Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   GU334_RS09565 Genome accession   NZ_CP047628
Coordinates   1976472..1977833 (-) Length   453 a.a.
NCBI ID   WP_167841545.1    Uniprot ID   A0AAE7CT37
Organism   Lactococcus raffinolactis strain Lr_19_14     
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 1975170..2007457 1976472..1977833 within 0


Gene organization within MGE regions


Location: 1975170..2007457
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GU334_RS09560 (GU334_09520) - 1975170..1976243 (-) 1074 WP_061774660.1 TRAM domain-containing protein -
  GU334_RS09565 (GU334_09525) radA 1976472..1977833 (-) 1362 WP_167841545.1 DNA repair protein RadA Machinery gene
  GU334_RS09570 (GU334_09530) - 1977835..1978281 (-) 447 WP_061774658.1 dUTP diphosphatase -
  GU334_RS09575 (GU334_09535) - 1978364..1980115 (-) 1752 WP_167839076.1 ABC transporter ATP-binding protein -
  GU334_RS09580 (GU334_09540) - 1980108..1981826 (-) 1719 WP_167841546.1 ABC transporter ATP-binding protein -
  GU334_RS09585 (GU334_09545) - 1982224..1983222 (+) 999 WP_001048115.1 IS5-like element IS1194 family transposase -
  GU334_RS09590 (GU334_09550) - 1983356..1983643 (+) 288 WP_071519144.1 helix-turn-helix domain-containing protein -
  GU334_RS11835 - 1983646..1984524 (+) 879 WP_209452113.1 IS3 family transposase -
  GU334_RS09600 (GU334_09560) - 1984755..1985387 (-) 633 WP_096815456.1 FusB/FusC family EF-G-binding protein -
  GU334_RS09605 (GU334_09565) - 1985623..1986303 (-) 681 WP_167841547.1 IS6-like element IS1216 family transposase -
  GU334_RS09610 (GU334_09570) - 1986387..1986764 (-) 378 WP_003129983.1 pyridoxamine 5'-phosphate oxidase family protein -
  GU334_RS09615 (GU334_09575) nrdF 1987037..1987987 (-) 951 WP_096040574.1 class 1b ribonucleoside-diphosphate reductase subunit beta -
  GU334_RS09620 (GU334_09580) tpx 1988071..1988562 (-) 492 Protein_1868 thiol peroxidase -
  GU334_RS09625 (GU334_09585) - 1988923..1989876 (-) 954 WP_096040575.1 ribonucleotide-diphosphate reductase subunit beta -
  GU334_RS09630 (GU334_09590) nrdE 1989886..1992042 (-) 2157 WP_167841548.1 class 1b ribonucleoside-diphosphate reductase subunit alpha -
  GU334_RS09635 (GU334_09595) nrdI 1992077..1992844 (-) 768 WP_096040577.1 class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI -
  GU334_RS09640 (GU334_09600) - 1993002..1993673 (+) 672 WP_096040578.1 Crp/Fnr family transcriptional regulator -
  GU334_RS09645 (GU334_09605) - 1993744..1994424 (-) 681 WP_001015311.1 IS6-like element IS1216 family transposase -
  GU334_RS09650 (GU334_09610) - 1995142..1995324 (+) 183 WP_167840890.1 hypothetical protein -
  GU334_RS09655 (GU334_09615) - 1995364..1996032 (-) 669 WP_021464853.1 type 1 glutamine amidotransferase -
  GU334_RS09660 (GU334_09620) - 1996172..1996852 (-) 681 WP_001015311.1 IS6-like element IS1216 family transposase -
  GU334_RS09665 (GU334_09625) - 1996929..1997027 (-) 99 Protein_1877 transposase -
  GU334_RS09670 (GU334_09630) - 1997163..1998068 (-) 906 WP_167840280.1 alpha/beta hydrolase -
  GU334_RS09675 (GU334_09635) - 1998511..1999035 (-) 525 WP_138492587.1 hypothetical protein -
  GU334_RS09680 (GU334_09640) - 1999081..1999308 (-) 228 WP_245325539.1 helix-turn-helix transcriptional regulator -
  GU334_RS09685 (GU334_09645) - 1999359..2000039 (+) 681 WP_047916692.1 IS6-like element ISS1N family transposase -
  GU334_RS09690 (GU334_09650) - 2000177..2000410 (-) 234 WP_167841549.1 thioredoxin family protein -
  GU334_RS09695 (GU334_09655) - 2000685..2001674 (-) 990 WP_167841550.1 permease -
  GU334_RS09700 (GU334_09660) - 2001674..2002006 (-) 333 WP_167841551.1 metalloregulator ArsR/SmtB family transcription factor -
  GU334_RS09705 (GU334_09665) - 2002325..2003005 (-) 681 WP_047916692.1 IS6-like element ISS1N family transposase -
  GU334_RS09710 (GU334_09670) - 2003079..2003237 (-) 159 Protein_1886 IS5/IS1182 family transposase -
  GU334_RS09715 (GU334_09675) - 2003362..2004642 (-) 1281 WP_167841552.1 McrC family protein -
  GU334_RS09720 (GU334_09680) - 2004644..2006674 (-) 2031 WP_245325540.1 AAA family ATPase -

