Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   GPY06_RS17905 Genome accession   NZ_CP046820
Coordinates   2625500..2626924 (-) Length   474 a.a.
NCBI ID   WP_158120563.1    Uniprot ID   -
Organism   Vibrio metoecus strain 2011V-1015     
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 2625094..2662782 2625500..2626924 within 0


Gene organization within MGE regions


Location: 2625094..2662782
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GPY06_RS17900 - 2625094..2625468 (-) 375 WP_032469900.1 CidA/LrgA family protein -
  GPY06_RS17905 sbcB 2625500..2626924 (-) 1425 WP_158120563.1 exodeoxyribonuclease I Machinery gene
  GPY06_RS17910 - 2627106..2628299 (+) 1194 WP_148522370.1 tyrosine-type recombinase/integrase -
  GPY06_RS17915 - 2628296..2628592 (-) 297 WP_002051850.1 helix-turn-helix transcriptional regulator -
  GPY06_RS17920 - 2628727..2628987 (-) 261 WP_002051851.1 hypothetical protein -
  GPY06_RS17925 - 2629022..2629570 (-) 549 WP_158120564.1 hypothetical protein -
  GPY06_RS17930 yejK 2629570..2630574 (-) 1005 WP_158120565.1 nucleoid-associated protein YejK -
  GPY06_RS17935 - 2630612..2631286 (-) 675 WP_158120566.1 hypothetical protein -
  GPY06_RS17940 - 2631290..2631523 (-) 234 WP_053033956.1 DUF7220 family protein -
  GPY06_RS17945 - 2631765..2632139 (-) 375 WP_148522380.1 hypothetical protein -
  GPY06_RS17950 - 2632136..2632393 (-) 258 WP_032468854.1 hypothetical protein -
  GPY06_RS17955 - 2632783..2633481 (-) 699 WP_158120567.1 LexA family protein -
  GPY06_RS17960 - 2633583..2633837 (+) 255 WP_032468855.1 hypothetical protein -
  GPY06_RS17965 - 2633877..2634422 (+) 546 WP_053033958.1 hypothetical protein -
  GPY06_RS17970 - 2634611..2635396 (+) 786 WP_238844738.1 helix-turn-helix domain-containing protein -
  GPY06_RS17975 - 2635408..2636124 (+) 717 WP_002051875.1 ATP-binding protein -
  GPY06_RS17980 - 2636124..2636756 (+) 633 WP_158120568.1 DNA N-6-adenine-methyltransferase -
  GPY06_RS17985 - 2636758..2637339 (+) 582 WP_148522383.1 hypothetical protein -
  GPY06_RS17990 - 2637524..2637814 (+) 291 WP_002051883.1 hypothetical protein -
  GPY06_RS17995 - 2637792..2638280 (+) 489 WP_158120569.1 hypothetical protein -
  GPY06_RS18000 - 2638319..2638633 (+) 315 WP_057568767.1 hypothetical protein -
  GPY06_RS18005 - 2638739..2638987 (+) 249 WP_158120570.1 hypothetical protein -
  GPY06_RS18010 - 2639321..2640550 (+) 1230 WP_148522387.1 tyrosine-type recombinase/integrase -
  GPY06_RS18015 - 2640984..2641553 (+) 570 WP_158120571.1 terminase small subunit -
  GPY06_RS18020 - 2641507..2643516 (+) 2010 WP_235618073.1 terminase gpA endonuclease subunit -
  GPY06_RS18025 - 2643510..2644037 (+) 528 WP_158120572.1 hypothetical protein -
  GPY06_RS18030 - 2644037..2645605 (+) 1569 WP_057568772.1 phage portal protein -
  GPY06_RS18035 - 2645562..2647541 (+) 1980 WP_088127474.1 phage major capsid protein -
  GPY06_RS18040 - 2647594..2647890 (+) 297 WP_158120573.1 hypothetical protein -
  GPY06_RS18045 - 2647883..2648233 (+) 351 WP_158120574.1 head-tail joining protein -
  GPY06_RS18050 - 2648196..2648816 (+) 621 WP_114774479.1 hypothetical protein -
  GPY06_RS18055 - 2648809..2649333 (+) 525 WP_158120575.1 hypothetical protein -
  GPY06_RS18060 - 2649330..2649977 (+) 648 WP_158120576.1 phage baseplate assembly protein V -
  GPY06_RS18065 - 2649979..2650320 (+) 342 WP_148522400.1 GPW/gp25 family protein -
  GPY06_RS18070 - 2650317..2651195 (+) 879 WP_158120577.1 baseplate assembly protein -
  GPY06_RS18075 - 2651195..2651752 (+) 558 WP_046121709.1 phage tail protein I -
  GPY06_RS18080 - 2651754..2652485 (+) 732 WP_158118984.1 hypothetical protein -
  GPY06_RS18085 - 2652485..2653027 (+) 543 WP_158118983.1 phage tail protein -
  GPY06_RS18090 - 2653115..2654581 (+) 1467 WP_158118982.1 phage tail sheath C-terminal domain-containing protein -
  GPY06_RS18095 - 2654581..2655096 (+) 516 WP_158118981.1 phage major tail tube protein -
  GPY06_RS18100 - 2655148..2655450 (+) 303 WP_158118980.1 phage tail assembly protein -
  GPY06_RS18105 - 2655554..2657335 (+) 1782 WP_158120578.1 phage tail protein -
  GPY06_RS18110 - 2657335..2657730 (+) 396 WP_000179074.1 phage tail protein -
  GPY06_RS18115 - 2657714..2657920 (+) 207 WP_000246642.1 tail protein X -
  GPY06_RS18120 - 2657911..2658915 (+) 1005 WP_158120579.1 contractile injection system protein, VgrG/Pvc8 family -
  GPY06_RS18125 - 2658912..2659328 (-) 417 WP_158120580.1 hypothetical protein -
  GPY06_RS18130 - 2659422..2660009 (-) 588 WP_156844164.1 phage antirepressor N-terminal domain-containing protein -
  GPY06_RS18140 - 2660314..2660661 (-) 348 WP_050559084.1 helix-turn-helix domain-containing protein -
  GPY06_RS18145 - 2660831..2661046 (+) 216 WP_002051960.1 hypothetical protein -
  GPY06_RS18150 - 2661119..2661526 (+) 408 WP_158120785.1 LexA family protein -
  GPY06_RS18155 - 2661526..2662782 (+) 1257 WP_158120582.1 Y-family DNA polymerase -

