Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   OKX02_RS12515 Genome accession   NZ_CP110214
Coordinates   2567255..2568619 (-) Length   454 a.a.
NCBI ID   WP_003580798.1    Uniprot ID   -
Organism   Lacticaseibacillus paracasei strain ATG-E1     
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 2558089..2569178 2567255..2568619 within 0


Gene organization within MGE regions


Location: 2558089..2569178
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  OKX02_RS12460 (OKX02_12460) - 2558089..2559360 (-) 1272 WP_003577830.1 MucBP domain-containing protein -
  OKX02_RS12465 (OKX02_12465) - 2559526..2561022 (-) 1497 WP_265013228.1 peptide cleavage/export ABC transporter -
  OKX02_RS12470 (OKX02_12470) - 2561069..2561989 (-) 921 WP_003574021.1 IS30 family transposase -
  OKX02_RS12475 (OKX02_12475) - 2562060..2562746 (-) 687 WP_265013229.1 cysteine peptidase family C39 domain-containing protein -
  OKX02_RS12480 (OKX02_12480) - 2562847..2562960 (-) 114 WP_003577835.1 bacteriocin -
  OKX02_RS12485 (OKX02_12485) - 2563004..2563108 (-) 105 WP_191994146.1 bacteriocin -
  OKX02_RS12490 (OKX02_12490) - 2563152..2563928 (-) 777 WP_003577837.1 ABC transporter permease -
  OKX02_RS12495 (OKX02_12495) - 2563932..2564837 (-) 906 WP_016366635.1 ATP-binding cassette domain-containing protein -
  OKX02_RS12500 (OKX02_12500) - 2564858..2564989 (-) 132 WP_003580794.1 hypothetical protein -
  OKX02_RS12505 (OKX02_12505) - 2565118..2566014 (+) 897 WP_003580795.1 helix-turn-helix domain-containing protein -
  OKX02_RS12510 (OKX02_12510) - 2566118..2567233 (-) 1116 WP_003567252.1 PIN/TRAM domain-containing protein -
  OKX02_RS12515 (OKX02_12515) radA 2567255..2568619 (-) 1365 WP_003580798.1 DNA repair protein RadA Machinery gene
  OKX02_RS12520 (OKX02_12520) - 2568636..2569178 (-) 543 WP_003567256.1 dUTP diphosphatase -

Sequence

Protein


Download         Length: 454 a.a.        Molecular weight: 49140.50 Da        Isoelectric Point: 7.4216

>NTDB_id=753105 OKX02_RS12515 WP_003580798.1 2567255..2568619(-) (radA) [Lacticaseibacillus paracasei strain ATG-E1]
MAKAKTQYVCQNCGYISATYLGRCPNCGGWNTLVEETVSSSKSVPRQTAAGSKIKPTRMNDVTITKETRVKTGLDELNRV
LGGGVVPGSLVLIGGDPGIGKSTLLLQVSGQLANTGGTVLYVSGEESASQIKMRAGRLGVANSGMYLYPETDMPSIEDVI
NQMQPDYVVIDSVQTMNVPEMNSAVGSVAQIREVTAELMRIAKSKGVTIFIVGHVTKEGAIAGPKILEHMVDTVLYFEGD
MHHTYRILRSVKNRFGSTNEIGIFEMHQDGLQEVANPSEIFLEERLAGATGSAVVVSMEGTRPILVEIQALISPTMYGNA
KRTSSGLDHNRVSLIMAVLEKRANLMLQNQDAYLKATGGVKLDEPAIDLAMAVAIASSYRDKEISPTDCFVGEIGLTGEV
RRVNRIEERVKEAAKLGFKRIFVPRNNLQGWHAPKDIQVIGVTSIAEALHKVFN

