Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   H6X83_RS06675 Genome accession   NZ_CP060696
Coordinates   1385482..1386855 (+) Length   457 a.a.
NCBI ID   WP_212508340.1    Uniprot ID   A0A7G9WKR1
Organism   Caproicibacterium amylolyticum strain LBM18003     
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)
Genomic island 1387105..1400542 1385482..1386855 flank 250


Gene organization within MGE regions


Location: 1385482..1400542
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  H6X83_RS06675 (H6X83_06665) radA 1385482..1386855 (+) 1374 WP_212508340.1 DNA repair protein RadA Machinery gene
  H6X83_RS06680 (H6X83_06670) - 1386815..1387006 (-) 192 WP_212508341.1 hypothetical protein -
  H6X83_RS06685 (H6X83_06675) - 1387105..1387890 (+) 786 WP_212508342.1 DUF6873 family GME fold protein -
  H6X83_RS06690 (H6X83_06680) - 1387931..1388917 (+) 987 WP_212508343.1 tyrosine recombinase XerC -
  H6X83_RS06695 (H6X83_06685) - 1388976..1389875 (-) 900 WP_212508344.1 YesL family protein -
  H6X83_RS06700 (H6X83_06690) - 1389954..1390847 (-) 894 WP_212508345.1 site-specific tyrosine recombinase -
  H6X83_RS06705 (H6X83_06695) - 1390866..1391507 (-) 642 WP_212508346.1 stage II sporulation protein M -
  H6X83_RS06710 (H6X83_06700) scfB 1391879..1393240 (-) 1362 WP_212508347.1 thioether cross-link-forming SCIFF peptide maturase -
  H6X83_RS06715 (H6X83_06705) scfA 1393349..1393495 (-) 147 WP_086035715.1 six-cysteine ranthipeptide SCIFF -
  H6X83_RS06720 (H6X83_06710) - 1393564..1393974 (-) 411 WP_212508348.1 TIGR04086 family membrane protein -
  H6X83_RS06725 (H6X83_06715) yajC 1394067..1394516 (-) 450 WP_212508349.1 preprotein translocase subunit YajC -
  H6X83_RS06730 (H6X83_06720) tgt 1394684..1395814 (-) 1131 WP_212508350.1 tRNA guanosine(34) transglycosylase Tgt -
  H6X83_RS06735 (H6X83_06725) queA 1395857..1396903 (-) 1047 WP_212508351.1 tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA -
  H6X83_RS06740 (H6X83_06730) asd 1397307..1398386 (+) 1080 WP_212508352.1 aspartate-semialdehyde dehydrogenase -
  H6X83_RS06745 (H6X83_06735) dapA 1398412..1399302 (+) 891 WP_212508353.1 4-hydroxy-tetrahydrodipicolinate synthase -
  H6X83_RS06750 (H6X83_06740) dapB 1399333..1400082 (+) 750 WP_212508354.1 4-hydroxy-tetrahydrodipicolinate reductase -
  H6X83_RS06755 (H6X83_06745) - 1400096..1400542 (+) 447 WP_212508355.1 hypothetical protein -

Sequence

Protein


Download         Length: 457 a.a.        Molecular weight: 49714.99 Da        Isoelectric Point: 5.9830

>NTDB_id=477746 H6X83_RS06675 WP_212508340.1 1385482..1386855(+) (radA) [Caproicibacterium amylolyticum strain LBM18003]
MAGKVKSVYVCSSCGYESAKWCGKCPDCGAWNTMTEELHEPVSAAKRNTSSLSAGMARVLPIREISMAEEPRYKTGVSEL
DRVLGGGIVKGSLILISGEPGIGKSTILLQICAYLGNTLKILYVSGEESSRQIKLRANRLQVDSENLYILTETDVQRVIE
HVREEKPDLLMVDSIQTMNYTELNSSPGSVAQVRECTNAIMHAAKELEIPAILVGHVNKDGAIAGPKVLEHIVDAVLYFE
GDRQMSYRILRAVKNRYGSTNEIGVFDMGENGLHQVENPSASMLTGRPEHVSGTCVTCVMEGSRPILAEIQALATTSGFG
NPRRMATGFDYNRMNLLLAVLEKRAGYYFSNLDAYLNVVGGLHLDEPACDLAVAVSLVSSLKDTALADDAVVFGEVGLTG
EIRSVLHVDQRITEAERLGFKKCVLPWHSLKQVSAAHEGIELIGVKNVRQAFEALQA

