Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   OCU42_RS06625 Genome accession   NZ_AP024905
Coordinates   1463023..1464447 (-) Length   474 a.a.
NCBI ID   WP_077335909.1    Uniprot ID   A0A1R4LK55
Organism   Vibrio ruber strain LMG 23124     
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 1462560..1483390 1463023..1464447 within 0


Gene organization within MGE regions


Location: 1462560..1483390
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  OCU42_RS06620 - 1462560..1462925 (-) 366 WP_038186233.1 CidA/LrgA family protein -
  OCU42_RS06625 sbcB 1463023..1464447 (-) 1425 WP_077335909.1 exodeoxyribonuclease I Machinery gene
  OCU42_RS06630 - 1464959..1465555 (+) 597 WP_077335911.1 transposase -
  OCU42_RS06635 - 1466223..1466783 (+) 561 WP_077335913.1 hypothetical protein -
  OCU42_RS06640 - 1466767..1467384 (+) 618 WP_159440451.1 phage baseplate assembly protein V -
  OCU42_RS06645 - 1467386..1467583 (+) 198 WP_077335915.1 hypothetical protein -
  OCU42_RS06650 - 1467583..1467942 (+) 360 WP_038186209.1 phage baseplate protein -
  OCU42_RS06655 - 1467914..1468915 (+) 1002 WP_077335917.1 baseplate J/gp47 family protein -
  OCU42_RS06660 - 1468875..1469639 (+) 765 WP_077335919.1 phage tail protein I -
  OCU42_RS06665 - 1469636..1470190 (+) 555 WP_077335921.1 phage tail protein -
  OCU42_RS06670 - 1470183..1471415 (+) 1233 WP_077335923.1 SUMF1/EgtB/PvdO family nonheme iron enzyme -
  OCU42_RS06675 - 1471430..1471705 (+) 276 WP_077335925.1 hypothetical protein -
  OCU42_RS06680 - 1472006..1473160 (+) 1155 WP_261855962.1 SUMF1/EgtB/PvdO family nonheme iron enzyme -
  OCU42_RS06685 - 1473175..1473450 (+) 276 WP_077335925.1 hypothetical protein -
  OCU42_RS06690 - 1474021..1474548 (+) 528 WP_077335931.1 phage tail protein -
  OCU42_RS06695 - 1474604..1475290 (+) 687 WP_077335933.1 hypothetical protein -
  OCU42_RS06700 - 1475395..1476189 (+) 795 WP_077335935.1 hypothetical protein -
  OCU42_RS06705 - 1476186..1476560 (+) 375 WP_077335937.1 phage tail assembly chaperone -
  OCU42_RS06710 - 1476659..1476859 (+) 201 WP_077335939.1 hypothetical protein -
  OCU42_RS06715 - 1476852..1478021 (+) 1170 WP_077335941.1 phage tail protein -
  OCU42_RS06720 - 1478021..1478527 (+) 507 WP_077335943.1 phage major tail tube protein -
  OCU42_RS06725 - 1478652..1479212 (+) 561 WP_077335945.1 phage tail assembly protein -
  OCU42_RS06730 - 1479335..1481797 (+) 2463 WP_077335947.1 phage tail tape measure protein -
  OCU42_RS06735 - 1481794..1482174 (+) 381 WP_038181569.1 phage tail protein -
  OCU42_RS06740 - 1482171..1482380 (+) 210 WP_038181572.1 tail protein X -
  OCU42_RS06745 - 1482371..1483390 (+) 1020 WP_077335949.1 phage tail protein -

Sequence

Protein


Download         Length: 474 a.a.        Molecular weight: 55156.38 Da        Isoelectric Point: 5.8184

