543..2278857
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  Vspart_RS09640 (Vspart_01990) - 2253543..2254505 (-) 963 WP_205410501.1 phage late control D family protein -
  Vspart_RS09645 (Vspart_01991) - 2254550..2254759 (-) 210 WP_074373495.1 tail protein X -
  Vspart_RS09650 (Vspart_01992) - 2254756..2255136 (-) 381 WP_074373494.1 phage tail protein -
  Vspart_RS09655 (Vspart_01993) - 2255133..2257655 (-) 2523 WP_182287456.1 phage tail tape measure protein -
  Vspart_RS09660 (Vspart_01994) - 2257796..2258338 (-) 543 WP_074373492.1 phage tail assembly protein -
  Vspart_RS09665 (Vspart_01995) - 2258427..2258933 (-) 507 WP_074373491.1 phage major tail tube protein -
  Vspart_RS09670 (Vspart_01996) - 2258933..2260102 (-) 1170 WP_074373490.1 phage tail protein -
  Vspart_RS09675 (Vspart_01997) - 2260095..2260292 (-) 198 WP_074373489.1 hypothetical protein -
  Vspart_RS09680 (Vspart_01998) - 2260389..2260565 (-) 177 WP_267129504.1 phage tail assembly chaperone -
  Vspart_RS09685 (Vspart_02000) - 2260816..2261502 (-) 687 WP_182287457.1 hypothetical protein -
  Vspart_RS09690 (Vspart_02001) - 2261523..2262062 (-) 540 WP_074373487.1 phage tail protein -
  Vspart_RS09695 (Vspart_02002) - 2262285..2262560 (-) 276 WP_182287458.1 hypothetical protein -
  Vspart_RS09700 (Vspart_02003) - 2262574..2263803 (-) 1230 WP_074373485.1 SUMF1/EgtB/PvdO family nonheme iron enzyme -
  Vspart_RS09705 (Vspart_02004) - 2263803..2264354 (-) 552 WP_074373484.1 phage tail protein -
  Vspart_RS09710 (Vspart_02005) - 2264576..2264851 (-) 276 WP_074373483.1 hypothetical protein -
  Vspart_RS09715 (Vspart_02006) - 2264865..2266097 (-) 1233 WP_074373482.1 SUMF1/EgtB/PvdO family nonheme iron enzyme -
  Vspart_RS09720 (Vspart_02007) - 2266097..2266648 (-) 552 WP_074373481.1 phage tail protein -
  Vspart_RS09725 (Vspart_02008) - 2266645..2267409 (-) 765 WP_074373480.1 phage tail protein I -
  Vspart_RS09730 (Vspart_02009) - 2267369..2268370 (-) 1002 WP_074373479.1 baseplate J/gp47 family protein -
  Vspart_RS09735 (Vspart_02010) - 2268342..2268704 (-) 363 WP_205410500.1 phage baseplate protein -
  Vspart_RS09740 (Vspart_02011) - 2268701..2268898 (-) 198 WP_074373477.1 hypothetical protein -
  Vspart_RS09745 (Vspart_02012) - 2268900..2269517 (-) 618 WP_074373476.1 phage baseplate assembly protein V -
  Vspart_RS09750 (Vspart_02013) - 2269501..2270058 (-) 558 WP_182287459.1 hypothetical protein -
  Vspart_RS09755 (Vspart_02014) - 2270887..2271483 (-) 597 WP_074373473.1 hypothetical protein -
  Vspart_RS09760 (Vspart_02015) - 2271694..2272440 (+) 747 WP_182287460.1 S24 family peptidase -
  Vspart_RS09765 (Vspart_02016) sbcB 2272691..2274115 (+) 1425 WP_182287461.1 exodeoxyribonuclease I Machinery gene
  Vspart_RS09770 (Vspart_02017) - 2274216..2274581 (+) 366 WP_182287462.1 CidA/LrgA family protein -
  Vspart_RS09775 (Vspart_02018) - 2274594..2275283 (+) 690 WP_074373469.1 CidB/LrgB family autolysis modulator -
  Vspart_RS09780 (Vspart_02019) cdd 2275431..2276318 (+) 888 WP_074373468.1 cytidine deaminase -
  Vspart_RS09785 (Vspart_02020) purT 2276462..2277637 (+) 1176 WP_182287463.1 formate-dependent phosphoribosylglycinamide formyltransferase -
  Vspart_RS09790 (Vspart_02021) - 2277783..2278427 (-) 645 WP_074373466.1 thiopurine S-methyltransferase -
  Vspart_RS09795 (Vspart_02022) - 2278558..2278857 (-) 300 WP_074373465.1 integration host factor subunit alpha -

