Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   DV129_RS07660 Genome accession   NZ_CP031247
Coordinates   1424401..1425762 (-) Length   453 a.a.
NCBI ID   WP_078065389.1    Uniprot ID   -
Organism   Streptococcus pneumoniae strain M23734     
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 1413576..1474830 1424401..1425762 within 0


Gene organization within MGE regions


Location: 1413576..1474830
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DV129_RS07590 recO 1413576..1414346 (-) 771 WP_000616164.1 DNA repair protein RecO -
  DV129_RS07595 - 1414343..1415512 (-) 1170 WP_000366352.1 pyridoxal phosphate-dependent aminotransferase -
  DV129_RS07600 - 1415661..1416671 (+) 1011 WP_000009173.1 YeiH family protein -
  DV129_RS12320 - 1416700..1416993 (-) 294 WP_012677093.1 hypothetical protein -
  DV129_RS07610 - 1417034..1417471 (-) 438 WP_000076480.1 CoA-binding protein -
  DV129_RS07615 polA 1417556..1420189 (-) 2634 WP_001844860.1 DNA polymerase I -
  DV129_RS12325 - 1420445..1421352 (+) 908 Protein_1441 Rpn family recombination-promoting nuclease/putative transposase -
  DV129_RS07635 - 1421479..1421760 (+) 282 Protein_1442 transposase family protein -
  DV129_RS07640 - 1421894..1422862 (-) 969 WP_000010163.1 ribose-phosphate diphosphokinase -
  DV129_RS07645 - 1423007..1423806 (-) 800 Protein_1444 PrsW family intramembrane metalloprotease -
  DV129_RS07655 - 1423831..1424328 (-) 498 WP_001809263.1 carbonic anhydrase -
  DV129_RS07660 radA 1424401..1425762 (-) 1362 WP_078065389.1 DNA repair protein RadA Machinery gene
  DV129_RS07665 - 1425776..1426291 (-) 516 WP_000691236.1 histidine phosphatase family protein -
  DV129_RS07670 - 1426293..1426736 (-) 444 WP_000701992.1 dUTP diphosphatase -
  DV129_RS07680 tadA 1426923..1427390 (-) 468 WP_000291875.1 tRNA adenosine(34) deaminase TadA -
  DV129_RS11755 - 1427672..1427821 (+) 150 WP_001030863.1 hypothetical protein -
  DV129_RS07685 - 1427963..1428142 (+) 180 WP_001209433.1 hypothetical protein -
  DV129_RS07690 - 1428412..1429368 (-) 957 WP_000350458.1 N-acetylmuramoyl-L-alanine amidase family protein -
  DV129_RS07695 - 1429368..1429703 (-) 336 WP_001186237.1 phage holin -
  DV129_RS07700 - 1429707..1430123 (-) 417 WP_001165344.1 phage holin family protein -
  DV129_RS07705 - 1430133..1430485 (-) 353 Protein_1455 hypothetical protein -
  DV129_RS07710 - 1430488..1430691 (-) 204 WP_001091109.1 hypothetical protein -
  DV129_RS12330 - 1430672..1430788 (-) 117 WP_001063632.1 hypothetical protein -
  DV129_RS12335 - 1430785..1431396 (-) 612 WP_001846937.1 tail fiber domain-containing protein -
  DV129_RS12340 - 1431356..1434004 (-) 2649 WP_012677074.1 hypothetical protein -
  DV129_RS07730 - 1434050..1437271 (-) 3222 WP_001846667.1 phage tail spike protein -
  DV129_RS07735 - 1437272..1437994 (-) 723 WP_000589852.1 hypothetical protein -
  DV129_RS07740 - 1437991..1440750 (-) 2760 WP_000918322.1 hypothetical protein -
  DV129_RS07745 - 1441028..1441447 (-) 420 WP_001227145.1 hypothetical protein -
  DV129_RS07750 - 1441459..1442037 (-) 579 WP_000191278.1 major tail protein -
  DV129_RS07755 - 1442049..1442372 (-) 324 WP_000777003.1 hypothetical protein -
  DV129_RS07760 - 1442369..1442716 (-) 348 WP_000063886.1 HK97 gp10 family phage protein -
  DV129_RS07765 - 1442713..1443012 (-) 300 WP_000267061.1 phage head closure protein -
  DV129_RS07770 - 1442999..1443280 (-) 282 WP_000371962.1 phage head-tail connector protein -
  DV129_RS07775 - 1443283..1443573 (-) 291 WP_000120767.1 hypothetical protein -
  DV129_RS07780 - 1443585..1444757 (-) 1173 WP_001037663.1 phage major capsid protein -