>NTDB_id=89343 OCU42_RS06625 WP_077335909.1 1463023..1464447(-) (sbcB) [Vibrio ruber strain LMG 23124]
MKNNEQPTFFFFDYETWGTHPAKDRPCQFAGVRTDMDFNIIGEPLVIFCRLPVDYLPAPEAALITGITPQQANSKGLSEP
EFIDRIHQELSHPNTTCLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVARACHALRPEGVVWPENEDGNT
SFKLEHLSVANGIEHTNAHDAMADVYATIELAKVIKNAQPKLFDYFYSMRHKRKLNALIDIVSMTPLMHVSGMLGSHCQY
TSWVVPLAWHPHNKNAVIMVDLAKDPQPLFDLNADEIRQRLYTKRDDLQEDELPIPVKLVHLNKCPILAPAKTLTAENAH
IIGIDRDKCLQHLSRMKQSQDIREKLVEVFNEEREYPTDTDVDTMLYHDFFNPADKAAMEIIRQTPPDALQDLSISFQDQ
RIKPLLFRYRARNWPETLTPHEQQQWQSHCQDYFSQHLDDYTLRLENLAHEHEQDPHKMQILKSIYHYVLSLTS

Nucleotide


Download         Length: 1425 bp        

>NTDB_id=89343 OCU42_RS06625 WP_077335909.1 1463023..1464447(-) (sbcB) [Vibrio ruber strain LMG 23124]
ATGAAAAACAACGAACAACCGACATTCTTCTTTTTTGATTATGAAACATGGGGTACACACCCCGCTAAAGATCGCCCCTG
TCAGTTTGCCGGGGTCAGAACTGATATGGACTTCAATATCATTGGTGAACCTCTGGTCATTTTTTGCCGACTGCCAGTAG
ATTATCTGCCTGCTCCGGAAGCTGCACTCATCACTGGTATTACGCCACAGCAAGCGAATAGCAAAGGTTTGTCAGAACCC
GAGTTTATTGATCGTATCCATCAGGAATTGTCTCATCCCAATACAACTTGTCTGGGCTATAACAGCATTCGTTTTGACGA
TGAAGTGACCCGTTATACCTGTTATCGCAATTTCATTGATCCTTATGCATGGAGCTGGCAAAACGGCAATTCGCGTTGGG
ATCTGCTCGACGTCGCGCGAGCCTGTCATGCATTACGCCCGGAAGGGGTTGTATGGCCTGAAAATGAAGACGGCAATACC
AGCTTTAAGCTCGAGCATCTTTCCGTTGCCAATGGTATCGAACATACCAATGCCCACGATGCGATGGCCGATGTCTATGC
AACCATTGAGTTGGCAAAAGTGATCAAAAATGCCCAGCCGAAATTATTCGATTATTTCTACTCAATGCGCCATAAGCGTA
AACTGAATGCACTGATCGACATTGTCAGTATGACGCCACTGATGCATGTTTCCGGTATGCTCGGCAGCCACTGTCAATAT
ACCAGTTGGGTTGTACCGCTTGCCTGGCATCCGCATAACAAAAATGCCGTGATCATGGTCGACTTGGCGAAAGATCCTCA
GCCTCTCTTTGATCTCAATGCTGACGAAATTCGGCAACGGCTCTACACAAAACGTGATGATTTACAAGAAGATGAGTTAC
CGATTCCGGTGAAACTGGTGCATCTCAATAAATGCCCGATCCTCGCTCCGGCCAAGACCTTGACGGCAGAAAATGCCCAT
ATAATCGGCATCGACAGAGACAAATGTTTGCAGCATTTGTCGCGTATGAAGCAATCTCAGGATATCAGAGAGAAACTGGT
CGAAGTATTTAATGAAGAGAGAGAGTATCCAACGGATACTGATGTCGATACGATGCTGTACCATGACTTTTTTAATCCGG
CAGATAAAGCTGCAATGGAGATTATCCGGCAAACACCGCCTGACGCATTACAAGATTTATCGATCTCTTTTCAGGATCAA
CGCATCAAGCCGCTGTTGTTCCGTTATCGGGCCAGAAACTGGCCTGAAACACTCACCCCGCATGAACAACAACAATGGCA
GTCGCACTGTCAGGATTATTTTTCCCAGCATCTGGATGATTACACTCTGCGTCTGGAAAATCTGGCTCATGAACATGAGC
AGGATCCACACAAAATGCAGATACTGAAATCAATCTACCATTATGTGCTCAGTCTGACATCATAA

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
  AlphaFold DB A0A1R4LK55

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

73.996

99.789

0.738

Multiple sequence alignment