Sequence

Protein


Download         Length: 474 a.a.        Molecular weight: 54967.33 Da        Isoelectric Point: 6.1457

>NTDB_id=402162 Vspart_RS09765 WP_182287461.1 2272691..2274115(+) (sbcB) [Vibrio spartinae strain 3.6]
MKNNEQPTFFFFDYETWGVHPAKDRPCQFAGVRTDMDFNIIGEPLVIFCQLPVDYLPAPEAALITGITPQQANSKGLSEP
EFIQRIHQELSHPNTTCLGYNNIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVARACHALRPEGVVWPQNENGNT
SFKLEHLSVANGIEHTNAHDAMADVYATIELAKVIKNAQPKLFDYFYSMRHKRKLNALIDIVSMTPLMHVSGMLGSHCQY
TSWVVPLAWHPHNKNAVIMVDLAKDPQPLFDLNADEIKERLYTKHEDLQDDELPIPVKLVHLNKCPILAPAKTLTAENAH
TIGIDRDKCLHHLSLMKQAQDIREKLVQVFGEEKDYPTNTDVDTMLYHNFFNPADKAAMEIIRQTSPEALRDLSISFQDS
RITPLLFRYRARNYPETLTMHEQKQWQSHCQDYFSQHMDDYILRLENLAHEHEQDSHKMQILKSIYQYVLNLTS

Nucleotide


Download         Length: 1425 bp        

>NTDB_id=402162 Vspart_RS09765 WP_182287461.1 2272691..2274115(+) (sbcB) [Vibrio spartinae strain 3.6]
ATGAAAAACAACGAACAACCAACATTCTTCTTTTTCGATTATGAAACTTGGGGAGTCCATCCCGCAAAAGATCGTCCCTG
TCAGTTTGCCGGGGTCAGAACGGATATGGACTTCAATATCATTGGCGAACCGCTGGTCATCTTCTGTCAACTACCGGTCG
ATTATCTGCCTGCACCGGAAGCTGCACTCATCACCGGTATCACCCCACAACAGGCCAATAGCAAAGGTTTATCAGAGCCA
GAATTTATTCAGCGTATCCATCAGGAATTGTCCCATCCCAATACAACCTGTCTGGGTTATAACAATATCCGTTTTGACGA
TGAAGTGACTCGTTATACCTGTTATCGCAATTTTATTGATCCTTATGCATGGAGCTGGCAAAACGGCAATTCGCGTTGGG
ATCTGCTGGACGTTGCTCGCGCCTGTCATGCATTACGTCCGGAAGGCGTTGTATGGCCTCAGAATGAAAATGGCAATACC
AGCTTTAAACTCGAACATCTTTCCGTTGCAAATGGTATCGAGCATACAAATGCCCATGATGCGATGGCTGACGTGTATGC
AACCATCGAATTGGCAAAAGTCATCAAAAATGCGCAACCGAAATTATTCGATTATTTCTATTCCATGCGCCATAAACGCA
AACTGAATGCGTTAATCGATATTGTCAGTATGACGCCATTAATGCATGTGTCCGGTATGCTCGGCAGCCACTGCCAATAT
ACCAGTTGGGTTGTGCCACTTGCTTGGCATCCGCATAATAAAAATGCGGTCATCATGGTTGATTTGGCGAAGGATCCCCA
GCCACTCTTTGATCTCAATGCTGATGAAATCAAAGAGCGTCTCTATACCAAACATGAAGACTTACAAGATGATGAGTTAC
CGATCCCGGTTAAGCTGGTTCATCTCAATAAATGCCCGATCCTCGCTCCTGCCAAGACGCTAACGGCAGAAAATGCACAT
ACCATCGGGATCGATAGAGACAAATGTTTACATCATTTATCTCTTATGAAGCAAGCTCAGGATATCAGAGAGAAGCTGGT
CCAAGTATTTGGTGAAGAGAAAGACTACCCAACGAATACTGACGTCGATACGATGTTATACCACAACTTTTTCAATCCCG
CGGACAAGGCTGCGATGGAGATTATCCGACAGACATCGCCTGAAGCTTTACGGGATTTATCGATCTCTTTCCAGGACTCA
CGGATCACCCCCTTATTGTTCCGTTATCGAGCCAGAAACTATCCTGAAACACTCACCATGCATGAACAGAAACAGTGGCA
ATCCCACTGTCAGGATTACTTCTCCCAACATATGGATGATTATATTCTTCGTCTGGAAAATCTGGCTCATGAACATGAGC
AGGATTCCCACAAGATGCAGATCCTAAAATCAATCTACCAATATGTGCTGAACCTGACATCATAA

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