Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   PH545_RS05970 Genome accession   NZ_CP116414
Coordinates   1173204..1174625 (-) Length   473 a.a.
NCBI ID   WP_289881280.1    Uniprot ID   -
Organism   Vibrio harveyi strain K2014767     
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 1164280..1192183 1173204..1174625 within 0


Gene organization within MGE regions


Location: 1164280..1192183
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PH545_RS05910 (PH545_05910) - 1164280..1164663 (-) 384 WP_005445549.1 hypothetical protein -
  PH545_RS05915 (PH545_05915) - 1164663..1164923 (-) 261 WP_005445548.1 hypothetical protein -
  PH545_RS05920 (PH545_05920) - 1165076..1165498 (-) 423 WP_017817999.1 hypothetical protein -
  PH545_RS05925 (PH545_05925) - 1165520..1165759 (-) 240 WP_005445546.1 hypothetical protein -
  PH545_RS05930 (PH545_05930) - 1165942..1166820 (-) 879 WP_289881276.1 AEC family transporter -
  PH545_RS05935 (PH545_05935) ihfA 1167347..1167643 (+) 297 WP_005445544.1 integration host factor subunit alpha -
  PH545_RS05940 (PH545_05940) - 1167787..1168560 (-) 774 WP_289881277.1 phosphoribosylglycinamide formyltransferase -
  PH545_RS05945 (PH545_05945) - 1168897..1169547 (+) 651 WP_252044321.1 thiopurine S-methyltransferase -
  PH545_RS05950 (PH545_05950) purT 1169625..1170800 (-) 1176 WP_289881278.1 formate-dependent phosphoribosylglycinamide formyltransferase -
  PH545_RS05955 (PH545_05955) cdd 1170949..1171836 (-) 888 WP_289881279.1 cytidine deaminase -
  PH545_RS05960 (PH545_05960) - 1172092..1172769 (-) 678 WP_005445538.1 LrgB family protein -
  PH545_RS05965 (PH545_05965) - 1172771..1173145 (-) 375 WP_050903240.1 CidA/LrgA family protein -
  PH545_RS05970 (PH545_05970) sbcB 1173204..1174625 (-) 1422 WP_289881280.1 exodeoxyribonuclease I Machinery gene
  PH545_RS05975 (PH545_05975) - 1174787..1175467 (-) 681 WP_005445535.1 DUF1826 domain-containing protein -
  PH545_RS05980 (PH545_05980) - 1175689..1177062 (-) 1374 WP_289881281.1 L-cystine transporter -
  PH545_RS05985 (PH545_05985) - 1177257..1177952 (-) 696 WP_289881282.1 oxidoreductase -
  PH545_RS05990 (PH545_05990) - 1178688..1179299 (+) 612 WP_274886399.1 flavin reductase family protein -
  PH545_RS05995 (PH545_05995) cobT 1179319..1180362 (+) 1044 WP_289881283.1 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase -
  PH545_RS06000 (PH545_06000) - 1180362..1181168 (+) 807 WP_289881284.1 adenosylcobinamide-GDP ribazoletransferase -
  PH545_RS06005 (PH545_06005) cobU 1181165..1181713 (+) 549 WP_289881285.1 bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase -
  PH545_RS06010 (PH545_06010) cobC 1181710..1182324 (+) 615 WP_289881286.1 alpha-ribazole phosphatase -
  PH545_RS06015 (PH545_06015) - 1182407..1184206 (+) 1800 WP_289881287.1 M3 family oligoendopeptidase -
  PH545_RS06020 (PH545_06020) - 1184445..1185473 (+) 1029 WP_005439838.1 succinylglutamate desuccinylase -
  PH545_RS06025 (PH545_06025) btuC 1185576..1186571 (+) 996 WP_005439842.1 vitamin B12 ABC transporter permease BtuC -
  PH545_RS06030 (PH545_06030) btuD 1186558..1187325 (+) 768 WP_289881288.1 vitamin B12 ABC transporter ATP-binding protein BtuD -
  PH545_RS06035 (PH545_06035) - 1187572..1188753 (+) 1182 WP_240694491.1 hypothetical protein -
  PH545_RS06040 (PH545_06040) - 1188812..1189333 (+) 522 WP_045452642.1 hypothetical protein -
  PH545_RS06045 (PH545_06045) - 1189387..1189743 (+) 357 WP_017190311.1 hypothetical protein -
  PH545_RS06050 (PH545_06050) - 1189907..1190323 (+) 417 WP_009697380.1 lysozyme inhibitor LprI family protein -
  PH545_RS06055 (PH545_06055) - 1190871..1191377 (+) 507 WP_289881289.1 AAA family ATPase -
  PH545_RS06060 (PH545_06060) - 1191410..1192183 (+) 774 WP_289881290.1 nucleotidyltransferase domain-containing protein -

