Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   HPY13_RS08245 Genome accession   NZ_CP053796
Coordinates   1818714..1820138 (+) Length   474 a.a.
NCBI ID   WP_175249783.1    Uniprot ID   -
Organism   Vibrio cholerae strain SL4G     
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 1782856..1820544 1818714..1820138 within 0


Gene organization within MGE regions


Location: 1782856..1820544
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  HPY13_RS08000 (HPY13_08005) - 1782856..1784112 (-) 1257 WP_175249768.1 Y-family DNA polymerase -
  HPY13_RS08005 (HPY13_08010) - 1784112..1784519 (-) 408 WP_032468873.1 LexA family transcriptional regulator -
  HPY13_RS08010 (HPY13_08015) - 1784592..1784807 (-) 216 WP_002051960.1 hypothetical protein -
  HPY13_RS08015 (HPY13_08020) - 1784998..1785324 (+) 327 WP_260608762.1 helix-turn-helix domain-containing protein -
  HPY13_RS08020 (HPY13_08025) - 1785425..1785964 (+) 540 WP_175249769.1 WYL domain-containing protein -
  HPY13_RS08025 (HPY13_08030) - 1785953..1786963 (-) 1011 WP_175249770.1 contractile injection system protein, VgrG/Pvc8 family -
  HPY13_RS08030 (HPY13_08035) - 1786954..1787160 (-) 207 WP_094392035.1 tail protein X -
  HPY13_RS08035 (HPY13_08040) - 1787144..1787539 (-) 396 WP_000179074.1 phage tail protein -
  HPY13_RS08040 (HPY13_08045) - 1787539..1789320 (-) 1782 WP_175249771.1 phage tail protein -
  HPY13_RS08045 (HPY13_08050) - 1789424..1789726 (-) 303 WP_088127481.1 phage tail assembly protein -
  HPY13_RS08050 (HPY13_08055) - 1789778..1790293 (-) 516 WP_175249772.1 phage major tail tube protein -
  HPY13_RS08055 (HPY13_08060) - 1790293..1791759 (-) 1467 WP_175249773.1 phage tail sheath C-terminal domain-containing protein -
  HPY13_RS08060 (HPY13_08065) - 1791848..1792372 (-) 525 WP_094392030.1 phage tail protein -
  HPY13_RS19175 - 1792372..1793502 (-) 1131 WP_254702159.1 hypothetical protein -
  HPY13_RS08070 (HPY13_08075) - 1793504..1794061 (-) 558 WP_094392029.1 phage tail protein I -
  HPY13_RS08075 (HPY13_08080) - 1794061..1794939 (-) 879 WP_094392028.1 baseplate J/gp47 family protein -
  HPY13_RS08080 (HPY13_08085) - 1794936..1795277 (-) 342 WP_094392027.1 GPW/gp25 family protein -
  HPY13_RS08085 (HPY13_08090) - 1795279..1795926 (-) 648 WP_175249774.1 phage baseplate assembly protein V -
  HPY13_RS08090 (HPY13_08095) - 1795923..1796447 (-) 525 WP_053033974.1 hypothetical protein -
  HPY13_RS08095 (HPY13_08100) - 1796440..1797045 (-) 606 WP_053033973.1 phage tail protein -
  HPY13_RS08100 (HPY13_08105) - 1797008..1797358 (-) 351 WP_057568775.1 head-tail joining protein -
  HPY13_RS08105 (HPY13_08110) - 1797351..1797647 (-) 297 WP_175249775.1 hypothetical protein -
  HPY13_RS08110 (HPY13_08115) - 1797700..1799679 (-) 1980 WP_175249776.1 phage major capsid protein -
