Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   EPB58_RS23345 Genome accession   NZ_CP035693
Coordinates   2748718..2750139 (-) Length   473 a.a.
NCBI ID   WP_154203624.1    Uniprot ID   -
Organism   Vibrio harveyi strain 2011V-1164     
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 2739801..2772446 2748718..2750139 within 0


Gene organization within MGE regions


Location: 2739801..2772446
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  EPB58_RS23285 - 2739801..2740178 (-) 378 WP_154203619.1 hypothetical protein -
  EPB58_RS23290 - 2740178..2740438 (-) 261 WP_005445548.1 hypothetical protein -
  EPB58_RS23295 - 2740591..2741013 (-) 423 WP_038897604.1 hypothetical protein -
  EPB58_RS23300 - 2741035..2741274 (-) 240 WP_154203620.1 hypothetical protein -
  EPB58_RS23305 - 2741457..2742335 (-) 879 WP_154203621.1 AEC family transporter -
  EPB58_RS23310 ihfA 2742862..2743158 (+) 297 WP_005445544.1 integration host factor subunit alpha -
  EPB58_RS23315 - 2743302..2744075 (-) 774 WP_005445543.1 phosphoribosylglycinamide formyltransferase -
  EPB58_RS23320 - 2744412..2745062 (+) 651 WP_154203622.1 thiopurine S-methyltransferase -
  EPB58_RS23325 purT 2745139..2746314 (-) 1176 WP_154203623.1 formate-dependent phosphoribosylglycinamide formyltransferase -
  EPB58_RS23330 cdd 2746463..2747350 (-) 888 WP_005445539.1 cytidine deaminase -
  EPB58_RS23335 - 2747606..2748283 (-) 678 WP_005445538.1 LrgB family protein -
  EPB58_RS23340 - 2748285..2748659 (-) 375 WP_005445537.1 CidA/LrgA family protein -
  EPB58_RS23345 sbcB 2748718..2750139 (-) 1422 WP_154203624.1 exodeoxyribonuclease I Machinery gene
  EPB58_RS23350 - 2750629..2750991 (-) 363 WP_050921748.1 cupin domain-containing protein -
  EPB58_RS23355 - 2751131..2751766 (-) 636 WP_154203625.1 LysE family translocator -
  EPB58_RS23360 - 2752360..2753055 (+) 696 WP_042606224.1 aspartate/glutamate racemase family protein -
  EPB58_RS23365 - 2753449..2754258 (+) 810 WP_042606225.1 LysR family transcriptional regulator -
  EPB58_RS23370 - 2755041..2755730 (-) 690 WP_101960465.1 DUF1826 domain-containing protein -
  EPB58_RS23375 - 2755952..2757325 (-) 1374 WP_154203626.1 L-cystine transporter -
  EPB58_RS23380 - 2757520..2758215 (-) 696 WP_017818004.1 NAD(P)H-binding protein -
  EPB58_RS23385 - 2758951..2759562 (+) 612 WP_154203627.1 flavin reductase family protein -
  EPB58_RS23390 cobT 2759582..2760625 (+) 1044 WP_154203628.1 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase -
  EPB58_RS23395 - 2760625..2761431 (+) 807 WP_154203629.1 adenosylcobinamide-GDP ribazoletransferase -
  EPB58_RS23400 cobU 2761428..2761961 (+) 534 WP_154203630.1 bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase -
  EPB58_RS23405 cobC 2761973..2762587 (+) 615 WP_154203631.1 alpha-ribazole phosphatase -
  EPB58_RS23410 - 2762670..2764469 (+) 1800 WP_154203632.1 M3 family oligoendopeptidase -
  EPB58_RS23415 - 2764708..2765736 (+) 1029 WP_154203633.1 succinylglutamate desuccinylase -
  EPB58_RS23420 btuC 2765839..2766834 (+) 996 WP_020197786.1 vitamin B12 ABC transporter permease BtuC -
  EPB58_RS23425 btuD 2766821..2767588 (+) 768 WP_080654225.1 vitamin B12 ABC transporter ATP-binding protein BtuD -
  EPB58_RS23430 - 2767835..2769016 (+) 1182 WP_241670074.1 hypothetical protein -
  EPB58_RS23435 - 2769075..2769596 (+) 522 WP_154203635.1 hypothetical protein -
  EPB58_RS23440 - 2769650..2770006 (+) 357 WP_154203636.1 hypothetical protein -
  EPB58_RS23445 - 2770170..2770586 (+) 417 WP_009697380.1 lysozyme inhibitor LprI family protein -
  EPB58_RS23450 - 2771134..2771640 (+) 507 WP_029791093.1 AAA family ATPase -
  EPB58_RS23455 - 2771673..2772446 (+) 774 WP_009701136.1 nucleotidyltransferase domain-containing protein -

