Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   PWS06_RS09195 Genome accession   NZ_CP118532
Coordinates   1843043..1844464 (-) Length   473 a.a.
NCBI ID   WP_274789931.1    Uniprot ID   -
Organism   Vibrio harveyi strain 160-19     
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 1833855..1856908 1843043..1844464 within 0


Gene organization within MGE regions


Location: 1833855..1856908
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PWS06_RS09135 - 1833855..1834238 (-) 384 WP_017817997.1 hypothetical protein -
  PWS06_RS09140 - 1834238..1834498 (-) 261 WP_005445548.1 hypothetical protein -
  PWS06_RS09145 - 1834651..1835073 (-) 423 WP_172580707.1 hypothetical protein -
  PWS06_RS09150 - 1835095..1835334 (-) 240 WP_047517048.1 hypothetical protein -
  PWS06_RS09155 - 1835517..1836395 (-) 879 WP_009701053.1 AEC family transporter -
  PWS06_RS09160 ihfA 1836922..1837218 (+) 297 WP_005445544.1 integration host factor subunit alpha -
  PWS06_RS09165 - 1837362..1838135 (-) 774 WP_005445543.1 phosphoribosylglycinamide formyltransferase -
  PWS06_RS09170 - 1838472..1839122 (+) 651 WP_239213188.1 thiopurine S-methyltransferase -
  PWS06_RS09175 purT 1839464..1840639 (-) 1176 WP_274789930.1 formate-dependent phosphoribosylglycinamide formyltransferase -
  PWS06_RS09180 cdd 1840788..1841675 (-) 888 WP_005445539.1 cytidine deaminase -
  PWS06_RS09185 - 1841931..1842608 (-) 678 WP_005445538.1 LrgB family protein -
  PWS06_RS09190 - 1842610..1842984 (-) 375 WP_005445537.1 CidA/LrgA family protein -
  PWS06_RS09195 sbcB 1843043..1844464 (-) 1422 WP_274789931.1 exodeoxyribonuclease I Machinery gene
  PWS06_RS09200 - 1844955..1845317 (-) 363 WP_050921748.1 cupin domain-containing protein -
  PWS06_RS09205 - 1845457..1846092 (-) 636 WP_050921745.1 LysE family translocator -
  PWS06_RS09210 - 1846686..1847381 (+) 696 WP_042606224.1 aspartate/glutamate racemase family protein -
  PWS06_RS09215 - 1847775..1848365 (+) 591 WP_274789932.1 LysR family transcriptional regulator -
  PWS06_RS09220 - 1849363..1850052 (-) 690 WP_274789934.1 DUF1826 domain-containing protein -
  PWS06_RS09225 - 1850274..1851647 (-) 1374 WP_274789935.1 L-cystine transporter -
  PWS06_RS09230 - 1851842..1852537 (-) 696 WP_274789936.1 NAD(P)H-binding protein -
  PWS06_RS09235 - 1853272..1853883 (+) 612 WP_017190319.1 flavin reductase family protein -
  PWS06_RS09240 cobT 1853903..1854946 (+) 1044 WP_274789937.1 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase -
  PWS06_RS09245 - 1854946..1855752 (+) 807 WP_274789938.1 adenosylcobinamide-GDP ribazoletransferase -
  PWS06_RS09250 cobU 1855749..1856297 (+) 549 WP_274789939.1 bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase -
  PWS06_RS09255 cobC 1856294..1856908 (+) 615 WP_274789940.1 alpha-ribazole phosphatase -

Sequence

Protein


Download         Length: 473 a.a.        Molecular weight: 54527.83 Da        Isoelectric Point: 4.9808

>NTDB_id=792989 PWS06_RS09195 WP_274789931.1 1843043..1844464(-) (sbcB) [Vibrio harveyi strain 160-19]
MHQDNQPTFFFFDYETWGTSPAKDRPSQFAGVRTDENFNIIGEPLVMYCRPPADYLPSPEAALITGITPQKAMQEGLPEP
EFIAKIHAELSKPKTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVMRACHALRPEGVEWPENDEGFT
SFKLEHLSVANGIEHSNAHDAMADVIATIEMAKKVKAAQPKLFDYFFSMRNKRKLNELVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELKERLYTKRDELGDLLPVPVKLVHLNKCPILAPAKTLTAENAEG
IGIDRQQCLNNLALLRQHPEIREKLISLFSIEREFEKSNDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARHYAGTLDEQEQRRWAQHCREVFESQIEEYMMNLENLVHEHESDEKKIAILKSVYRYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=792989 PWS06_RS09195 WP_274789931.1 1843043..1844464(-) (sbcB) [Vibrio harveyi strain 160-19]
ATGCACCAAGATAATCAGCCCACTTTTTTCTTTTTTGATTACGAGACTTGGGGAACAAGTCCAGCCAAAGATCGTCCAAG
CCAGTTCGCAGGCGTTCGCACTGATGAAAACTTCAATATCATCGGTGAACCTTTGGTCATGTACTGTCGCCCACCTGCTG
ATTACCTTCCTTCGCCAGAAGCAGCTTTGATCACTGGTATTACACCACAAAAAGCAATGCAAGAAGGCTTACCTGAACCT
GAGTTTATTGCCAAAATTCATGCCGAATTGTCTAAACCAAAGACGACTAGCCTTGGCTACAACAGCATACGTTTTGATGA
TGAAGTCACTCGTTACACTTGCTACCGAAACTTCATCGACCCATACGCATGGAGCTGGCAAAACGGCAACTCACGATGGG
ATTTGCTTGACGTGATGCGAGCATGTCATGCCCTGCGTCCTGAAGGCGTAGAATGGCCAGAGAACGATGAAGGCTTTACA
AGCTTCAAGCTAGAGCATTTATCCGTAGCGAATGGCATTGAACACAGCAATGCTCACGATGCGATGGCCGACGTGATTGC
CACGATTGAAATGGCGAAGAAAGTTAAAGCCGCCCAACCTAAGCTATTTGACTACTTTTTCTCGATGCGTAACAAGCGCA
AACTCAATGAGCTGGTTGATATTGTCAATATGACTCCGTTGATGCATGTATCAGGCATGCTTGGGCGTGAATGCCAATAC
ACAAGCTGGATTGTGCCAGTGGCTTGGCATCCAACCAACAATAACGCTGTTATCACGATTGATTTAGCCAAAGATCCTCA
GCCGATCCTTGAACTTTCAGCGGAAGAACTGAAAGAACGCTTGTACACCAAGCGTGACGAATTGGGCGACTTACTGCCTG
TACCAGTGAAGCTAGTGCATCTGAACAAGTGCCCTATTCTCGCTCCAGCAAAAACATTAACCGCGGAAAATGCGGAAGGC
ATTGGTATTGACCGCCAACAATGTTTAAACAATTTAGCGTTGTTGCGCCAACACCCAGAGATCCGAGAGAAGCTGATTAG
TCTATTCTCTATAGAACGTGAATTCGAAAAGAGTAATGACGTTGATACGCAGCTTTACGATGGTTTTTTCTCGCCTGCTG
ATCGCGCTGCTATGGACATCATTCGTGAAACCGATCCGAATAACTTAGCCGCACTGGACATTGAATTCGATGATAAACGA
ATCAAGCCATTGCTTTTCCGTTACCGTGCTCGCCATTATGCAGGCACATTAGATGAACAAGAACAAAGACGCTGGGCACA
ACATTGTCGTGAAGTTTTCGAAAGTCAGATTGAAGAGTACATGATGAATTTGGAAAACTTAGTTCACGAACATGAAAGTG
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