Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   MNQ96_RS17620 Genome accession   NZ_CP093335
Coordinates   3768065..3769426 (-) Length   453 a.a.
NCBI ID   WP_241941753.1    Uniprot ID   -
Organism   Sphingopyxis granuli strain A2-E30     
Function   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 3736652..3770290 3768065..3769426 within 0


Gene organization within MGE regions


Location: 3736652..3770290
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  MNQ96_RS17445 (MNQ96_17445) - 3736652..3736921 (-) 270 Protein_3457 integrase core domain-containing protein -
  MNQ96_RS17450 (MNQ96_17450) istA 3737112..3738626 (+) 1515 WP_420854228.1 IS21 family transposase -
  MNQ96_RS17455 (MNQ96_17455) istB 3738623..3739459 (+) 837 WP_241940839.1 IS21-like element helper ATPase IstB -
  MNQ96_RS17460 (MNQ96_17460) - 3739553..3740523 (-) 971 Protein_3460 IS3 family transposase -
  MNQ96_RS17465 (MNQ96_17465) - 3740574..3741269 (-) 696 WP_241943310.1 patatin-like phospholipase family protein -
  MNQ96_RS17470 (MNQ96_17470) - 3741668..3742570 (+) 903 WP_241941734.1 hypothetical protein -
  MNQ96_RS18870 - 3742508..3742753 (-) 246 Protein_3463 integrase core domain-containing protein -
  MNQ96_RS17480 (MNQ96_17480) - 3742707..3743126 (-) 420 Protein_3464 nucleotidyltransferase domain-containing protein -
  MNQ96_RS17485 (MNQ96_17485) - 3743190..3744131 (-) 942 WP_241941735.1 DUF2493 domain-containing protein -
  MNQ96_RS17490 (MNQ96_17490) - 3744680..3745446 (+) 767 Protein_3466 IS5 family transposase -
  MNQ96_RS17495 (MNQ96_17495) - 3745443..3746690 (-) 1248 WP_241941736.1 type II toxin-antitoxin system HipA family toxin -
  MNQ96_RS17500 (MNQ96_17500) - 3746687..3746905 (-) 219 WP_104959934.1 type II toxin-antitoxin system Y4mF family antitoxin -
  MNQ96_RS17505 (MNQ96_17505) - 3747244..3748281 (-) 1038 WP_104959935.1 DUF7146 domain-containing protein -
  MNQ96_RS17510 (MNQ96_17510) - 3748345..3749562 (-) 1218 Protein_3470 strawberry notch-like NTP hydrolase domain-containing protein -
  MNQ96_RS17515 (MNQ96_17515) - 3749714..3750622 (+) 909 WP_241941737.1 prolyl oligopeptidase family serine peptidase -
  MNQ96_RS17520 (MNQ96_17520) - 3750634..3752361 (-) 1728 WP_241941738.1 asparagine synthetase B family protein -
  MNQ96_RS17525 (MNQ96_17525) - 3752361..3753002 (-) 642 WP_241941739.1 lasso peptide biosynthesis B2 protein -
  MNQ96_RS18775 - 3753062..3753193 (-) 132 WP_267894964.1 hypothetical protein -
  MNQ96_RS17535 (MNQ96_17535) - 3753830..3754303 (-) 474 WP_241941740.1 DUF1178 family protein -
  MNQ96_RS17540 (MNQ96_17540) grxC 3754300..3754566 (-) 267 WP_241941741.1 glutaredoxin 3 -
  MNQ96_RS17545 (MNQ96_17545) - 3754571..3755371 (-) 801 WP_241941742.1 double zinc ribbon domain-containing protein -
  MNQ96_RS17550 (MNQ96_17550) - 3755495..3756361 (+) 867 WP_241941743.1 class I SAM-dependent methyltransferase -
  MNQ96_RS17555 (MNQ96_17555) - 3756552..3756944 (-) 393 WP_241941744.1 (deoxy)nucleoside triphosphate pyrophosphohydrolase -
  MNQ96_RS17560 (MNQ96_17560) - 3757048..3757227 (+) 180 WP_241941745.1 Flp family type IVb pilin -
  MNQ96_RS17565 (MNQ96_17565) - 3757366..3757545 (+) 180 WP_241941746.1 Flp family type IVb pilin -
  MNQ96_RS17570 (MNQ96_17570) - 3757619..3759121 (-) 1503 WP_241941747.1 M48 family metalloprotease -
  MNQ96_RS17575 (MNQ96_17575) - 3759370..3760317 (-) 948 WP_067106173.1 acetyl-CoA carboxylase carboxyltransferase subunit alpha -
  MNQ96_RS17580 (MNQ96_17580) - 3760381..3761268 (-) 888 WP_276516797.1 tyrosine recombinase -
  MNQ96_RS17585 (MNQ96_17585) - 3761261..3763081 (-) 1821 WP_241941748.1 hypothetical protein -
  MNQ96_RS17590 (MNQ96_17590) - 3763078..3763248 (-) 171 WP_158682313.1 hypothetical protein -
  MNQ96_RS17595 (MNQ96_17595) - 3763356..3763919 (+) 564 WP_067187173.1 shikimate kinase -
  MNQ96_RS17600 (MNQ96_17600) aroB 3763907..3765013 (+) 1107 WP_241941749.1 3-dehydroquinate synthase -
  MNQ96_RS17605 (MNQ96_17605) - 3765042..3766928 (-) 1887 WP_241941750.1 cation:proton antiporter -
  MNQ96_RS17610 (MNQ96_17610) - 3766925..3767350 (-) 426 WP_241941751.1 iron-sulfur cluster assembly scaffold protein -
  MNQ96_RS17615 (MNQ96_17615) - 3767347..3767922 (-) 576 WP_241941752.1 CvpA family protein -
  MNQ96_RS17620 (MNQ96_17620) radA 3768065..3769426 (-) 1362 WP_241941753.1 DNA repair protein RadA Machinery gene
  MNQ96_RS17625 (MNQ96_17625) fsa 3769640..3770290 (+) 651 WP_076076901.1 fructose-6-phosphate aldolase -