Nucleotide


Download         Length: 1374 bp        

>NTDB_id=477746 H6X83_RS06675 WP_212508340.1 1385482..1386855(+) (radA) [Caproicibacterium amylolyticum strain LBM18003]
ATGGCGGGAAAAGTGAAGAGTGTATATGTGTGTTCCTCCTGCGGCTATGAGTCCGCGAAATGGTGTGGCAAGTGTCCTGA
CTGCGGCGCATGGAATACCATGACAGAGGAACTGCATGAGCCTGTCAGCGCGGCAAAACGAAACACAAGCAGCCTTTCAG
CTGGTATGGCCAGAGTGCTGCCGATTCGTGAAATCAGCATGGCAGAGGAACCTCGATACAAAACAGGTGTTTCCGAGCTG
GACCGTGTCTTAGGCGGCGGGATTGTAAAAGGTTCACTTATATTAATCAGCGGTGAGCCGGGCATTGGGAAGTCTACGAT
TTTACTGCAGATTTGTGCCTATTTGGGAAACACACTAAAAATTTTATATGTATCCGGAGAAGAGTCCAGTCGGCAGATCA
AACTGCGCGCAAACCGTTTGCAGGTAGATTCAGAGAACCTGTATATTTTGACGGAAACAGACGTACAGCGTGTGATTGAA
CATGTGCGTGAAGAGAAACCAGATTTGTTGATGGTCGATTCCATTCAGACAATGAACTATACTGAATTGAATTCTTCTCC
GGGAAGTGTAGCACAAGTACGCGAGTGTACAAATGCAATTATGCACGCGGCTAAGGAGTTGGAAATTCCAGCAATTTTGG
TTGGCCACGTCAATAAAGATGGCGCCATTGCCGGCCCTAAGGTACTGGAGCATATTGTGGATGCGGTGCTTTACTTTGAA
GGTGACCGGCAAATGAGCTACCGTATTTTGCGTGCAGTAAAGAACCGCTATGGCTCTACCAATGAAATTGGCGTTTTTGA
TATGGGAGAAAACGGTCTACACCAGGTTGAAAATCCGTCTGCATCCATGCTGACTGGTCGGCCTGAACACGTTTCTGGTA
CCTGTGTCACTTGCGTGATGGAGGGCAGTCGCCCGATTCTTGCCGAAATACAAGCATTAGCAACAACGTCCGGTTTCGGC
AACCCGCGCCGCATGGCAACGGGTTTCGATTATAATCGTATGAATCTGCTTTTGGCAGTACTGGAAAAAAGAGCAGGCTA
TTATTTCTCTAATTTGGACGCGTATTTAAATGTAGTTGGCGGTCTGCATTTAGATGAACCAGCCTGCGATCTTGCAGTGG
CAGTATCCCTGGTTTCCAGCTTGAAAGATACAGCGTTGGCAGATGATGCTGTTGTATTTGGCGAAGTTGGATTAACTGGA
GAAATTCGTTCCGTACTGCATGTAGACCAGCGCATAACAGAGGCAGAACGTCTTGGATTTAAAAAATGTGTGTTGCCCTG
GCACAGCTTAAAGCAGGTCAGTGCAGCACATGAAGGAATTGAGCTAATTGGTGTTAAAAATGTACGGCAGGCATTTGAGG
CTCTGCAGGCATAG

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(365-426)

AAA domain (AAA_25)

(78-222)

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(9-36)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A7G9WKR1

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

53.88

98.687

0.532
  radA Streptococcus mitis NCTC 12261

49.451

99.562

0.492
  radA Streptococcus mitis SK321

49.451

99.562

0.492
  radA Streptococcus pneumoniae Rx1

49.451

99.562

0.492
  radA Streptococcus pneumoniae D39

49.451

99.562

0.492
  radA Streptococcus pneumoniae R6

49.451

99.562

0.492
  radA Streptococcus pneumoniae TIGR4

49.451

99.562

0.492