  HPY13_RS08115 (HPY13_08120) - 1799636..1801204 (-) 1569 WP_095461693.1 phage portal protein -
  HPY13_RS08120 (HPY13_08125) - 1801204..1801731 (-) 528 WP_000236573.1 hypothetical protein -
  HPY13_RS08125 (HPY13_08130) - 1801725..1803734 (-) 2010 WP_254702160.1 terminase gpA endonuclease subunit -
  HPY13_RS08130 (HPY13_08135) - 1803688..1804257 (-) 570 WP_175249777.1 terminase small subunit -
  HPY13_RS08135 (HPY13_08140) - 1804702..1805931 (-) 1230 WP_148524536.1 tyrosine-type recombinase/integrase -
  HPY13_RS08140 (HPY13_08145) - 1806215..1806697 (-) 483 WP_119299414.1 lysis protein -
  HPY13_RS08145 (HPY13_08150) - 1806670..1807158 (-) 489 WP_053033964.1 lysozyme -
  HPY13_RS08150 (HPY13_08155) - 1807145..1807336 (-) 192 WP_053033963.1 hypothetical protein -
  HPY13_RS08155 (HPY13_08160) - 1807578..1808159 (-) 582 WP_002051880.1 hypothetical protein -
  HPY13_RS08160 (HPY13_08165) - 1808161..1808676 (-) 516 WP_175249778.1 class I SAM-dependent methyltransferase -
  HPY13_RS08165 (HPY13_08170) - 1808673..1809305 (-) 633 WP_053033960.1 DNA N-6-adenine-methyltransferase -
  HPY13_RS08170 (HPY13_08175) - 1809305..1809724 (-) 420 WP_156844150.1 hypothetical protein -
  HPY13_RS08175 (HPY13_08180) - 1809693..1810676 (-) 984 WP_080371333.1 hypothetical protein -
  HPY13_RS08180 (HPY13_08185) - 1810865..1811410 (-) 546 WP_053033958.1 hypothetical protein -
  HPY13_RS08185 (HPY13_08190) - 1811450..1811704 (-) 255 WP_254702161.1 hypothetical protein -
  HPY13_RS08190 (HPY13_08195) - 1811806..1812504 (+) 699 WP_175249779.1 LexA family transcriptional regulator -
  HPY13_RS08195 (HPY13_08200) - 1812894..1813151 (+) 258 WP_032468854.1 hypothetical protein -
  HPY13_RS08200 (HPY13_08205) - 1813148..1813525 (+) 378 WP_053033957.1 hypothetical protein -
  HPY13_RS08205 (HPY13_08210) - 1813589..1813822 (+) 234 WP_053033956.1 hypothetical protein -
  HPY13_RS08210 (HPY13_08215) - 1813826..1814560 (+) 735 WP_175249780.1 hypothetical protein -
  HPY13_RS08215 (HPY13_08220) yejK 1814598..1815599 (+) 1002 WP_053033954.1 nucleoid-associated protein YejK -
  HPY13_RS08220 (HPY13_08225) - 1815610..1815975 (+) 366 WP_175249781.1 hypothetical protein -
  HPY13_RS08225 (HPY13_08230) - 1816026..1816598 (+) 573 WP_175249782.1 3'-5' exoribonuclease -
  HPY13_RS08230 (HPY13_08235) - 1816651..1816911 (+) 261 WP_002051851.1 hypothetical protein -
  HPY13_RS08235 (HPY13_08240) - 1817046..1817342 (+) 297 WP_002051850.1 AlpA family transcriptional regulator -
  HPY13_RS08240 (HPY13_08245) - 1817339..1818532 (-) 1194 WP_002051848.1 site-specific integrase -
  HPY13_RS08245 (HPY13_08250) sbcB 1818714..1820138 (+) 1425 WP_175249783.1 exodeoxyribonuclease I Machinery gene
  HPY13_RS08250 (HPY13_08255) - 1820170..1820544 (+) 375 WP_046127346.1 CidA/LrgA family protein -