Sequence

Protein


Download         Length: 453 a.a.        Molecular weight: 47457.27 Da        Isoelectric Point: 6.2631

>NTDB_id=663760 MNQ96_RS17620 WP_241941753.1 3768065..3769426(-) (radA) [Sphingopyxis granuli strain A2-E30]
MAKAKRQYVCQNCGAVSYRWQGQCADCGEWNTLVEEAAETVFSAKHDLSKGGRTLALETLDEQSAMPERMLCGIAEFDRA
LGGGFVAGSATLIGGDPGIGKSTLLLQAAGRIARAGRSVVYISGEEAAAQVRLRAQRLGLGDAPVALASATSVRDILATL
EGRGADFVVIDSIQTMHSDLIDSAPGTVSQVRASAQELIRYAKDSGAAIVLVGHVTKDGTIAGPRVLEHMVDTVLAFEGE
RSHQYRILRAVKNRFGGTDEIGVFAMGEEGLGEVANPSSLFLTDRSRDVPGSVVFPALEGTRPVLVEVQALTVRLASGAT
PRRAVVGWDSGRLAMVLAVLEARCGLQMGSAEVYLNIAGGYRLTDPAADLAVAAALISAFSERPVPADAIVFGELSLSGE
VRPVAHDALRLREAAKLGFSSGWGPKGMKGVKGIGVTGFGRLGELVDLMLGRA

Nucleotide


Download         Length: 1362 bp        

>NTDB_id=663760 MNQ96_RS17620 WP_241941753.1 3768065..3769426(-) (radA) [Sphingopyxis granuli strain A2-E30]
ATGGCCAAAGCGAAACGCCAATATGTCTGCCAGAATTGCGGCGCTGTCAGTTATCGCTGGCAGGGCCAGTGCGCCGATTG
CGGCGAGTGGAACACGCTGGTCGAGGAAGCGGCCGAAACGGTCTTCTCCGCGAAGCACGACCTGTCGAAGGGCGGCCGCA
CGCTCGCGCTCGAAACGCTCGACGAACAGAGCGCGATGCCCGAGCGGATGCTGTGCGGCATCGCCGAGTTCGACCGTGCG
CTCGGCGGCGGTTTCGTCGCCGGGTCGGCGACGCTGATCGGCGGCGATCCGGGGATCGGCAAATCGACCTTGCTGCTTCA
GGCCGCGGGCCGGATCGCCAGGGCGGGCAGGTCGGTCGTCTATATCAGCGGCGAGGAAGCGGCGGCGCAGGTCCGGCTGC
GCGCGCAGCGGCTGGGGCTCGGCGACGCGCCGGTGGCGCTCGCCAGCGCGACTTCGGTGCGCGACATCCTCGCGACGCTG
GAGGGGCGCGGCGCCGATTTCGTCGTCATCGATTCGATCCAGACGATGCACAGCGACCTGATCGACAGTGCGCCGGGTAC
CGTCAGCCAGGTGCGCGCGAGCGCGCAGGAACTGATCCGCTATGCCAAGGACAGCGGCGCGGCGATCGTGCTCGTCGGCC
ATGTGACGAAGGACGGGACGATCGCGGGACCGCGCGTGCTCGAACATATGGTCGACACCGTACTGGCGTTCGAGGGCGAG
CGCAGCCACCAGTATCGCATCCTGCGCGCGGTCAAGAACCGCTTCGGCGGCACCGACGAGATCGGGGTGTTCGCGATGGG
CGAGGAGGGGCTGGGCGAGGTCGCCAACCCGTCGAGCCTGTTCCTGACCGACCGCAGCCGCGACGTGCCGGGGTCGGTGG
TGTTCCCCGCGCTGGAGGGCACGCGGCCGGTGCTGGTCGAGGTACAGGCGCTGACCGTACGCCTTGCGAGCGGCGCGACG
CCGCGCCGCGCCGTCGTCGGCTGGGACAGCGGGCGGCTCGCGATGGTGCTCGCGGTGCTCGAGGCGCGCTGCGGGCTCCA
GATGGGGAGCGCCGAAGTCTATCTGAACATCGCGGGCGGCTATCGCCTCACCGATCCGGCGGCCGACCTAGCGGTCGCGG
CGGCGCTGATCTCGGCGTTCAGCGAGCGACCGGTGCCCGCCGACGCGATCGTCTTCGGCGAACTGTCGCTGTCGGGCGAG
GTGCGCCCGGTCGCGCACGACGCGCTGCGCCTGCGCGAGGCGGCGAAGCTCGGCTTTTCAAGCGGCTGGGGGCCAAAGGG
GATGAAGGGCGTGAAGGGGATCGGCGTCACCGGCTTCGGCCGGCTCGGCGAACTCGTTGACCTGATGCTCGGGCGTGCCT
AG

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(342-419)

AAA domain (AAA_25)

(81-219)

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)


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
  radA Bacillus subtilis subsp. subtilis str. 168

47.629

100

0.488
  radA Streptococcus pneumoniae Rx1

47.072

98.013

0.461
  radA Streptococcus pneumoniae D39

47.072

98.013

0.461
  radA Streptococcus pneumoniae TIGR4

47.072

98.013

0.461
  radA Streptococcus pneumoniae R6

47.072

98.013

0.461
  radA Streptococcus mitis NCTC 12261

46.444

99.338

0.461
  radA Streptococcus mitis SK321

47.775

94.26

0.45