Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   RND59_RS12600 Genome accession   NZ_CP134780
Coordinates   2758914..2760338 (-) Length   474 a.a.
NCBI ID   WP_311844872.1    Uniprot ID   -
Organism   Vibrio ruber strain HNIBRBA4764     
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 2758450..2776393 2758914..2760338 within 0


Gene organization within MGE regions


Location: 2758450..2776393
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RND59_RS12595 (RND59_12595) - 2758450..2758815 (-) 366 WP_038186233.1 CidA/LrgA family protein -
  RND59_RS12600 (RND59_12600) sbcB 2758914..2760338 (-) 1425 WP_311844872.1 exodeoxyribonuclease I Machinery gene
  RND59_RS12605 (RND59_12605) - 2760850..2761443 (+) 594 WP_311844873.1 transposase -
  RND59_RS12610 (RND59_12610) - 2762246..2762803 (+) 558 WP_311844874.1 hypothetical protein -
  RND59_RS12615 (RND59_12615) - 2762787..2763404 (+) 618 WP_169739391.1 phage baseplate assembly protein V -
  RND59_RS12620 (RND59_12620) - 2763406..2763603 (+) 198 WP_077335915.1 hypothetical protein -
  RND59_RS12625 (RND59_12625) - 2763603..2763962 (+) 360 WP_311844875.1 phage baseplate protein -
  RND59_RS12630 (RND59_12630) - 2763934..2764935 (+) 1002 WP_311844876.1 baseplate J/gp47 family protein -
  RND59_RS12635 (RND59_12635) - 2764895..2765659 (+) 765 WP_311844877.1 phage tail protein I -
  RND59_RS12640 (RND59_12640) - 2765656..2766210 (+) 555 WP_311844878.1 phage tail protein -
  RND59_RS12645 (RND59_12645) - 2766203..2767435 (+) 1233 WP_311844879.1 SUMF1/EgtB/PvdO family nonheme iron enzyme -
  RND59_RS12650 (RND59_12650) - 2767450..2767725 (+) 276 WP_311844880.1 hypothetical protein -
  RND59_RS12655 (RND59_12655) - 2767794..2768066 (+) 273 WP_311844881.1 hypothetical protein -
  RND59_RS12660 (RND59_12660) - 2768059..2769291 (+) 1233 WP_311844882.1 SUMF1/EgtB/PvdO family nonheme iron enzyme -
  RND59_RS12665 (RND59_12665) - 2769306..2769581 (+) 276 WP_311844883.1 hypothetical protein -
  RND59_RS12670 (RND59_12670) - 2769660..2769863 (+) 204 WP_311844884.1 hypothetical protein -
  RND59_RS12675 (RND59_12675) - 2769856..2771025 (+) 1170 WP_059120928.1 hypothetical protein -
  RND59_RS12680 (RND59_12680) - 2771025..2771531 (+) 507 WP_059120927.1 phage major tail tube protein -
  RND59_RS12685 (RND59_12685) - 2771655..2772215 (+) 561 WP_311844885.1 phage tail assembly protein -
  RND59_RS12690 (RND59_12690) - 2772338..2774800 (+) 2463 WP_311844886.1 phage tail tape measure protein -
  RND59_RS12695 (RND59_12695) - 2774797..2775177 (+) 381 WP_038181569.1 phage tail protein -
  RND59_RS12700 (RND59_12700) - 2775174..2775383 (+) 210 WP_038181572.1 tail protein X -
  RND59_RS12705 (RND59_12705) - 2775374..2776393 (+) 1020 WP_311844887.1 phage late control D family protein -

Sequence

Protein


Download         Length: 474 a.a.        Molecular weight: 55225.51 Da        Isoelectric Point: 5.9358

