Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   NQ540_RS00435 Genome accession   NZ_CP102283
Coordinates   74982..76367 (+) Length   461 a.a.
NCBI ID   WP_039849307.1    Uniprot ID   -
Organism   Granulicatella adiacens ATCC 49175     
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 25014..74969 74982..76367 flank 13


Gene organization within MGE regions


Location: 25014..76367
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  NQ540_RS00090 (NQ540_00090) ssb 25014..25511 (+) 498 WP_005608180.1 single-stranded DNA-binding protein Machinery gene
  NQ540_RS00095 (NQ540_00095) rpsR 25534..25776 (+) 243 WP_005608178.1 30S ribosomal protein S18 -
  NQ540_RS00100 (NQ540_00100) - 26030..28057 (+) 2028 WP_005608177.1 DHH family phosphoesterase -
  NQ540_RS00105 (NQ540_00105) rplI 28073..28525 (+) 453 WP_005608175.1 50S ribosomal protein L9 -
  NQ540_RS00110 (NQ540_00110) dnaB 28712..30097 (+) 1386 WP_005608173.1 replicative DNA helicase -
  NQ540_RS00115 (NQ540_00115) - 30130..31419 (+) 1290 WP_005608172.1 adenylosuccinate synthase -
  NQ540_RS00120 (NQ540_00120) yycF 31447..32163 (+) 717 WP_005608170.1 response regulator YycF -
  NQ540_RS00125 (NQ540_00125) walK 32246..34102 (+) 1857 WP_005608168.1 cell wall metabolism sensor histidine kinase WalK -
  NQ540_RS00130 (NQ540_00130) - 34092..35444 (+) 1353 WP_005608166.1 YycH family regulatory protein -
  NQ540_RS00135 (NQ540_00135) - 35434..36297 (+) 864 WP_005608164.1 two-component system regulatory protein YycI -
  NQ540_RS00140 (NQ540_00140) - 36310..37113 (+) 804 WP_005608162.1 MBL fold metallo-hydrolase -
  NQ540_RS00145 (NQ540_00145) - 37221..38456 (+) 1236 WP_005608160.1 S1C family serine protease -
  NQ540_RS00150 (NQ540_00150) rlmH 38972..39451 (+) 480 WP_005608158.1 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH -
  NQ540_RS00155 (NQ540_00155) - 39607..40788 (-) 1182 WP_005608156.1 tyrosine-type recombinase/integrase -
  NQ540_RS00160 (NQ540_00160) - 40904..41578 (-) 675 WP_005608154.1 NYN domain-containing protein -
  NQ540_RS00165 (NQ540_00165) - 41746..42156 (-) 411 WP_005608152.1 ImmA/IrrE family metallo-endopeptidase -
  NQ540_RS00170 (NQ540_00170) - 42355..42600 (-) 246 Protein_33 helix-turn-helix domain-containing protein -
  NQ540_RS00175 (NQ540_00175) - 42772..42963 (+) 192 WP_005608146.1 helix-turn-helix transcriptional regulator -
  NQ540_RS00180 (NQ540_00180) - 43138..43302 (-) 165 WP_083789029.1 YjzC family protein -
  NQ540_RS00185 (NQ540_00185) - 43390..43692 (+) 303 WP_005608142.1 hypothetical protein -
  NQ540_RS00190 (NQ540_00190) - 43696..43989 (-) 294 WP_005608140.1 hypothetical protein -
  NQ540_RS00195 (NQ540_00195) - 44045..44320 (+) 276 WP_005608138.1 hypothetical protein -
  NQ540_RS00200 (NQ540_00200) - 44317..44595 (+) 279 WP_005608136.1 hypothetical protein -
  NQ540_RS00205 (NQ540_00205) - 44812..45054 (+) 243 WP_005608133.1 hypothetical protein -
  NQ540_RS00210 (NQ540_00210) - 45076..45864 (+) 789 WP_005608132.1 conserved phage C-terminal domain-containing protein -
  NQ540_RS00215 (NQ540_00215) - 45866..47122 (+) 1257 WP_005608131.1 replicative DNA helicase -
  NQ540_RS00220 (NQ540_00220) - 47119..47493 (+) 375 WP_005608130.1 hypothetical protein -
  NQ540_RS00225 (NQ540_00225) - 47477..47965 (+) 489 WP_005608129.1 hypothetical protein -
  NQ540_RS00230 (NQ540_00230) - 47962..48297 (+) 336 WP_005608128.1 MazG-like family protein -
  NQ540_RS00235 (NQ540_00235) - 48297..48566 (+) 270 WP_005608127.1 DUF3310 domain-containing protein -
  NQ540_RS00240 (NQ540_00240) - 48569..48808 (+) 240 WP_005608125.1 hypothetical protein -
  NQ540_RS00245 (NQ540_00245) - 48792..49340 (+) 549 WP_005608123.1 hypothetical protein -