Sequence

Protein


Download         Length: 473 a.a.        Molecular weight: 54601.95 Da        Isoelectric Point: 4.9808

>NTDB_id=777281 PH545_RS05970 WP_289881280.1 1173204..1174625(-) (sbcB) [Vibrio harveyi strain K2014767]
MHQDNQPTFFFFDYETWGTSPAKDRPSQFAGVRTDENFNIIGEPLVMYCRPPADYLPSPEAALITGITPQKAMQEGLPEP
EFIAKIHAELSKPKTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVMRACHALRPEGIEWSENDEGFT
SFKLEHLSVANGIEHSNAHDAMVDVIATIEMAKKVKAAQPKLFDYFFSMRNKRKLNELVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELKERLYTKRDELGDLLPVPVKLVHLNKCPILAPAKTLTAENAEV
IGIDRQQCLNNLALLRQHPEIREKLISLFSIEREFEKSNDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARHYAGTLDEQEQRRWAQHCREVFESQIEEYMMNLENLVHEHESDEKKIAILKSVYRYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=777281 PH545_RS05970 WP_289881280.1 1173204..1174625(-) (sbcB) [Vibrio harveyi strain K2014767]
ATGCACCAAGACAATCAGCCCACTTTTTTCTTTTTCGATTACGAGACTTGGGGAACAAGTCCAGCCAAAGACCGCCCAAG
CCAGTTTGCTGGCGTTCGCACTGATGAAAACTTCAATATCATTGGTGAACCTTTGGTGATGTACTGTCGTCCACCTGCTG
ATTACCTTCCTTCGCCAGAAGCAGCTTTGATCACTGGTATTACACCACAAAAAGCAATGCAAGAAGGCTTACCTGAACCT
GAGTTTATCGCCAAAATTCATGCTGAATTGTCTAAACCAAAGACGACTAGCCTTGGCTACAACAGCATACGTTTTGATGA
TGAAGTCACTCGTTACACTTGCTACCGAAACTTCATCGACCCATACGCATGGAGCTGGCAAAACGGCAACTCACGATGGG
ATTTGCTTGACGTGATGCGAGCATGTCATGCCCTGCGTCCTGAAGGTATTGAATGGTCGGAGAACGATGAAGGCTTTACA
AGCTTCAAGCTAGAGCATTTATCCGTAGCGAATGGCATTGAACACAGCAATGCTCACGATGCGATGGTAGACGTGATTGC
CACGATTGAAATGGCGAAGAAAGTTAAAGCCGCCCAACCTAAGCTATTTGACTACTTTTTCTCGATGCGTAACAAGCGCA
AACTCAATGAGCTGGTTGATATTGTCAATATGACTCCGTTGATGCATGTATCAGGCATGCTTGGGCGTGAATGCCAATAC
ACAAGCTGGATTGTGCCTGTGGCTTGGCACCCAACCAACAACAACGCTGTTATCACGATTGATTTAGCCAAAGATCCTCA
GCCGATCCTTGAACTTTCAGCGGAAGAACTGAAAGAACGCTTGTACACCAAGCGTGATGAATTGGGCGACTTACTGCCTG
TACCAGTGAAGCTAGTGCATCTGAACAAGTGCCCTATTCTCGCTCCAGCAAAAACATTAACCGCGGAAAATGCGGAAGTC
ATTGGTATTGACCGCCAACAATGTTTAAACAATTTAGCGTTGTTGCGCCAACACCCAGAGATCCGAGAGAAGCTGATTAG
TCTATTCTCTATAGAACGTGAATTCGAAAAGAGTAATGACGTTGATACGCAGCTTTACGATGGTTTTTTCTCGCCTGCTG
ATCGCGCTGCTATGGACATCATTCGTGAAACCGATCCGAATAACTTAGCCGCACTGGACATTGAATTCGATGATAAACGA
ATCAAGCCATTGCTTTTCCGTTACCGTGCTCGCCATTATGCAGGCACATTAGATGAACAAGAACAAAGACGCTGGGCACA
ACATTGTCGTGAAGTTTTCGAAAGTCAGATTGAAGAGTACATGATGAATTTAGAAAACTTAGTTCACGAACATGAAAGTG
ACGAAAAGAAGATAGCAATATTAAAATCCGTCTATCGCTATGTAGAGAGCCTAGCCTCCTAA

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

79.07

100

0.791