Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   ACFBML_RS09010 Genome accession   NZ_CP170491
Coordinates   2015916..2017337 (+) Length   473 a.a.
NCBI ID   WP_390337773.1    Uniprot ID   -
Organism   Vibrio harveyi strain LcV6     
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 2000852..2027519 2015916..2017337 within 0


Gene organization within MGE regions


Location: 2000852..2027519
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ACFBML_RS08935 (ACFBML_08935) - 2000852..2001625 (-) 774 WP_017190308.1 nucleotidyltransferase domain-containing protein -
  ACFBML_RS08940 (ACFBML_08940) - 2001658..2002164 (-) 507 WP_390337766.1 AAA family ATPase -
  ACFBML_RS08945 (ACFBML_08945) - 2002712..2003128 (-) 417 WP_047517001.1 lysozyme inhibitor LprI family protein -
  ACFBML_RS08950 (ACFBML_08950) btuD 2003216..2003983 (-) 768 WP_080654225.1 vitamin B12 ABC transporter ATP-binding protein BtuD -
  ACFBML_RS08955 (ACFBML_08955) btuC 2003970..2004965 (-) 996 WP_390337767.1 vitamin B12 ABC transporter permease BtuC -
  ACFBML_RS08960 (ACFBML_08960) - 2005068..2006096 (-) 1029 WP_005439838.1 succinylglutamate desuccinylase -
  ACFBML_RS08965 (ACFBML_08965) - 2006335..2008134 (-) 1800 WP_050907537.1 M3 family oligoendopeptidase -
  ACFBML_RS08970 (ACFBML_08970) cobC 2008216..2008830 (-) 615 WP_390337768.1 alpha-ribazole phosphatase -
  ACFBML_RS08975 (ACFBML_08975) cobU 2008827..2009375 (-) 549 WP_390337769.1 bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase -
  ACFBML_RS08980 (ACFBML_08980) - 2009372..2010178 (-) 807 WP_390337770.1 adenosylcobinamide-GDP ribazoletransferase -
  ACFBML_RS08985 (ACFBML_08985) cobT 2010178..2011221 (-) 1044 WP_390337771.1 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase -
  ACFBML_RS08990 (ACFBML_08990) - 2011241..2011852 (-) 612 WP_390337772.1 flavin reductase family protein -
  ACFBML_RS08995 (ACFBML_08995) - 2012588..2013283 (+) 696 WP_017190320.1 NAD(P)H-binding protein -
  ACFBML_RS09000 (ACFBML_09000) - 2013478..2014851 (+) 1374 WP_053050855.1 L-cystine transporter -
  ACFBML_RS09005 (ACFBML_09005) - 2015073..2015753 (+) 681 WP_005445535.1 DUF1826 domain-containing protein -
  ACFBML_RS09010 (ACFBML_09010) sbcB 2015916..2017337 (+) 1422 WP_390337773.1 exodeoxyribonuclease I Machinery gene
  ACFBML_RS09015 (ACFBML_09015) - 2017396..2017770 (+) 375 WP_050903240.1 CidA/LrgA family protein -
  ACFBML_RS09020 (ACFBML_09020) - 2017772..2018449 (+) 678 WP_005445538.1 LrgB family protein -
  ACFBML_RS09025 (ACFBML_09025) cdd 2018705..2019592 (+) 888 WP_005445539.1 cytidine deaminase -
  ACFBML_RS09030 (ACFBML_09030) purT 2019741..2020916 (+) 1176 WP_009697365.1 formate-dependent phosphoribosylglycinamide formyltransferase -
  ACFBML_RS09035 (ACFBML_09035) - 2020994..2021644 (-) 651 WP_042606219.1 thiopurine S-methyltransferase -
  ACFBML_RS09040 (ACFBML_09040) - 2021981..2022754 (+) 774 WP_005445543.1 phosphoribosylglycinamide formyltransferase -
  ACFBML_RS09045 (ACFBML_09045) ihfA 2022898..2023194 (-) 297 WP_005445544.1 integration host factor subunit alpha -
  ACFBML_RS09050 (ACFBML_09050) - 2023721..2024599 (+) 879 WP_222326295.1 AEC family transporter -
  ACFBML_RS09055 (ACFBML_09055) - 2024782..2025021 (+) 240 WP_222326297.1 hypothetical protein -
  ACFBML_RS09060 (ACFBML_09060) - 2025043..2025465 (+) 423 WP_222326299.1 hypothetical protein -
  ACFBML_RS09065 (ACFBML_09065) - 2025618..2025878 (+) 261 WP_005445548.1 hypothetical protein -
  ACFBML_RS09070 (ACFBML_09070) - 2025878..2026261 (+) 384 WP_005445549.1 hypothetical protein -
  ACFBML_RS09075 (ACFBML_09075) - 2026252..2026590 (+) 339 WP_222326301.1 hypothetical protein -
  ACFBML_RS09080 (ACFBML_09080) - 2026794..2027519 (+) 726 WP_017817995.1 metallophosphoesterase -