Sequence

Protein


Download         Length: 453 a.a.        Molecular weight: 49398.93 Da        Isoelectric Point: 5.4218

>NTDB_id=414705 GU334_RS09565 WP_167841545.1 1976472..1977833(-) (radA) [Lactococcus raffinolactis strain Lr_19_14]
MAKAKSKFVCQSCGYQSPKYLGRCPNCGAWNSFVEEIEAKEVKNARVTLTGEKTRPVKLGEVESLDTPRVLTDMGEFNRV
LGGGVVPGSLILIGGDPGIGKSTILLQVSVQLANLGRVLYVSGEESAQQIKMRAERLGDLDSDFYLYAENNMQNIRAEIE
KLQPDFLVIDSIQTVMSPEITGVQGSVSQVREVTAELLQIAKTNNIATFIVGHVTKEGSLAGPRMLEHMVDTVLYFEGER
QHTFRILRAVKNRFGSTNEIGIFEMQSQGLVEVTNPSEIFLEERLEGATGSAIVVSMEGTRPILVEIQALVTPTIFGNAR
RTTSGLDFNRVSLIMAVLEKRANLLLQNQDAYLKSAGGVKLDEPAIDLAIAVAIVSSYKEKPTAPDVAFIGEIGLTGEIR
RVNRIESRINEVAKLGFKKLYAPKNSLAGLEIPPSIEVIGVTTLAEVLQKVFS

Nucleotide


Download         Length: 1362 bp        

>NTDB_id=414705 GU334_RS09565 WP_167841545.1 1976472..1977833(-) (radA) [Lactococcus raffinolactis strain Lr_19_14]
ATGGCGAAAGCAAAATCAAAATTCGTCTGCCAATCCTGTGGGTATCAGTCGCCCAAATATCTGGGGCGCTGTCCTAATTG
TGGCGCTTGGAACTCTTTTGTCGAAGAAATTGAAGCCAAAGAGGTCAAAAATGCGCGCGTGACCCTGACTGGGGAGAAAA
CACGACCTGTTAAACTAGGAGAAGTCGAAAGTCTAGATACACCCCGTGTTTTGACAGATATGGGCGAGTTTAACCGCGTT
CTTGGCGGTGGCGTTGTACCGGGGAGCTTGATTCTTATCGGTGGTGATCCAGGGATTGGGAAGTCAACCATTCTCTTACA
AGTTTCTGTGCAGCTGGCAAATCTCGGGCGTGTCCTTTATGTGTCAGGCGAGGAATCAGCCCAACAAATCAAGATGCGAG
CTGAACGTTTGGGTGATTTGGATTCTGATTTCTACCTCTACGCAGAAAATAATATGCAAAATATCCGAGCTGAAATTGAA
AAATTGCAGCCAGATTTTCTGGTCATTGACTCCATCCAAACCGTCATGAGCCCCGAAATTACAGGCGTACAAGGCTCGGT
CAGTCAAGTTCGAGAAGTGACCGCAGAACTACTCCAAATCGCAAAAACCAATAATATTGCTACCTTTATCGTCGGTCACG
TCACCAAGGAAGGCAGTCTTGCCGGCCCGAGAATGCTAGAGCATATGGTAGATACGGTGCTTTATTTTGAAGGGGAGCGC
CAGCATACTTTTCGGATTCTTCGTGCGGTGAAAAACCGGTTCGGCTCAACCAATGAAATCGGAATTTTTGAGATGCAATC
TCAAGGACTGGTCGAAGTGACCAATCCCAGCGAGATTTTCTTGGAGGAACGTTTAGAAGGTGCAACTGGCTCAGCTATTG
TTGTTTCAATGGAAGGGACCAGACCTATTTTGGTAGAAATCCAAGCGCTTGTCACACCAACGATTTTTGGTAATGCTAGA
CGGACAACCTCAGGTCTTGATTTTAATCGCGTCAGCTTGATTATGGCAGTGCTTGAAAAACGTGCCAATCTATTGCTCCA
AAATCAAGACGCCTACCTCAAATCAGCTGGTGGTGTCAAATTAGATGAACCAGCCATTGATTTAGCCATTGCGGTTGCCA
TTGTTTCAAGTTATAAAGAAAAACCGACAGCACCAGATGTCGCCTTTATCGGTGAAATTGGCTTGACAGGCGAAATTCGC
AGGGTCAACCGCATCGAGAGTCGAATCAATGAAGTAGCTAAACTGGGCTTTAAAAAACTTTATGCCCCTAAAAATTCCTT
GGCTGGTTTAGAAATCCCACCATCTATAGAAGTCATTGGTGTCACGACTTTAGCCGAAGTCTTGCAGAAGGTCTTTTCTT
AA

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(360-425)

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

AAA domain (AAA_25)

(82-218)


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

81.015

100

0.81
  radA Streptococcus pneumoniae D39

81.015

100

0.81
  radA Streptococcus pneumoniae R6

81.015

100

0.81
  radA Streptococcus pneumoniae TIGR4

81.015

100

0.81
  radA Streptococcus mitis SK321

81.015

100

0.81
  radA Streptococcus mitis NCTC 12261

80.795

100

0.808
  radA Bacillus subtilis subsp. subtilis str. 168

64.238

100

0.642

Multiple sequence alignment