  NQ540_RS00250 (NQ540_00250) - 49341..49673 (+) 333 WP_005608121.1 hypothetical protein -
  NQ540_RS00255 (NQ540_00255) - 49823..50035 (+) 213 WP_005608119.1 hypothetical protein -
  NQ540_RS00260 (NQ540_00260) - 50037..50273 (+) 237 WP_005608117.1 hypothetical protein -
  NQ540_RS00265 (NQ540_00265) - 50274..50477 (+) 204 WP_005608115.1 hypothetical protein -
  NQ540_RS00270 (NQ540_00270) - 50479..50775 (+) 297 WP_005608114.1 hypothetical protein -
  NQ540_RS00275 (NQ540_00275) nrdH 50967..51203 (+) 237 WP_005608112.1 glutaredoxin-like protein NrdH -
  NQ540_RS00280 (NQ540_00280) - 51203..51535 (+) 333 WP_005608110.1 hypothetical protein -
  NQ540_RS00285 (NQ540_00285) ssb 51532..51933 (+) 402 WP_005608108.1 single-stranded DNA-binding protein Machinery gene
  NQ540_RS00290 (NQ540_00290) - 51953..52414 (+) 462 WP_050755113.1 ArpU family phage packaging/lysis transcriptional regulator -
  NQ540_RS00295 (NQ540_00295) - 52646..53188 (+) 543 WP_005608105.1 site-specific integrase -
  NQ540_RS00300 (NQ540_00300) - 53341..53658 (+) 318 WP_005608102.1 HNH endonuclease -
  NQ540_RS00305 (NQ540_00305) - 53764..54132 (+) 369 WP_005608099.1 P27 family phage terminase small subunit -
  NQ540_RS00310 (NQ540_00310) - 54129..55880 (+) 1752 WP_005608097.1 terminase large subunit -
  NQ540_RS00315 (NQ540_00315) - 55882..57081 (+) 1200 WP_005608094.1 phage portal protein -
  NQ540_RS00320 (NQ540_00320) - 57074..57649 (+) 576 WP_050755115.1 HK97 family phage prohead protease -
  NQ540_RS00325 (NQ540_00325) - 57639..57974 (+) 336 WP_005608086.1 hypothetical protein -
  NQ540_RS00330 (NQ540_00330) - 57950..58804 (+) 855 WP_327050066.1 phage major capsid protein -
  NQ540_RS00335 (NQ540_00335) - 58817..59113 (+) 297 WP_050755112.1 hypothetical protein -
  NQ540_RS00340 (NQ540_00340) - 59013..59363 (+) 351 WP_211204711.1 hypothetical protein -
  NQ540_RS00345 (NQ540_00345) - 59353..59670 (+) 318 WP_005608082.1 phage head closure protein -
  NQ540_RS00350 (NQ540_00350) - 59660..60013 (+) 354 WP_050755111.1 HK97 gp10 family phage protein -
  NQ540_RS00355 (NQ540_00355) - 60059..60334 (+) 276 WP_259912550.1 hypothetical protein -
  NQ540_RS00360 (NQ540_00360) - 60349..60942 (+) 594 WP_005608079.1 major tail protein -
  NQ540_RS00365 (NQ540_00365) - 60955..61347 (+) 393 WP_005608078.1 hypothetical protein -
  NQ540_RS00370 (NQ540_00370) - 61569..64460 (+) 2892 WP_005608077.1 phage tail tape measure protein -
  NQ540_RS00375 (NQ540_00375) - 64457..65212 (+) 756 WP_005608076.1 phage distal tail protein -
  NQ540_RS00380 (NQ540_00380) - 65209..67290 (+) 2082 WP_039849309.1 phage tail spike protein -
  NQ540_RS00385 (NQ540_00385) - 67283..69322 (+) 2040 WP_005608074.1 DUF859 family phage minor structural protein -
  NQ540_RS00390 (NQ540_00390) - 69335..69550 (+) 216 WP_005608073.1 hypothetical protein -
  NQ540_RS00395 (NQ540_00395) - 69554..69979 (+) 426 WP_005608071.1 phage holin family protein -
  NQ540_RS00400 (NQ540_00400) - 69985..70242 (+) 258 WP_039849314.1 phage holin -
  NQ540_RS00405 (NQ540_00405) - 70306..71286 (+) 981 WP_039849308.1 N-acetylmuramoyl-L-alanine amidase family protein -
  NQ540_RS00410 (NQ540_00410) - 71695..71889 (+) 195 WP_005608064.1 hypothetical protein -
  NQ540_RS00420 (NQ540_00420) - 72652..72990 (+) 339 WP_005608062.1 hypothetical protein -
  NQ540_RS00425 (NQ540_00425) - 73051..74154 (-) 1104 WP_005608060.1 ABC transporter ATP-binding protein -
  NQ540_RS00430 (NQ540_00430) - 74406..74969 (+) 564 WP_005608058.1 dUTP diphosphatase -
  NQ540_RS00435 (NQ540_00435) radA 74982..76367 (+) 1386 WP_039849307.1 DNA repair protein RadA Machinery gene

