Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   NQD60_RS04150 Genome accession   NZ_CP102085
Coordinates   1020028..1021410 (+) Length   460 a.a.
NCBI ID   WP_257101179.1    Uniprot ID   -
Organism   Mycoavidus sp. SF9855     
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 1010377..1022125 1020028..1021410 within 0


Gene organization within MGE regions


Location: 1010377..1022125
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  NQD60_RS04090 (NQD60_04090) - 1010377..1011078 (+) 702 WP_257101170.1 peptidoglycan DD-metalloendopeptidase family protein -
  NQD60_RS04100 (NQD60_04100) tsaB 1011223..1012005 (+) 783 WP_257101171.1 tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB -
  NQD60_RS04105 (NQD60_04105) rimI 1012022..1012504 (+) 483 WP_257101265.1 ribosomal protein S18-alanine N-acetyltransferase -
  NQD60_RS04110 (NQD60_04110) - 1012491..1013243 (+) 753 WP_257101172.1 uracil-DNA glycosylase family protein -
  NQD60_RS04115 (NQD60_04115) - 1013388..1013588 (-) 201 WP_257101173.1 hypothetical protein -
  NQD60_RS04120 (NQD60_04120) - 1013645..1013893 (-) 249 WP_257101174.1 hypothetical protein -
  NQD60_RS04125 (NQD60_04125) - 1014025..1015416 (+) 1392 WP_257100571.1 ISNCY family transposase -
  NQD60_RS04130 (NQD60_04130) - 1015590..1016330 (-) 741 WP_257101175.1 Rpn family recombination-promoting nuclease/putative transposase -
  NQD60_RS09165 - 1016559..1016777 (+) 219 WP_368736115.1 hypothetical protein -
  NQD60_RS04135 (NQD60_04135) thiD 1016674..1017480 (-) 807 WP_257101176.1 bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase -
  NQD60_RS04140 (NQD60_04140) lplT 1017515..1018819 (-) 1305 WP_257101177.1 lysophospholipid transporter LplT -
  NQD60_RS04145 (NQD60_04145) alr 1018956..1020026 (+) 1071 WP_257101178.1 alanine racemase -
  NQD60_RS04150 (NQD60_04150) radA 1020028..1021410 (+) 1383 WP_257101179.1 DNA repair protein RadA Machinery gene
  NQD60_RS04155 (NQD60_04155) - 1021521..1021781 (-) 261 WP_257101180.1 hypothetical protein -
  NQD60_RS04160 (NQD60_04160) - 1021778..1022125 (-) 348 WP_257101181.1 holin -

Sequence

Protein


Download         Length: 460 a.a.        Molecular weight: 48925.64 Da        Isoelectric Point: 8.1113

>NTDB_id=714183 NQD60_RS04150 WP_257101179.1 1020028..1021410(+) (radA) [Mycoavidus sp. SF9855]
MAKKTLYACGVCGAQSPKWQGQCLACNAWNSLIETVAEAPATHRYQALAKTAPVQKLAAIEAADVPRFSSGIQEFDRVLG
GGLVAGGVVLIGGDPGIGKSTLLLQSLAVLARERRALYVSGEESSAQIALRAQRLGLMESTAPASELHLLAEIQLEKIQA
AITAERPAVAVIDSIQTVYSEALSSAPGSVAQVRECAAQLTRLAKQMGVTIIMVGHVTKEGSLAGPRVLEHIVDTVLYFE
GDTHSAYRLVRAFKNRFGAVNELGVFAMTERGLRGVANPSALFLSQHEHRVPGSCVLVTQEGSRPLLVEIQALVDTAHIP
NPRRLAVGLEQNRLAMLLAVLNRHAGIACFDQDVFLNAVGGVKISEPAADLAVLLAIQSSLRNKPLPNGLVVFGEIGLAG
EIRPCPRGQERLKEAAKLGFSMALIPAANAPKQPIEGLEIIAVDRIEKAIEQIRARNNNS