Nucleotide


Download         Length: 1365 bp        

>NTDB_id=753105 OKX02_RS12515 WP_003580798.1 2567255..2568619(-) (radA) [Lacticaseibacillus paracasei strain ATG-E1]
ATGGCGAAAGCAAAAACACAATATGTTTGCCAAAACTGTGGCTATATTTCAGCCACTTATCTAGGCCGGTGTCCAAATTG
CGGCGGCTGGAACACCTTAGTGGAAGAAACCGTCAGTTCAAGCAAGTCTGTGCCGCGACAAACCGCAGCCGGAAGCAAGA
TAAAGCCGACGCGGATGAACGATGTGACGATCACCAAAGAAACGCGCGTCAAGACTGGCTTAGATGAACTGAACCGGGTG
CTTGGCGGCGGAGTGGTGCCAGGGTCACTGGTGCTGATCGGCGGGGATCCGGGGATTGGTAAATCAACCTTGCTATTACA
AGTATCAGGGCAGTTGGCTAATACCGGCGGAACGGTTTTGTATGTCTCTGGCGAAGAAAGTGCCAGTCAGATCAAAATGC
GGGCTGGCCGGCTTGGCGTGGCAAATTCGGGGATGTACTTGTATCCCGAAACCGACATGCCGAGTATTGAAGACGTCATC
AACCAAATGCAGCCGGATTATGTTGTGATCGACTCCGTTCAAACTATGAATGTGCCAGAAATGAATTCAGCGGTCGGTTC
TGTGGCACAGATTCGCGAAGTGACGGCAGAACTGATGCGCATTGCCAAGTCCAAAGGCGTGACCATTTTCATCGTTGGCC
ATGTCACTAAGGAAGGGGCGATTGCCGGGCCGAAGATTCTTGAGCATATGGTCGACACGGTGCTCTATTTTGAAGGCGAC
ATGCACCACACGTATCGAATCTTAAGATCCGTCAAAAATCGATTTGGATCGACCAATGAAATCGGCATTTTTGAAATGCA
TCAAGACGGGTTACAGGAAGTCGCCAATCCCTCGGAAATCTTCTTGGAAGAACGCTTGGCGGGGGCAACCGGTTCTGCGG
TGGTTGTTTCGATGGAAGGCACCCGACCAATCTTAGTCGAGATTCAAGCCTTGATCAGTCCAACGATGTATGGCAATGCT
AAACGGACGAGCAGTGGGTTGGATCACAATCGAGTGAGCTTGATCATGGCCGTTCTTGAGAAGCGGGCTAACTTGATGTT
GCAAAATCAGGACGCCTATCTCAAGGCAACAGGCGGTGTGAAACTCGATGAGCCGGCGATTGACCTCGCCATGGCTGTGG
CAATTGCGTCATCTTATCGAGATAAGGAGATTTCACCGACAGATTGTTTTGTCGGTGAAATCGGATTGACGGGGGAAGTG
CGCCGCGTCAATCGGATCGAAGAACGTGTCAAAGAGGCGGCCAAACTGGGTTTCAAACGGATTTTTGTACCCCGTAACAA
CTTGCAAGGCTGGCATGCGCCAAAAGATATTCAAGTCATTGGTGTTACAAGCATTGCCGAAGCGCTGCATAAGGTCTTTA
ATTAA

Domains

Predicted by InterproScan.

AAA domain (AAA_25)

(69-219)

Subunit ChlI of Mg-chelatase (ChlI)

(363-427)

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 Streptococcus mitis NCTC 12261

68.212

99.78

0.681
  radA Streptococcus pneumoniae Rx1

68.212

99.78

0.681
  radA Streptococcus pneumoniae D39

68.212

99.78

0.681
  radA Streptococcus pneumoniae R6

68.212

99.78

0.681
  radA Streptococcus pneumoniae TIGR4

68.212

99.78

0.681
  radA Streptococcus mitis SK321

67.991

99.78

0.678
  radA Bacillus subtilis subsp. subtilis str. 168

64.537

100

0.645