Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   DXE35_RS02460 Genome accession   NZ_LT606949
Coordinates   428164..429528 (+) Length   454 a.a.
NCBI ID   WP_114689462.1    Uniprot ID   -
Organism   Polynucleobacter necessarius isolate PPGSP7     
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 416343..429528 428164..429528 within 0


Gene organization within MGE regions


Location: 416343..429528
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DXE35_RS02400 recJ 417466..419241 (-) 1776 WP_114689454.1 single-stranded-DNA-specific exonuclease RecJ -
  DXE35_RS02405 - 419249..420208 (-) 960 WP_231969929.1 hypothetical protein -
  DXE35_RS02410 - 420276..421538 (+) 1263 WP_114689456.1 lipoprotein-releasing ABC transporter permease subunit -
  DXE35_RS02415 - 421531..422238 (+) 708 WP_114689457.1 ABC transporter ATP-binding protein -
  DXE35_RS02420 - 422250..423086 (+) 837 WP_114690354.1 TatD family hydrolase -
  DXE35_RS02425 - 423206..423727 (+) 522 WP_269459848.1 ComEC/Rec2 family competence protein -
  DXE35_RS10080 comA 423758..423868 (+) 111 WP_331851951.1 MBL fold metallo-hydrolase Machinery gene
  DXE35_RS02430 - 423865..424251 (+) 387 WP_114689458.1 recombinase family protein -
  DXE35_RS02435 - 424309..424923 (+) 615 WP_114689459.1 recombinase family protein -
  DXE35_RS02440 - 424933..425316 (+) 384 WP_162784943.1 hypothetical protein -
  DXE35_RS02450 - 425778..427618 (+) 1841 Protein_505 potassium transporter Kup -
  DXE35_RS02455 - 427678..428124 (+) 447 WP_231969932.1 hypothetical protein -
  DXE35_RS02460 radA 428164..429528 (+) 1365 WP_114689462.1 DNA repair protein RadA Machinery gene

Sequence

Protein


Download         Length: 454 a.a.        Molecular weight: 48326.11 Da        Isoelectric Point: 7.3471

>NTDB_id=1145198 DXE35_RS02460 WP_114689462.1 428164..429528(+) (radA) [Polynucleobacter necessarius isolate PPGSP7]
MAKVKTVYICQSCGGTSAKWQGQCPSCQAWNTLEEGLPETTSNSRFQGLVQSLPRQKLSAITAEDLPRFSTGVEEFDRVL
GGGLVPGGVVLLGGDPGIGKSTLFLQALAEMSAAGMNVLYSSGEESAAQIALRAKRIGLDAPQLEVLAEIQLEKLISIMD
TVRPQVLVVDSIQTLYSEVLSSAPGSVAQVRECAAQLTRAAKSSGICVLMVGHVTKDGHLAGPRVLEHIVDTVLYFEGDT
HSSFRLVRSIKNRFGAVNELGVFAMTEKGLRGVTNPSAIFLSQHEQMVPGACVLVTQEGSRPLLVEIQALVDTAHVPNPR
RLAVGLEQARLAMLLAVLHRHAGVACFDQDVFLNAVGGVKIAEPAADLAVLLAIQSSIRNRALPKELIVFGEVGLAGEIR
PCPRGQERLKEAAKLGFTVTIIPKTNMPKTKIPGLKVIPVERIDQAIAAAAELS

Nucleotide


Download         Length: 1365 bp        

>NTDB_id=1145198 DXE35_RS02460 WP_114689462.1 428164..429528(+) (radA) [Polynucleobacter necessarius isolate PPGSP7]
TTGGCTAAAGTCAAAACGGTTTATATCTGTCAATCTTGTGGCGGCACCTCAGCCAAGTGGCAAGGTCAGTGCCCGTCTTG
CCAGGCTTGGAATACCCTAGAAGAAGGCCTTCCTGAAACGACGTCGAATTCTCGTTTTCAGGGTTTGGTGCAATCATTGC
CAAGACAAAAGCTTTCCGCGATTACTGCTGAAGATTTGCCAAGATTTAGTACGGGCGTTGAAGAGTTCGATCGCGTACTG
GGTGGCGGCTTAGTTCCAGGCGGCGTAGTGCTCTTAGGCGGTGATCCTGGTATTGGTAAGTCGACCTTGTTTCTTCAGGC
CTTAGCGGAGATGAGTGCTGCGGGGATGAATGTACTCTACAGCAGTGGCGAAGAATCGGCGGCTCAGATTGCCTTGCGCG
CAAAGCGGATTGGATTGGATGCGCCGCAGTTAGAAGTGTTGGCGGAAATTCAGCTGGAAAAACTGATTTCAATTATGGAT
ACAGTGAGGCCACAGGTATTGGTGGTGGATTCGATTCAGACTTTGTATTCGGAAGTGCTAAGTTCAGCCCCAGGTTCTGT
AGCTCAAGTGCGCGAATGTGCGGCGCAATTAACAAGAGCAGCCAAATCCAGTGGGATTTGCGTGTTAATGGTGGGTCACG
TAACCAAGGACGGCCATCTTGCGGGCCCTCGAGTGCTCGAGCATATTGTTGACACCGTTTTATATTTTGAGGGTGATACC
CACTCCTCTTTCCGCTTAGTGCGCTCCATCAAGAATCGCTTTGGCGCGGTTAATGAGTTGGGCGTCTTTGCAATGACTGA
GAAAGGTCTACGCGGCGTCACCAATCCTTCGGCGATCTTTTTGTCACAGCACGAGCAAATGGTTCCTGGCGCCTGTGTAT
TGGTGACTCAAGAGGGCAGCAGACCTTTGTTGGTTGAGATTCAGGCTCTGGTGGATACGGCGCACGTGCCCAATCCTCGT
CGCTTAGCTGTTGGTTTGGAGCAGGCGCGTTTAGCAATGCTCTTGGCTGTATTGCATCGTCATGCTGGTGTCGCTTGTTT
TGATCAAGACGTGTTCTTAAATGCTGTTGGCGGCGTCAAAATTGCCGAGCCAGCGGCTGACTTGGCGGTACTGCTCGCGA
TTCAGTCATCTATTCGCAATCGAGCTTTGCCTAAAGAATTGATTGTGTTTGGCGAGGTTGGTTTAGCAGGAGAAATTCGC
CCTTGTCCACGCGGTCAGGAGCGTTTGAAGGAGGCTGCTAAGCTAGGCTTTACTGTGACAATCATTCCAAAAACCAATAT
GCCTAAGACAAAGATTCCTGGATTGAAAGTCATTCCAGTTGAACGAATTGATCAGGCAATCGCTGCAGCAGCTGAGTTAA
GTTAA

Domains

Predicted by InterproScan.

AAA domain (AAA_25)

(78-218)

Lon protease (S16) C-terminal proteolytic domain (Lon_C)

(359-450)

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

49.336

99.559

0.491
  radA Streptococcus pneumoniae Rx1

45.778

99.119

0.454
  radA Streptococcus pneumoniae D39

45.778

99.119

0.454
  radA Streptococcus pneumoniae R6

45.778

99.119

0.454
  radA Streptococcus pneumoniae TIGR4

45.778

99.119

0.454
  radA Streptococcus mitis NCTC 12261

45.778

99.119

0.454
  radA Streptococcus mitis SK321

45.778

99.119

0.454

Multiple sequence alignment