  DV129_RS07785 - 1444754..1445329 (-) 576 WP_001172113.1 HK97 family phage prohead protease -
  DV129_RS07790 - 1445313..1446515 (-) 1203 WP_114865984.1 phage portal protein -
  DV129_RS07795 - 1446533..1446751 (-) 219 WP_001002923.1 hypothetical protein -
  DV129_RS07800 - 1446759..1448489 (-) 1731 WP_000527303.1 terminase large subunit -
  DV129_RS07805 - 1448482..1448874 (-) 393 WP_001118282.1 P27 family phage terminase small subunit -
  DV129_RS07810 - 1449012..1449332 (-) 321 WP_000282422.1 HNH endonuclease -
  DV129_RS07815 - 1449452..1449643 (-) 192 WP_000238198.1 hypothetical protein -
  DV129_RS07820 - 1449807..1450349 (-) 543 WP_000397552.1 site-specific integrase -
  DV129_RS07825 - 1450538..1450939 (-) 402 WP_000736391.1 transcriptional activator -
  DV129_RS11760 - 1451151..1451309 (-) 159 WP_153231720.1 hypothetical protein -
  DV129_RS07830 - 1451306..1451542 (-) 237 WP_001067627.1 DUF3310 domain-containing protein -
  DV129_RS07835 - 1451542..1451931 (-) 390 WP_000612387.1 YopX family protein -
  DV129_RS07840 - 1451928..1452442 (-) 515 Protein_1483 class I SAM-dependent methyltransferase -
  DV129_RS07845 - 1452442..1452867 (-) 426 WP_000772905.1 DUF1642 domain-containing protein -
  DV129_RS07850 - 1452857..1453186 (-) 330 WP_000969678.1 hypothetical protein -
  DV129_RS11970 - 1453354..1453521 (-) 168 WP_000233203.1 hypothetical protein -
  DV129_RS07865 - 1453648..1453875 (-) 228 WP_000891963.1 hypothetical protein -
  DV129_RS07870 - 1453875..1454069 (-) 195 WP_000470303.1 hypothetical protein -
  DV129_RS07875 - 1454084..1454854 (-) 771 WP_000228214.1 ATP-binding protein -
  DV129_RS07880 - 1454994..1455821 (-) 828 WP_001289767.1 phage replisome organizer N-terminal domain-containing protein -
  DV129_RS07885 - 1455814..1456110 (-) 297 WP_001156934.1 hypothetical protein -
  DV129_RS07890 - 1456126..1456446 (-) 321 WP_000462827.1 hypothetical protein -
  DV129_RS07895 - 1456532..1456789 (-) 258 WP_000370958.1 hypothetical protein -
  DV129_RS07900 - 1456802..1457515 (-) 714 WP_001002346.1 ORF6C domain-containing protein -
  DV129_RS07905 - 1457569..1457994 (+) 426 WP_000456433.1 hypothetical protein -
  DV129_RS11975 - 1457989..1458150 (-) 162 WP_001004503.1 hypothetical protein -
  DV129_RS07910 - 1458161..1458358 (-) 198 WP_001057654.1 hypothetical protein -
  DV129_RS07915 - 1458375..1458578 (-) 204 WP_000032100.1 hypothetical protein -
  DV129_RS07920 - 1458571..1458945 (-) 375 WP_000573356.1 hypothetical protein -
  DV129_RS11980 - 1458989..1459135 (-) 147 WP_001001334.1 hypothetical protein -
  DV129_RS07925 - 1459420..1459788 (+) 369 WP_000495824.1 helix-turn-helix transcriptional regulator -
  DV129_RS07930 - 1459788..1460021 (+) 234 WP_000156422.1 hypothetical protein -
  DV129_RS07935 - 1460021..1460284 (+) 264 WP_000285962.1 type II toxin-antitoxin system RelE/ParE family toxin -
  DV129_RS07940 - 1460297..1460677 (+) 381 Protein_1504 ImmA/IrrE family metallo-endopeptidase -
  DV129_RS07945 - 1460715..1461527 (+) 813 WP_001174227.1 HIRAN domain-containing protein -
  DV129_RS07950 - 1461702..1462850 (+) 1149 WP_000876726.1 site-specific integrase -
  DV129_RS07955 - 1463082..1464368 (-) 1287 WP_000205044.1 adenylosuccinate synthase -
  DV129_RS07960 comW 1464599..1464835 (-) 237 WP_000939546.1 sigma(X)-activator ComW Regulator
  DV129_RS07965 - 1465100..1465897 (+) 798 Protein_1509 transposase -
  DV129_RS07970 - 1465932..1466778 (-) 847 Protein_1510 IS630 family transposase -
  DV129_RS08010 comX/comX2 1472271..1472750 (-) 480 WP_000588897.1 sigma-70 family RNA polymerase sigma factor Regulator
  DV129_RS08015 ftsH 1472872..1474830 (-) 1959 WP_000744537.1 ATP-dependent zinc metalloprotease FtsH -