Sequence

Protein


Download         Length: 473 a.a.        Molecular weight: 54583.94 Da        Isoelectric Point: 4.9808

>NTDB_id=343803 EPB58_RS23345 WP_154203624.1 2748718..2750139(-) (sbcB) [Vibrio harveyi strain 2011V-1164]
MHQDNQPTFFFFDYETWGTSPAKDRPSQFAGVRTDENFNIIGEPLVMYCRPPADYLPSPEAALITGITPQKAMQEGLPEP
EFIAKIHAELSKPKTTSLGYNSIRFDDEVTRYTCYRNFIDPYAWSWQNGNSRWDLLDVMRACHALRPEGIEWPENDEGFT
SFKLEHLSVANGIEHSNAHDAMADVIATIEMAKKVKAAQPKLFDYFFSMRNKRKLNELVDIVNMTPLMHVSGMLGRECQY
TSWIVPVAWHPTNNNAVITIDLAKDPQPILELSAEELKERLYTKRDELGDLLPVPVKLVHLNKCPILAPAKTLTAENAEV
IGIDRQQCLNNLALLRQHPEIREKLISLFSIEREFEKSNDVDTQLYDGFFSPADRAAMDIIRETDPNNLAALDIEFDDKR
IKPLLFRYRARHYAGTLDEQEQRRWAQHCREVFESQIEEYMMNLENLVHEHESDEKKIAILKSVYRYVESLAS

Nucleotide


Download         Length: 1422 bp        

>NTDB_id=343803 EPB58_RS23345 WP_154203624.1 2748718..2750139(-) (sbcB) [Vibrio harveyi strain 2011V-1164]
ATGCACCAAGACAATCAGCCCACTTTTTTCTTTTTCGATTACGAGACTTGGGGAACAAGTCCAGCCAAAGACCGCCCAAG
CCAGTTTGCTGGCGTTCGCACTGATGAAAACTTCAATATCATTGGTGAACCTTTGGTGATGTACTGTCGTCCACCTGCTG
ATTACCTTCCTTCGCCAGAAGCAGCTTTGATCACTGGTATTACACCACAAAAAGCAATGCAAGAAGGCTTACCTGAACCT
GAGTTTATCGCCAAAATTCATGCTGAATTGTCTAAACCAAAGACGACTAGCCTTGGCTACAACAGCATACGTTTTGATGA
TGAAGTCACTCGTTACACTTGCTACCGAAACTTCATCGACCCATACGCATGGAGCTGGCAAAACGGCAACTCACGATGGG
ATTTGCTTGACGTGATGCGAGCATGTCATGCCCTGCGTCCTGAAGGTATTGAATGGCCGGAGAACGATGAAGGCTTTACA
AGCTTCAAGCTAGAGCATTTATCCGTAGCGAATGGCATTGAACACAGCAATGCTCACGATGCGATGGCCGACGTGATTGC
CACGATTGAAATGGCGAAGAAAGTTAAAGCCGCCCAACCTAAGCTATTTGACTACTTTTTCTCGATGCGTAACAAGCGCA
AACTCAATGAGCTGGTTGATATTGTCAATATGACTCCGTTGATGCATGTATCAGGCATGCTTGGGCGTGAATGCCAATAC
ACAAGCTGGATTGTGCCTGTGGCTTGGCACCCAACCAACAACAACGCTGTTATCACGATTGATTTAGCCAAAGATCCTCA
GCCGATCCTTGAACTTTCAGCGGAAGAACTGAAAGAACGCTTGTACACCAAGCGTGATGAATTGGGCGACTTACTGCCTG
TACCAGTGAAGCTAGTGCATCTGAACAAGTGCCCTATTCTCGCTCCAGCAAAAACATTAACCGCGGAAAATGCGGAAGTC
ATTGGTATTGACCGCCAACAATGTTTAAACAATTTAGCGTTGTTGCGCCAACACCCAGAGATCCGAGAGAAGCTGATTAG
TCTATTCTCTATAGAACGTGAATTCGAAAAGAGTAATGACGTTGATACGCAGCTTTACGATGGCTTTTTCTCGCCTGCTG
ATCGCGCTGCTATGGACATCATTCGTGAAACCGATCCGAATAACTTAGCCGCACTGGACATTGAATTCGATGATAAACGA
ATCAAGCCATTGCTTTTCCGTTACCGTGCTCGCCATTATGCAGGCACATTAGATGAACAAGAACAAAGACGCTGGGCACA
ACATTGTCGTGAAGTTTTCGAAAGTCAGATTGAAGAGTACATGATGAATTTAGAAAACTTAGTTCACGAACATGAAAGTG
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

79.493

100

0.795

Multiple sequence alignment