Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   LXG94_RS13825 Genome accession   NZ_CP090179
Coordinates   679777..681198 (-) Length   473 a.a.
NCBI ID   WP_005445536.1    Uniprot ID   A0A9X3ML51
Organism   Vibrio harveyi strain XH2145     
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 656478..696248 679777..681198 within 0


Gene organization within MGE regions


Location: 656478..696248
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LXG94_RS13700 (LXG94_13700) - 656478..656867 (+) 390 WP_009697353.1 VOC family protein -
  LXG94_RS13705 (LXG94_13705) - 656869..657183 (+) 315 WP_005443150.1 heavy metal-binding domain-containing protein -
  LXG94_RS13710 (LXG94_13710) - 657328..657777 (+) 450 WP_038897610.1 hypothetical protein -
  LXG94_RS13715 (LXG94_13715) - 658125..658934 (+) 810 WP_005445576.1 helix-turn-helix transcriptional regulator -
  LXG94_RS13720 (LXG94_13720) - 659105..659893 (+) 789 WP_009697355.1 TetR/AcrR family transcriptional regulator -
  LXG94_RS13725 (LXG94_13725) - 660095..662470 (+) 2376 WP_038897609.1 RND family transporter -
  LXG94_RS13730 (LXG94_13730) - 662512..663303 (+) 792 WP_026000346.1 outer membrane lipoprotein-sorting protein -
  LXG94_RS13735 (LXG94_13735) - 663313..664494 (+) 1182 WP_038897608.1 hypothetical protein -
  LXG94_RS13740 (LXG94_13740) - 664672..665796 (+) 1125 WP_038897607.1 GGDEF domain-containing protein -
  LXG94_RS13745 (LXG94_13745) pheS 666081..667064 (+) 984 WP_005439802.1 phenylalanine--tRNA ligase subunit alpha -
  LXG94_RS13750 (LXG94_13750) pheT 667083..669470 (+) 2388 WP_038897606.1 phenylalanine--tRNA ligase subunit beta -
  LXG94_RS13755 (LXG94_13755) - 669595..670320 (-) 726 WP_038897605.1 metallophosphoesterase -
  LXG94_RS13760 (LXG94_13760) - 670524..670862 (-) 339 WP_029791121.1 hypothetical protein -
  LXG94_RS13765 (LXG94_13765) - 670853..671236 (-) 384 WP_005445549.1 hypothetical protein -
  LXG94_RS13770 (LXG94_13770) - 671236..671496 (-) 261 WP_005445548.1 hypothetical protein -
  LXG94_RS13775 (LXG94_13775) - 671649..672071 (-) 423 WP_038897604.1 hypothetical protein -
  LXG94_RS13780 (LXG94_13780) - 672093..672332 (-) 240 WP_038897603.1 hypothetical protein -
  LXG94_RS13785 (LXG94_13785) - 672515..673393 (-) 879 WP_009701053.1 AEC family transporter -
  LXG94_RS13790 (LXG94_13790) ihfA 673920..674216 (+) 297 WP_005445544.1 integration host factor subunit alpha -
  LXG94_RS13795 (LXG94_13795) - 674360..675133 (-) 774 WP_005445543.1 phosphoribosylglycinamide formyltransferase -
  LXG94_RS13800 (LXG94_13800) - 675470..676120 (+) 651 WP_038897602.1 thiopurine S-methyltransferase -
  LXG94_RS13805 (LXG94_13805) purT 676198..677373 (-) 1176 WP_038897600.1 formate-dependent phosphoribosylglycinamide formyltransferase -
  LXG94_RS13810 (LXG94_13810) cdd 677522..678409 (-) 888 WP_005445539.1 cytidine deaminase -
  LXG94_RS13815 (LXG94_13815) - 678665..679342 (-) 678 WP_005445538.1 LrgB family protein -
  LXG94_RS13820 (LXG94_13820) - 679344..679718 (-) 375 WP_005445537.1 CidA/LrgA family protein -
  LXG94_RS13825 (LXG94_13825) sbcB 679777..681198 (-) 1422 WP_005445536.1 exodeoxyribonuclease I Machinery gene
  LXG94_RS13830 (LXG94_13830) - 681360..682040 (-) 681 WP_005445535.1 DUF1826 domain-containing protein -
  LXG94_RS13835 (LXG94_13835) - 682262..683635 (-) 1374 WP_038897599.1 L-cystine transporter -
  LXG94_RS13840 (LXG94_13840) - 683830..684525 (-) 696 WP_038897598.1 NAD(P)H-binding protein -
  LXG94_RS13845 (LXG94_13845) - 685247..685858 (+) 612 WP_017190319.1 flavin reductase family protein -
  LXG94_RS13850 (LXG94_13850) cobT 685878..686921 (+) 1044 WP_080640343.1 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase -
  LXG94_RS13855 (LXG94_13855) - 686921..687727 (+) 807 WP_026000344.1 adenosylcobinamide-GDP ribazoletransferase -
  LXG94_RS13860 (LXG94_13860) cobU 687724..688257 (+) 534 WP_038897596.1 bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase -
  LXG94_RS13865 (LXG94_13865) cobC 688269..688883 (+) 615 WP_038897595.1 alpha-ribazole phosphatase family protein -
  LXG94_RS13870 (LXG94_13870) - 688966..690765 (+) 1800 WP_038897594.1 M3 family oligoendopeptidase -
  LXG94_RS13875 (LXG94_13875) - 691004..692032 (+) 1029 WP_038897593.1 succinylglutamate desuccinylase -
  LXG94_RS13880 (LXG94_13880) btuC 692135..693130 (+) 996 WP_009697375.1 vitamin B12 ABC transporter permease BtuC -
  LXG94_RS13885 (LXG94_13885) btuD 693117..693884 (+) 768 WP_080640342.1 vitamin B12 ABC transporter ATP-binding protein BtuD -
  LXG94_RS13890 (LXG94_13890) - 693972..694388 (+) 417 WP_009697380.1 lysozyme inhibitor LprI family protein -
  LXG94_RS13895 (LXG94_13895) - 694643..694876 (+) 234 WP_038897592.1 hypothetical protein -
  LXG94_RS13900 (LXG94_13900) - 694936..695442 (+) 507 WP_009697382.1 AAA family ATPase -
  LXG94_RS13905 (LXG94_13905) - 695475..696248 (+) 774 WP_009701136.1 nucleotidyltransferase domain-containing protein -