Sequence

Protein


Download         Length: 474 a.a.        Molecular weight: 54695.23 Da        Isoelectric Point: 6.1360

>NTDB_id=408386 GPY06_RS17905 WP_158120563.1 2625500..2626924(-) (sbcB) [Vibrio metoecus strain 2011V-1015]
MKNDEQPSFFFFDYETWGVNPAKDRPSQFAGVRTDMDFNIIGEPLVIYCQLPNDYLPAPEAALITGITPQKANSLGLPEP
EFIARIHAELSTPKTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQHGNSRWDLLDVIRACHALRPEGMEWPENEDGFT
SFKLERLSVANGIEHSNAHDAMADVIATIELAKKIKAAQPKLFDYFFNMRHKRKLTELIDIVNQTPLMHVSGMLGRERHY
TSWIVPIAWHPTNQNAVIVVDLGKDPQPLLELDAEALQARLYTRYEDLAPDELPIPVKLVHLNKCPILAPAKTLTAENAQ
KIGIDREQCLAHLNVIRQHPQIREKLVSVFSQEREFAKENNVDSQLYDGFFSPADRAAMDIIRTTEPENLGNLDIKVADK
RIEPLLFRYRARHYPHTLTDAEQRRWAAHCRDYFERNLESYMLNLENLVHEHQADPKKMAILKSVYHYVEKLAC

Nucleotide


Download         Length: 1425 bp        

>NTDB_id=408386 GPY06_RS17905 WP_158120563.1 2625500..2626924(-) (sbcB) [Vibrio metoecus strain 2011V-1015]
ATGAAAAATGATGAACAGCCGTCATTCTTCTTTTTCGACTACGAGACTTGGGGAGTCAATCCTGCCAAGGATCGTCCAAG
TCAGTTTGCGGGTGTTCGTACCGATATGGATTTCAACATTATTGGTGAGCCTCTGGTCATCTATTGCCAATTGCCAAATG
ATTATTTACCTGCGCCTGAAGCGGCACTGATCACCGGCATTACCCCGCAAAAGGCGAATAGCCTCGGCTTGCCAGAACCA
GAATTTATCGCCCGTATTCATGCCGAGCTTTCCACTCCGAAGACCACCAGCCTAGGCTACAACAGCATTCGTTTTGATGA
TGAAGTAACGCGCTACACCTGTTATCGCAACTTTATCGACCCGTATGCCTGGAGCTGGCAACACGGCAATTCACGTTGGG
ATCTACTGGATGTGATCCGCGCTTGTCATGCTCTGCGCCCTGAAGGCATGGAATGGCCAGAAAATGAAGATGGTTTTACC
AGCTTCAAGCTAGAACGTCTTTCTGTTGCCAACGGCATTGAACACAGCAACGCGCACGATGCGATGGCCGATGTGATTGC
CACGATTGAACTGGCGAAAAAAATCAAAGCAGCGCAACCGAAACTGTTTGATTACTTTTTCAACATGCGCCACAAACGCA
AGCTGACGGAGCTGATTGATATCGTGAACCAAACCCCATTGATGCATGTTTCTGGCATGCTGGGACGCGAACGTCACTAT
ACCAGTTGGATTGTGCCAATCGCTTGGCATCCTACCAACCAAAATGCGGTCATTGTGGTGGATTTGGGTAAAGACCCTCA
GCCCCTGCTGGAACTGGATGCAGAAGCATTGCAAGCGCGCCTCTATACACGTTATGAAGATTTAGCACCCGATGAACTGC
CGATCCCAGTGAAGTTAGTGCATCTCAACAAATGTCCTATTCTGGCTCCGGCCAAAACCTTGACCGCAGAAAATGCACAA
AAGATTGGTATTGACCGCGAACAGTGTCTCGCGCACTTGAATGTGATTCGTCAGCATCCACAAATTCGTGAAAAGCTAGT
CTCCGTATTCAGTCAAGAGCGTGAGTTTGCCAAGGAAAACAACGTAGATAGCCAATTGTATGATGGTTTTTTCTCTCCGG
CCGATCGCGCAGCGATGGATATTATTCGAACCACTGAACCGGAGAACCTCGGAAACCTTGACATAAAAGTGGCAGATAAA
CGGATTGAACCACTTCTCTTTCGCTACCGCGCACGCCATTATCCACATACCTTAACCGATGCCGAACAACGGCGTTGGGC
GGCGCATTGTCGTGACTATTTCGAACGCAATCTGGAAAGCTATATGTTGAATTTGGAAAATCTGGTGCATGAACATCAAG
CTGATCCAAAGAAAATGGCGATTTTAAAATCCGTCTACCATTACGTGGAAAAACTCGCTTGCTAA

Domains

Predicted by InterproScan.

Exonuclease C-terminal (Exonuc_X-T_C)

(210-470)

Exonuclease (RNase_T)

(11-191)


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

93.249

100

0.932

Multiple sequence alignment