Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   PDMSB3_RS12025 Genome accession   NZ_LR699553
Coordinates   2700179..2701555 (-) Length   458 a.a.
NCBI ID   WP_007181410.1    Uniprot ID   A0A5Q4ZE98
Organism   Paraburkholderia dioscoreae strain Msb3     
Function   homologous recombination (predicted from homology)   
Homologous recombination

Genomic Context

Location: 2695179..2706555
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PDMSB3_RS12005 (PDMSB3_2612) - 2695860..2696339 (-) 480 WP_007181414.1 glutathione peroxidase -
  PDMSB3_RS12010 (PDMSB3_2613) - 2696475..2698448 (+) 1974 WP_007181413.1 ATP-binding cassette domain-containing protein -
  PDMSB3_RS12015 (PDMSB3_2614) - 2698558..2699616 (+) 1059 WP_165187468.1 CaiB/BaiF CoA-transferase family protein -
  PDMSB3_RS12020 (PDMSB3_2615) - 2699757..2700035 (-) 279 WP_007181411.1 DUF2866 domain-containing protein -
  PDMSB3_RS12025 (PDMSB3_2616) radA 2700179..2701555 (-) 1377 WP_007181410.1 DNA repair protein RadA Machinery gene
  PDMSB3_RS12030 (PDMSB3_2617) alr 2701663..2702733 (-) 1071 WP_007181409.1 alanine racemase -
  PDMSB3_RS12035 (PDMSB3_2619) lplT 2702952..2704259 (+) 1308 WP_007181408.1 lysophospholipid transporter LplT -
  PDMSB3_RS12040 (PDMSB3_2620) thiD 2704318..2705124 (+) 807 WP_007181407.1 bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase -
  PDMSB3_RS12045 (PDMSB3_2621) - 2705184..2706254 (-) 1071 WP_165186274.1 DUF1853 family protein -

Sequence

Protein


Download         Length: 458 a.a.        Molecular weight: 48656.06 Da        Isoelectric Point: 7.3834

>NTDB_id=1129342 PDMSB3_RS12025 WP_007181410.1 2700179..2701555(-) (radA) [Paraburkholderia dioscoreae strain Msb3]
MAKPKTVYICSECGGQSPKWAGQCPSCNAWNTLVESVAEAPSTHRFQSLAKSAPVRRLADIEASDIPRFTTGVSEFDRVL
GGGLVPGGVVLIGGDPGIGKSTLLLQSLAEIAADKRALYISGEESAAQIALRAQRLSLLEPGSKASELQLLAEIQLEKIQ
ATIAEQRPDVAVIDSIQTVYSDALTSAPGSVAQVRECAAQLTRIAKQSGTTIIMVGHVTKEGALAGPRVLEHIVDTVLYF
EGDTHSSYRLVRAIKNRFGAVNELGVFAMTERGLRGVANPSALFLSQHEQSVPGSCVLVTQEGTRPLLVEVQALVDAANA
PNPRRLAVGLEQNRLAMLLAVLHRHAGIACFDQDVFLNAVGGVKITEPAADLAVLLAIHSSMRNKPLPKGLVVFGEVGLA
GEIRPSPRGQERLKEAAKLGFSVAVIPKANAPKQPIEGLQVVAVERIEQAIDRVRTLE

Nucleotide


Download         Length: 1377 bp        

>NTDB_id=1129342 PDMSB3_RS12025 WP_007181410.1 2700179..2701555(-) (radA) [Paraburkholderia dioscoreae strain Msb3]
GTGGCTAAACCCAAGACGGTGTACATCTGTAGTGAATGCGGCGGGCAATCGCCGAAATGGGCCGGCCAGTGCCCCTCGTG
CAATGCGTGGAACACGCTGGTCGAGTCGGTGGCGGAAGCGCCTTCCACGCATCGTTTCCAGTCGCTCGCGAAGAGCGCGC
CGGTGCGCCGTCTCGCCGATATCGAAGCGTCCGACATACCGCGCTTCACCACCGGCGTGAGCGAGTTCGACCGCGTGCTG
GGCGGCGGTCTGGTGCCGGGCGGCGTGGTGCTGATCGGCGGCGATCCGGGCATCGGCAAATCGACGCTGTTGCTGCAATC
GCTCGCGGAAATCGCCGCCGACAAACGCGCGCTCTATATCAGCGGCGAAGAATCCGCTGCGCAGATTGCGTTGCGCGCGC
AACGACTTTCGTTGCTGGAGCCGGGCTCGAAGGCGAGCGAGCTGCAACTGCTGGCGGAAATCCAGCTGGAAAAAATCCAG
GCGACGATCGCCGAACAGCGACCCGATGTCGCGGTGATCGACTCGATCCAGACGGTCTATTCCGACGCGCTGACTTCCGC
GCCGGGCTCGGTCGCCCAGGTGCGCGAGTGCGCCGCGCAGCTTACACGGATCGCCAAGCAGTCGGGCACCACCATCATCA
TGGTCGGCCACGTGACTAAGGAAGGCGCGCTGGCGGGGCCGCGCGTGCTCGAACACATCGTCGACACGGTGTTGTACTTC
GAGGGCGACACGCATTCGTCGTACCGTCTGGTGCGCGCGATCAAGAACCGCTTCGGCGCGGTCAACGAACTCGGCGTGTT
CGCCATGACCGAGCGCGGCTTGCGCGGCGTGGCCAATCCGTCGGCGCTGTTTCTGTCGCAGCACGAGCAGTCGGTGCCGG
GTTCCTGCGTGCTGGTGACGCAGGAGGGCACGCGGCCGCTGCTGGTCGAAGTGCAGGCGCTCGTGGACGCCGCCAACGCG
CCGAATCCGCGGCGCCTCGCGGTCGGTCTGGAACAGAACCGGCTCGCGATGCTGCTGGCGGTGCTGCATCGTCACGCCGG
CATCGCCTGTTTCGATCAGGACGTGTTCCTGAACGCCGTGGGTGGGGTGAAGATTACCGAGCCCGCTGCCGACTTGGCCG
TGCTGCTCGCGATCCATTCGTCCATGCGCAACAAGCCGCTGCCCAAGGGCCTGGTGGTGTTCGGAGAAGTGGGCCTCGCC
GGCGAAATCCGGCCGTCGCCGCGCGGTCAGGAACGTTTGAAGGAAGCCGCCAAACTGGGCTTTTCCGTCGCGGTGATTCC
CAAGGCCAATGCGCCAAAGCAGCCGATAGAAGGCTTACAGGTCGTTGCGGTCGAGCGGATCGAACAGGCCATCGACCGGG
TCCGCACGCTCGAATAG

Domains

Predicted by InterproScan.

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

AAA domain (AAA_25)

(79-222)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A5Q4ZE98

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

49.892

100

0.502
  radA Streptococcus pneumoniae Rx1

47.289

100

0.476
  radA Streptococcus pneumoniae D39

47.289

100

0.476
  radA Streptococcus pneumoniae R6

47.289

100

0.476
  radA Streptococcus pneumoniae TIGR4

47.289

100

0.476
  radA Streptococcus mitis SK321

47.598

100

0.476
  radA Streptococcus mitis NCTC 12261

47.265

99.782

0.472

Multiple sequence alignment