Sequence

Protein


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

>NTDB_id=640960 LXG94_RS13825 WP_005445536.1 679777..681198(-) (sbcB) [Vibrio harveyi strain XH2145]
MHQDNQPTFFFFDYETWGTSPAKDRPSQFAGVRTDENFNIIGEPLVMYCRPPADYLPSPEAALITGITPQKAMQEGLPEP
EFIAKIHAELSKPKTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVMRACHALRPEGVEWPENDEGFT
SFKLEHLSVANGIEHSNAHDAMADVIATIEMAKKVKAAQPKLFDYFFSMRNKRKLNELVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELKERLYTKRDELGDLLPVPVKLVHLNKCPILAPAKTLTAENAEV
IGIDRQQCLNNLALLRQHPEIREKLISLFSIEREFEKSNDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARHYAGTLDEQEQRRWAQHCREVFESQIEEYMMNLENLVHEHESDEKKIAILKSVYRYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=640960 LXG94_RS13825 WP_005445536.1 679777..681198(-) (sbcB) [Vibrio harveyi strain XH2145]
ATGCACCAAGACAATCAGCCCACTTTTTTCTTTTTCGATTACGAGACTTGGGGAACAAGTCCAGCCAAAGACCGCCCAAG
CCAGTTTGCAGGCGTTCGCACTGATGAAAACTTCAATATCATTGGTGAACCTTTGGTGATGTACTGTCGTCCACCTGCTG
ATTACCTTCCTTCGCCAGAAGCAGCTTTGATCACTGGTATTACACCACAAAAAGCAATGCAAGAAGGCTTACCTGAACCT
GAGTTTATTGCCAAAATTCATGCTGAATTGTCTAAACCAAAGACGACTAGCCTTGGCTACAACAGCATACGTTTTGATGA
TGAAGTCACTCGTTACACTTGCTACCGAAACTTCATCGACCCATACGCATGGAGCTGGCAAAACGGCAACTCACGATGGG
ATTTGCTTGACGTGATGCGAGCATGTCACGCCCTGCGTCCTGAAGGCGTAGAATGGCCAGAGAACGATGAAGGCTTTACA
AGCTTCAAGCTAGAGCATTTATCCGTAGCGAATGGCATTGAACACAGCAATGCTCACGATGCGATGGCCGACGTGATTGC
CACGATTGAAATGGCGAAGAAAGTTAAAGCCGCCCAACCTAAGCTATTTGACTACTTTTTCTCGATGCGTAACAAGCGCA
AACTCAATGAGCTGGTTGATATTGTCAATATGACTCCGTTGATGCATGTATCAGGCATGCTTGGGCGTGAATGCCAATAC
ACAAGCTGGATTGTGCCTGTGGCTTGGCACCCAACCAACAACAACGCTGTTATCACGATTGATTTAGCCAAAGATCCTCA
GCCGATCCTTGAACTTTCAGCGGAAGAACTGAAAGAACGCTTGTACACCAAGCGTGACGAATTGGGCGACTTACTGCCCG
TACCAGTGAAGCTAGTGCATCTGAACAAGTGCCCTATTCTCGCTCCAGCAAAAACATTAACCGCGGAAAATGCGGAAGTC
ATTGGTATTGACCGCCAACAATGTTTAAACAATTTAGCGTTGTTGCGCCAACACCCAGAGATCCGAGAGAAGCTGATTAG
TCTATTCTCTATAGAACGTGAATTCGAAAAGAGTAATGACGTTGATACGCAGCTTTACGATGGCTTTTTCTCGCCTGCTG
ATCGCGCTGCTATGGACATCATTCGTGAAACCGATCCGAATAACTTAGCCGCACTGGACATTGAATTCGATGATAAACGA
ATCAAGCCATTGCTTTTCCGTTACCGTGCTCGCCATTATGCAGGCACATTAGATGAACAAGAACAAAGACGCTGGGCACA
ACATTGTCGTGAAGTTTTCGAAAGTCAGATTGAAGAGTACATGATGAATTTAGAAAACTTAGTTCACGAACATGAAAGTG
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