Nucleotide


Download         Length: 1383 bp        

>NTDB_id=714183 NQD60_RS04150 WP_257101179.1 1020028..1021410(+) (radA) [Mycoavidus sp. SF9855]
ATGGCAAAAAAAACGCTTTATGCCTGTGGTGTTTGTGGCGCGCAGTCGCCCAAATGGCAAGGGCAGTGTCTTGCCTGCAA
TGCATGGAATTCACTGATTGAGACCGTAGCTGAAGCACCCGCCACCCACCGCTATCAAGCGCTAGCCAAGACCGCTCCGG
TGCAAAAACTGGCGGCCATCGAGGCCGCCGATGTGCCACGCTTTTCAAGTGGCATTCAAGAGTTTGACCGGGTGCTTGGT
GGTGGTTTAGTGGCAGGTGGGGTGGTCCTAATTGGCGGAGACCCGGGCATTGGTAAATCAACCCTGTTATTGCAATCGCT
TGCCGTCTTGGCCCGTGAGCGTCGCGCGCTTTATGTGAGCGGCGAAGAGTCGTCTGCACAAATCGCTTTGCGCGCGCAGC
GCTTGGGTTTAATGGAAAGCACGGCGCCCGCAAGCGAGCTGCATTTGCTAGCCGAGATTCAGCTCGAGAAAATACAAGCA
GCAATTACTGCTGAACGGCCGGCAGTGGCGGTGATTGATTCGATCCAAACCGTCTATTCAGAGGCGCTGAGCTCAGCGCC
TGGCTCAGTTGCCCAAGTCCGCGAATGTGCCGCGCAACTCACGCGCTTAGCCAAGCAAATGGGCGTGACTATCATTATGG
TCGGCCATGTGACCAAAGAAGGCAGTCTGGCCGGGCCGCGGGTGCTGGAACATATTGTTGACACAGTGCTGTATTTTGAG
GGGGATACTCATTCCGCCTACCGGCTGGTGCGGGCCTTTAAAAATCGCTTTGGCGCAGTCAATGAGCTCGGGGTGTTTGC
GATGACCGAGCGCGGTTTGCGCGGGGTAGCGAACCCCTCTGCGCTTTTTCTATCACAACATGAACACAGAGTGCCCGGCT
CTTGTGTGTTAGTCACGCAAGAAGGCTCGCGGCCATTGTTGGTTGAGATTCAGGCCTTAGTCGACACCGCTCATATACCC
AATCCCCGTCGACTCGCAGTAGGGCTTGAGCAAAATCGGCTGGCGATGTTATTGGCGGTATTAAACCGGCATGCAGGCAT
TGCGTGTTTTGATCAAGACGTGTTTTTAAATGCCGTAGGGGGCGTCAAAATCTCTGAGCCAGCCGCGGATCTTGCAGTGT
TGCTGGCAATTCAATCCTCCCTGCGCAACAAACCGTTGCCTAACGGCTTAGTGGTATTTGGCGAAATTGGGCTGGCTGGC
GAAATCCGCCCTTGCCCACGCGGACAAGAGCGCTTGAAGGAAGCGGCCAAGCTTGGTTTTTCAATGGCTTTGATTCCAGC
CGCAAACGCCCCTAAGCAGCCGATTGAAGGGCTTGAAATAATTGCTGTTGACCGGATTGAAAAAGCGATTGAACAGATAC
GGGCACGCAATAATAATTCATGA

Domains

Predicted by InterproScan.

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(7-34)

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

(362-452)

AAA domain (AAA_25)

(63-221)


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

49.567

100

0.498
  radA Streptococcus mitis SK321

46.608

99.348

0.463
  radA Streptococcus pneumoniae Rx1

46.304

100

0.463
  radA Streptococcus pneumoniae D39

46.304

100

0.463
  radA Streptococcus pneumoniae R6

46.304

100

0.463
  radA Streptococcus pneumoniae TIGR4

46.304

100

0.463
  radA Streptococcus mitis NCTC 12261

46.272

99.13

0.459