Sequence

Protein


Download         Length: 473 a.a.        Molecular weight: 54500.80 Da        Isoelectric Point: 4.9221

>NTDB_id=1057681 ACFBML_RS09010 WP_390337773.1 2015916..2017337(+) (sbcB) [Vibrio harveyi strain LcV6]
MHQDNQPTFFFFDYETWGTSPAKDRPSQFAGVRTDENFNIIGEPLVMYCRPPADYLPSPEAALITGITPQKAMQEGLPEP
EFIAKIHAELSKPKTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVMRACHALRPEGVEWPENDEGFT
SFKLEHLSVANGIEHSNAHDAMADVIATIEMAKKVKAAQPKLFDYFFSMRNKRKLNELVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELKERLYTKRDELGDLLPVPVKLVHLNKCPILAPAKTLTAENAEV
IGIDRQQCLNNLALLRQHPEIREKLISLFSIEREFEKSNDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARHYAGTLDEQEQRSWAQHCREVFESQIEEYMMNLENLVHEHESDEKKIAILKSVYRYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=1057681 ACFBML_RS09010 WP_390337773.1 2015916..2017337(+) (sbcB) [Vibrio harveyi strain LcV6]
ATGCACCAAGATAATCAGCCCACTTTTTTCTTTTTTGATTACGAGACTTGGGGAACAAGTCCAGCCAAAGATCGTCCAAG
CCAGTTTGCTGGCGTTCGCACTGATGAAAACTTCAATATCATTGGTGAACCTTTGGTGATGTACTGTCGTCCACCTGCTG
ATTACCTTCCTTCGCCAGAAGCAGCTTTGATCACTGGTATTACACCACAAAAAGCAATGCAAGAAGGCTTACCTGAACCT
GAGTTTATCGCCAAAATTCATGCCGAATTGTCTAAACCAAAGACGACTAGCCTTGGCTACAACAGCATACGTTTTGATGA
TGAAGTCACTCGTTACACTTGCTACCGAAACTTCATCGACCCATACGCATGGAGCTGGCAAAACGGCAACTCACGATGGG
ATTTGCTTGACGTGATGCGAGCATGTCATGCCCTTCGTCCTGAAGGTGTGGAATGGCCGGAGAATGATGAAGGCTTTACG
AGTTTCAAGCTTGAGCATTTATCCGTGGCTAACGGCATTGAACACAGCAATGCTCACGATGCGATGGCCGACGTGATTGC
CACGATTGAAATGGCGAAGAAAGTTAAAGCCGCCCAACCTAAGCTATTTGACTACTTTTTCTCGATGCGTAACAAGCGCA
AACTCAATGAGCTGGTTGATATTGTCAATATGACTCCATTGATGCATGTATCAGGCATGCTTGGGCGTGAATGCCAATAC
ACAAGCTGGATTGTGCCTGTGGCTTGGCACCCAACCAACAACAACGCTGTTATCACGATTGATTTAGCCAAAGATCCTCA
GCCGATCCTTGAACTTTCAGCGGAAGAACTGAAAGAACGCTTGTACACCAAGCGTGACGAATTGGGCGACTTACTGCCTG
TACCAGTGAAGCTGGTGCATCTGAACAAGTGCCCTATTCTCGCTCCAGCAAAAACATTAACCGCGGAAAATGCGGAAGTC
ATTGGTATTGACCGCCAACAATGTTTAAACAATTTAGCGTTGTTGCGCCAACACCCAGAGATCCGAGAGAAGCTGATTAG
TCTATTCTCTATAGAACGTGAATTCGAAAAGAGTAATGACGTTGATACGCAGCTTTACGATGGTTTTTTCTCGCCTGCTG
ATCGCGCTGCGATGGACATCATTCGTGAAACCGATCCGAATAACTTAGCCGCACTGGACATTGAATTCGATGATAAACGA
ATCAAGCCATTGCTTTTCCGTTACCGTGCTCGCCATTATGCAGGCACATTAGATGAACAAGAACAAAGAAGCTGGGCACA
ACATTGTCGTGAAGTTTTCGAAAGTCAGATTGAAGAGTACATGATGAATTTAGAAAACTTAGTTCACGAACATGAAAGTG
ACGAAAAGAAGATAGCAATATTAAAATCCGTCTATCGTTATGTAGAGAGCCTAGCCTCCTAA

Domains

Predicted by InterproScan.

Exonuclease (RNase_T)

(11-190)

Exonuclease C-terminal (Exonuc_X-T_C)

(210-469)


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

Multiple sequence alignment