Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   FD971_RS06740 Genome accession   NZ_CP061318
Coordinates   1300497..1301861 (-) Length   454 a.a.
NCBI ID   WP_215333498.1    Uniprot ID   -
Organism   Polynucleobacter sp. AP-Ainpum-60-G11     
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 1300497..1317794 1300497..1301861 within 0


Gene organization within MGE regions


Location: 1300497..1317794
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  FD971_RS06740 (FD971_06740) radA 1300497..1301861 (-) 1365 WP_215333498.1 DNA repair protein RadA Machinery gene
  FD971_RS06745 (FD971_06745) - 1301867..1302325 (-) 459 WP_251368599.1 hypothetical protein -
  FD971_RS06750 (FD971_06750) - 1302373..1304217 (-) 1845 WP_251368710.1 potassium transporter Kup -
  FD971_RS06760 (FD971_06760) - 1304776..1306539 (+) 1764 WP_215333501.1 tetratricopeptide repeat protein -
  FD971_RS06765 (FD971_06765) - 1306894..1307862 (+) 969 WP_215333502.1 tripartite tricarboxylate transporter substrate binding protein BugE -
  FD971_RS06770 (FD971_06770) - 1307938..1308330 (-) 393 WP_215333503.1 type II toxin-antitoxin system HicB family antitoxin -
  FD971_RS06775 (FD971_06775) - 1308327..1308521 (-) 195 WP_215333504.1 type II toxin-antitoxin system HicA family toxin -
  FD971_RS06780 (FD971_06780) - 1308567..1311056 (-) 2490 WP_251368600.1 DNA internalization-related competence protein ComEC/Rec2 -
  FD971_RS06785 (FD971_06785) - 1311061..1311921 (-) 861 WP_215333505.1 TatD family hydrolase -
  FD971_RS06790 (FD971_06790) - 1311918..1312625 (-) 708 WP_251368601.1 ABC transporter ATP-binding protein -
  FD971_RS06795 (FD971_06795) - 1312630..1313889 (-) 1260 WP_215335270.1 lipoprotein-releasing ABC transporter permease subunit -
  FD971_RS06800 (FD971_06800) - 1313939..1314919 (+) 981 WP_215333507.1 hypothetical protein -
  FD971_RS06805 (FD971_06805) recJ 1314916..1316661 (+) 1746 WP_215333508.1 single-stranded-DNA-specific exonuclease RecJ -
  FD971_RS06810 (FD971_06810) prfB 1316690..1317794 (+) 1105 WP_215333509.1 peptide chain release factor 2 -

Sequence

Protein


Download         Length: 454 a.a.        Molecular weight: 48130.97 Da        Isoelectric Point: 7.3470

>NTDB_id=481794 FD971_RS06740 WP_215333498.1 1300497..1301861(-) (radA) [Polynucleobacter sp. AP-Ainpum-60-G11]
MAKIKTIYICQSCGGTSAKWQGQCPSCQAWNTLEEGLPEVSSNTRFQGLAQSLPRQKLSAISAEDLPRFSTGVEEFDRVL
GGGLVPGGVVLLGGDPGIGKSTLLLQALAEMSAAGMNVLYSSGEESAAQIALRAKRIALDAPQLEVLAEIQLEKLLSIMD
TVKPQVLVVDSIQTLYSEVLSSAPGSVAQVRECAAQLTRAAKSSGICVLMVGHVTKDGHLAGPRVLEHIVDTVLYFEGDT
HSSFRLVRSIKNRFGAVNELGVFAMTEKGLRGVANPSAIFLSQHAEMVPGACVLVTQEGSRPLLVEIQALVDTAHIPNPR
RLAVGLEQARLAMLLAVLHRHAGVACFDQDVFLNAVGGVKISEPAADLAVLLAIQSSIRNKALPKELIVFGEVGLAGEIR
PCPRGQERLKEAAKLGFTVAIIPKANMPKAKIPGLRVIPVERIDQAISAAAELS

Nucleotide


Download         Length: 1365 bp        

>NTDB_id=481794 FD971_RS06740 WP_215333498.1 1300497..1301861(-) (radA) [Polynucleobacter sp. AP-Ainpum-60-G11]
TTGGCCAAGATTAAAACAATTTATATCTGCCAGTCATGCGGTGGAACTTCTGCTAAGTGGCAAGGACAGTGCCCTTCCTG
TCAGGCGTGGAACACGCTTGAGGAGGGCTTGCCTGAGGTGAGCTCAAACACACGCTTTCAGGGTTTAGCGCAATCACTAC
CGCGTCAAAAGCTTTCTGCTATTTCAGCCGAAGACCTTCCTCGCTTTAGTACTGGGGTTGAAGAGTTTGATCGCGTATTG
GGTGGCGGCTTAGTTCCTGGTGGGGTTGTGCTTTTGGGCGGCGATCCTGGTATTGGCAAATCCACTTTGTTATTGCAAGC
ACTAGCTGAGATGAGTGCTGCAGGTATGAACGTTCTTTACAGTAGTGGTGAGGAGTCTGCTGCGCAAATCGCATTACGTG
CAAAACGCATTGCACTCGATGCGCCTCAATTAGAAGTGCTTGCAGAAATTCAATTAGAAAAACTCTTATCCATCATGGAT
ACTGTGAAGCCACAGGTCTTGGTGGTGGATTCTATTCAGACCTTATATTCAGAGGTATTGAGTTCAGCGCCAGGGTCAGT
TGCCCAAGTACGAGAGTGTGCTGCGCAACTCACTAGGGCAGCTAAATCTAGCGGTATTTGTGTCTTGATGGTGGGTCACG
TTACTAAAGATGGTCACTTGGCTGGTCCCCGCGTACTCGAACACATTGTTGATACCGTTCTGTACTTTGAAGGTGATACC
CATTCTTCATTTAGATTGGTGCGCTCGATTAAAAACCGTTTTGGCGCAGTCAATGAGCTCGGCGTCTTTGCTATGACTGA
AAAAGGGTTGCGTGGTGTTGCTAATCCTTCAGCTATTTTCCTATCCCAGCATGCTGAGATGGTGCCAGGTGCCTGTGTGT
TAGTGACCCAAGAAGGTAGTCGCCCGCTCTTGGTAGAAATTCAGGCTCTGGTCGATACGGCCCACATCCCAAATCCACGC
CGCTTGGCGGTGGGTTTAGAACAGGCGCGTTTAGCGATGCTTTTGGCGGTTTTACATCGTCACGCAGGTGTAGCTTGCTT
TGATCAAGACGTCTTCTTAAATGCAGTAGGCGGTGTGAAGATCTCAGAGCCGGCTGCTGACTTAGCAGTGTTGTTGGCAA
TTCAGTCTTCAATTCGTAATAAAGCGCTACCTAAAGAGTTGATCGTATTTGGAGAGGTTGGTTTGGCCGGAGAAATTCGT
CCATGCCCACGAGGTCAGGAGCGCTTGAAAGAAGCGGCTAAGCTAGGCTTCACTGTAGCAATTATTCCAAAAGCCAATAT
GCCTAAGGCAAAGATTCCAGGTTTAAGGGTGATACCTGTAGAGCGCATTGATCAGGCTATTTCTGCTGCTGCAGAACTCA
GTTAA

Domains

Predicted by InterproScan.

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

(357-450)

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

AAA domain (AAA_25)

(78-218)


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

48.791

100

0.489
  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