>NTDB_id=883676 RND59_RS12600 WP_311844872.1 2758914..2760338(-) (sbcB) [Vibrio ruber strain HNIBRBA4764]
MKNNEQPTFFFFDYETWGTRPAKDRPCQFAGVRTDMDFNIIGEPLVIFCRLPVDYLPAPEAALITGITPQQANSKGLSEP
EFIDRIHQELSHPNTTCLGYNNIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVARACHALRPEGVVWPENEDGNT
SFKLEHLSVANGIEHTNAHDAMADVYATIELAKVIKNAQPKLFDYFYSMRHKRKLNALIDIVSMTPLMHVSGMLGSHCQY
TSWVVPLAWHPHNKNAVIMVDLAKDPQPLFDLNADEIRQRLYTKRDDLQEDELQIPVKLVHLNKCPILAPAKTLTAENAH
IIGIDRDKCLQHLSRMKQSQDIREKLVEVFNEEREYPTDTDVDTMLYHDFFNPADKAAMEIIRQTPPDALQDLSISFQDP
RIKPLLFRYRARNYPETLTPHEQQQWQSHCQDYFSRHMDDYTLRLENLAHEHEQDPHKMQILKSIYHYVLSLTS

Nucleotide


Download         Length: 1425 bp        

>NTDB_id=883676 RND59_RS12600 WP_311844872.1 2758914..2760338(-) (sbcB) [Vibrio ruber strain HNIBRBA4764]
ATGAAAAACAACGAACAACCGACATTCTTCTTTTTTGATTATGAAACATGGGGCACACGCCCCGCTAAAGATCGCCCCTG
TCAGTTTGCCGGGGTCAGAACTGATATGGACTTCAATATCATCGGTGAACCACTGGTCATTTTTTGCCGACTGCCAGTAG
ATTATCTGCCTGCTCCGGAAGCGGCACTCATCACTGGTATTACGCCACAGCAAGCGAATAGCAAAGGTTTGTCAGAACCC
GAGTTTATTGATCGTATCCATCAGGAATTGTCTCATCCCAATACAACTTGTCTGGGCTATAACAACATTCGTTTTGACGA
TGAAGTGACCCGTTATACCTGTTATCGCAATTTCATTGATCCTTATGCATGGAGCTGGCAAAACGGCAATTCGCGTTGGG
ATCTGCTCGACGTCGCGCGAGCCTGTCATGCATTACGCCCGGAAGGGGTTGTATGGCCTGAAAATGAAGACGGCAATACC
AGCTTTAAGCTCGAGCATCTTTCCGTTGCCAATGGTATCGAACATACCAATGCCCACGATGCGATGGCCGATGTCTATGC
AACCATTGAGTTGGCAAAAGTGATCAAAAATGCCCAACCGAAATTGTTCGATTATTTCTACTCAATGCGCCATAAGCGTA
AACTGAATGCACTGATCGACATTGTCAGTATGACGCCCCTGATGCATGTTTCCGGTATGCTTGGCAGCCACTGTCAATAT
ACCAGTTGGGTTGTACCGCTTGCCTGGCATCCGCATAACAAAAATGCCGTGATCATGGTCGACTTGGCGAAAGATCCTCA
GCCTCTCTTTGATCTCAATGCTGACGAAATTCGGCAACGGCTCTACACAAAACGTGATGATTTACAAGAAGATGAGTTAC
AGATTCCGGTGAAGCTGGTTCATCTCAATAAATGCCCGATCCTCGCTCCGGCGAAGACCTTGACGGCAGAAAATGCGCAT
ATAATCGGCATCGACAGAGACAAATGTTTGCAGCATTTGTCGCGTATGAAGCAATCTCAGGATATCAGAGAGAAACTGGT
CGAAGTATTTAATGAAGAGAGAGAGTATCCAACGGATACTGATGTCGATACGATGCTGTACCATGATTTTTTTAATCCGG
CAGATAAAGCTGCAATGGAGATTATCCGGCAAACACCGCCTGACGCATTACAAGATTTATCGATCTCTTTTCAGGATCCA
CGTATCAAGCCGCTGCTGTTCCGTTATCGGGCCAGAAACTATCCTGAAACACTCACCCCGCATGAACAACAACAATGGCA
ATCGCACTGTCAGGATTATTTTTCCCGGCATATGGATGATTACACTCTGCGTCTGGAAAATCTGGCTCATGAACATGAGC
AGGATCCACACAAAATGCAGATACTGAAATCCATCTACCATTATGTGCTCAGCCTGACATCATAA

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

73.784

99.789

0.736