Sequence

Protein


Download         Length: 453 a.a.        Molecular weight: 49466.97 Da        Isoelectric Point: 6.5137

>NTDB_id=304772 DV129_RS07660 WP_078065389.1 1424401..1425762(-) (radA) [Streptococcus pneumoniae strain M23734]
MAKKKATFVCQNCGYNSPKYLGRCPNCGSWSSFVEEVEVAEVKNARVSLTGEKTKPMKLAEVTSINVNRTKTEMEEFNRV
LGGGVVPGSLVLIGGDPGIGKSTLLLQVSTQLSQVGTVLYVSGEESAQQIKLRAERLGDIDSEFYLYAETNMQSVRAEVE
RIQPDFFIIDSIQTIMSPEISGVQGSVSQVREVTAELMQLAKTNNIAIFIVGHVTKEGTLAGPRMLEHMVDTVLYFEGER
HHTFRILRAVKNRFGSTNEIGIFEMQSGGLVEVLNPSQVFLEERLDGATGSSIVVTMEGTRPILAEVQALVTPTMFGNAK
RTTTGLDFNRASLIMAVLEKRAGLLLQNQDAYLKSAGGVKLDEPAIDLAVAVAIASSYKDKPTNPQECFVGELGLTGEIR
RVNRIEQRINEAAKLGFTKIYVPKNSLTGITLPKEIQVIGVTTIQEVLKKVFA

Nucleotide


Download         Length: 1362 bp        

>NTDB_id=304772 DV129_RS07660 WP_078065389.1 1424401..1425762(-) (radA) [Streptococcus pneumoniae strain M23734]
ATCGCAAAGAAAAAAGCGACATTTGTATGTCAAAATTGTGGGTATAATTCCCCTAAATATCTGGGACGTTGCCCCAACTG
TGGGTCTTGGTCTTCTTTTGTGGAAGAGGTTGAGGTTGCCGAGGTCAAGAATGCGCGTGTGTCCTTGACAGGTGAGAAAA
CCAAGCCCATGAAACTAGCTGAGGTGACTTCCATCAATGTCAATCGAACCAAGACGGAGATGGAGGAATTCAACCGTGTG
CTTGGAGGCGGAGTGGTACCAGGAAGTCTCGTCCTCATCGGTGGGGATCCTGGGATTGGGAAATCAACTCTTCTCCTACA
AGTCTCAACCCAGTTGTCCCAAGTGGGGACAGTTCTCTATGTCAGTGGGGAGGAGTCTGCCCAGCAGATTAAATTACGTG
CAGAGCGCTTAGGTGATATTGATAGTGAGTTTTATCTCTATGCAGAGACCAATATGCAGAGTGTTCGTGCAGAAGTGGAG
CGTATCCAGCCAGACTTCTTCATTATTGACTCTATCCAGACCATTATGTCTCCTGAGATTTCAGGGGTGCAGGGGTCTGT
TTCTCAGGTGCGTGAAGTGACCGCTGAACTCATGCAGTTGGCCAAGACCAATAACATTGCCATCTTTATCGTAGGTCATG
TGACCAAAGAAGGAACCTTGGCTGGGCCTCGTATGTTGGAGCATATGGTGGATACGGTGCTTTACTTTGAAGGGGAGCGT
CACCACACCTTTCGTATTTTGAGAGCGGTCAAAAATCGTTTTGGTTCCACTAATGAGATTGGGATTTTTGAGATGCAGTC
GGGCGGCTTGGTTGAGGTACTCAATCCGAGTCAAGTTTTCCTAGAAGAGCGTTTGGATGGGGCGACTGGTTCCTCCATCG
TTGTAACCATGGAAGGGACGCGTCCGATTTTGGCGGAGGTTCAGGCTTTAGTAACACCGACCATGTTTGGAAATGCCAAG
CGTACTACGACAGGACTTGATTTTAACCGTGCTAGCTTGATTATGGCTGTTTTGGAAAAACGGGCAGGGCTTCTCTTGCA
AAATCAGGATGCCTATCTCAAATCTGCTGGTGGTGTTAAATTGGATGAACCTGCCATTGACTTGGCTGTTGCAGTTGCTA
TTGCTTCGAGCTACAAAGACAAACCAACTAATCCTCAGGAATGTTTTGTCGGAGAACTGGGCTTGACAGGAGAGATTCGG
CGCGTGAATCGTATTGAGCAACGCATCAACGAAGCTGCTAAACTGGGCTTTACTAAGATTTATGTACCTAAGAATTCCTT
GACAGGAATCACTCTGCCTAAGGAAATTCAGGTCATTGGCGTGACAACGATTCAGGAAGTTTTGAAAAAGGTCTTTGCAT
AA

Domains

Predicted by InterproScan.

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

Subunit ChlI of Mg-chelatase (ChlI)

(360-425)

AAA domain (AAA_25)

(63-218)


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 Streptococcus pneumoniae Rx1

99.779

100

0.998
  radA Streptococcus pneumoniae D39

99.779

100

0.998
  radA Streptococcus pneumoniae R6

99.779

100

0.998
  radA Streptococcus pneumoniae TIGR4

99.779

100

0.998
  radA Streptococcus mitis SK321

99.338

100

0.993
  radA Streptococcus mitis NCTC 12261

99.338

100

0.993
  radA Bacillus subtilis subsp. subtilis str. 168

63.135

100

0.631

Multiple sequence alignment