Sequence

Protein


Download         Length: 474 a.a.        Molecular weight: 54480.88 Da        Isoelectric Point: 5.9006

>NTDB_id=447372 HPY13_RS08245 WP_175249783.1 1818714..1820138(+) (sbcB) [Vibrio cholerae strain SL4G]
MKNDEQPSFFFFDYETWGVNPAKDRPSQFAGVRTDMDFNIIGEPLVIYCQLPNDYLPAPEAALITGITPQKANSQGLAEP
EFIARIHAELSTPNTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQHGNSRWDLLDVLRACHALRPEGIEWPENDDGFT
SFKLEHLSVANGIEHSNAHDAMADVIATIELAKKVKAAQPKLFDYFFTMRHKRKLTELIDIVNQTPLMHVSGMLGRERHY
TSWIVPIAWHPTNQNAVIVVDLGKDPQPLLELDAETLQARLYMRYEDLAPDELPVPVKLVHLNKCPILAPAKTLTAENAQ
KIGIDREQCLAHLNVIRQHPEIREKLVTVFSQEREFNQESDVDSQLYAGFFSPADRAAMEIIRTTAPENLGSLAIQVADK
RIEPLLFRYRARHYPHTLTDAEQRRWAAHCRDYFERNLEGYMLNLENLVHEHQADPKKMAILKSVYHYVEKLAC

Nucleotide


Download         Length: 1425 bp        

>NTDB_id=447372 HPY13_RS08245 WP_175249783.1 1818714..1820138(+) (sbcB) [Vibrio cholerae strain SL4G]
ATGAAAAATGATGAACAGCCGTCATTCTTCTTTTTCGACTACGAGACTTGGGGAGTCAATCCCGCCAAAGATCGTCCTAG
TCAGTTTGCGGGTGTGCGTACCGATATGGACTTCAACATCATCGGTGAGCCTTTGGTGATTTACTGTCAACTGCCCAACG
ACTATTTGCCCGCTCCTGAAGCCGCATTGATCACAGGGATCACCCCTCAAAAAGCCAATAGCCAAGGTCTGGCGGAGCCC
GAATTTATCGCGCGTATTCATGCAGAACTCTCCACACCCAATACCACCAGCCTAGGTTATAACAGCATACGTTTTGATGA
TGAAGTGACGCGCTACACCTGCTATCGCAACTTTATCGACCCCTATGCTTGGAGCTGGCAACACGGCAATTCCCGTTGGG
ATCTGCTGGATGTGCTTCGCGCGTGTCATGCTTTGCGTCCTGAAGGTATCGAGTGGCCGGAAAATGATGACGGCTTTACC
AGCTTTAAACTGGAACATCTTTCTGTTGCCAACGGCATTGAGCACAGCAACGCGCACGATGCGATGGCCGATGTGATTGC
CACCATTGAACTGGCGAAAAAAGTCAAAGCCGCGCAGCCGAAATTGTTCGACTACTTCTTCACTATGCGCCACAAACGCA
AGCTGACAGAACTGATTGATATTGTGAACCAAACTCCGCTGATGCATGTTTCTGGCATGCTTGGGCGTGAGCGCCACTAC
ACCAGCTGGATTGTGCCGATTGCTTGGCATCCGACCAATCAAAATGCGGTGATTGTGGTGGATTTGGGTAAAGACCCTCA
GCCGCTGCTGGAGCTCGATGCCGAAACGCTGCAAGCGCGTCTCTATATGCGGTATGAAGACCTAGCACCGGATGAGCTAC
CAGTACCCGTGAAATTGGTGCATCTCAATAAATGCCCTATTCTGGCTCCGGCCAAAACCTTGACCGCAGAAAATGCACAA
AAGATTGGTATTGACCGCGAACAGTGTCTCGCGCACTTGAATGTGATTCGTCAACATCCCGAGATTCGTGAAAAGCTGGT
GACGGTATTTAGCCAAGAGCGCGAGTTTAACCAAGAGAGTGATGTGGATAGCCAACTCTATGCCGGCTTTTTCTCCCCAG
CCGATCGCGCGGCGATGGAGATCATCCGCACCACTGCACCGGAGAATCTGGGCAGCTTAGCGATACAGGTGGCAGATAAG
CGCATTGAACCACTGCTGTTTCGTTATCGTGCGCGCCATTATCCCCATACCTTAACCGATGCCGAGCAACGCCGCTGGGC
AGCGCATTGCCGTGACTATTTCGAGCGCAATCTAGAAGGTTATATGTTGAATTTGGAAAATCTGGTCCATGAACATCAAG
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

97.89

100

0.979