Sequence

Protein


Download         Length: 461 a.a.        Molecular weight: 50701.99 Da        Isoelectric Point: 6.9560

>NTDB_id=715829 NQ540_RS00435 WP_039849307.1 74982..76367(+) (radA) [Granulicatella adiacens ATCC 49175]
MAKTATSFVCRECGYNSPKYLGKCPNCGNWSTMEEFKETTSNTKRPSLVQQSEEAHKTKPMRLDQVSYERVNRVKTSISE
LDRVLGGGVVPGSLVLIGGDPGIGKSTLLLQVSSELQQTQGTVLYVSGEESASQIKMRAERLGMQADGFYIYAETNLEDI
VAQVEALKPDYVIIDSIQTMTHPQANGVAGSVSHVREATATLMRLAKLNQIAIFIVGHVTKEGALAGPRMLEHMVDTVLY
FEGDKHHSFRVLRSVKNRFGSTNEIGVFEMHQEGLNEVTNPSEVFLEERLAGATGSAIVVSLEGTRPILTEVQCLLSPTA
FGNARRTTSGLDYNRVALLMAVLEKRAGLLLQNQDAYFKSTGGLKLGEPAVDLAIAMSIVSSYKEKETQMGDCFIGEIGL
TGEIRKVNRVYDRVREAEKLGFKRVFIPKNNLDGWKIPENIEVVGVSSVKEAIYKAFNHEK

Nucleotide


Download         Length: 1386 bp        

>NTDB_id=715829 NQ540_RS00435 WP_039849307.1 74982..76367(+) (radA) [Granulicatella adiacens ATCC 49175]
ATGGCAAAAACAGCCACAAGTTTTGTATGTAGAGAATGTGGATATAATTCACCAAAATATTTAGGAAAATGTCCAAACTG
TGGAAATTGGTCCACAATGGAAGAGTTTAAGGAAACGACGAGTAACACGAAACGACCTTCTTTAGTCCAACAGTCAGAAG
AAGCCCATAAAACAAAACCGATGCGACTGGACCAGGTTTCTTATGAACGCGTCAACCGTGTAAAAACATCCATTAGCGAA
CTCGACCGTGTGCTTGGTGGTGGCGTGGTGCCAGGCTCCTTAGTATTAATCGGTGGGGACCCTGGGATTGGAAAATCGAC
TTTATTATTACAAGTTTCTAGTGAATTACAACAAACACAAGGGACCGTTCTCTATGTATCCGGAGAGGAAAGTGCGTCTC
AAATTAAAATGCGTGCAGAGCGTCTTGGGATGCAAGCAGACGGATTTTATATTTATGCGGAGACAAACTTAGAAGATATC
GTTGCGCAAGTGGAAGCCTTAAAACCAGACTATGTCATTATCGACTCGATTCAAACGATGACACATCCGCAAGCAAATGG
GGTTGCAGGAAGCGTGTCTCATGTTCGTGAGGCAACGGCAACACTCATGCGACTTGCGAAACTCAATCAGATCGCCATCT
TTATTGTGGGTCACGTGACAAAAGAGGGAGCGTTGGCAGGTCCTCGTATGTTGGAACATATGGTGGACACCGTTCTTTAT
TTTGAAGGGGATAAGCATCATAGTTTCCGAGTGCTTCGCTCTGTGAAAAACCGTTTTGGGTCAACGAACGAGATTGGGGT
CTTCGAAATGCATCAAGAAGGGCTGAATGAAGTAACCAATCCTTCGGAAGTCTTTTTAGAAGAACGTTTGGCTGGCGCAA
CTGGTTCCGCAATTGTCGTGTCTCTTGAAGGGACAAGACCAATTTTAACCGAGGTGCAATGTCTATTGTCCCCAACAGCC
TTTGGAAATGCACGCCGTACGACAAGTGGTCTAGACTATAATCGTGTTGCGCTCTTGATGGCGGTACTTGAGAAACGTGC
AGGTCTTCTATTGCAAAACCAAGATGCTTACTTTAAATCAACAGGCGGCTTGAAACTGGGCGAACCCGCAGTCGATTTAG
CGATTGCGATGAGTATCGTTTCAAGCTATAAGGAAAAAGAAACGCAGATGGGGGATTGCTTTATCGGCGAAATTGGCTTG
ACAGGTGAAATTCGAAAAGTAAACCGTGTCTATGACCGTGTCCGTGAAGCAGAAAAACTCGGATTCAAGCGTGTCTTCAT
TCCAAAAAACAACTTAGATGGATGGAAAATTCCTGAAAATATCGAAGTTGTCGGTGTATCTTCTGTCAAAGAGGCTATTT
ATAAAGCCTTCAATCATGAAAAATAG

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(369-431)

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

AAA domain (AAA_25)

(68-223)


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

66.594

99.349

0.662
  radA Streptococcus pneumoniae D39

66.594

99.349

0.662
  radA Streptococcus pneumoniae R6

66.594

99.349

0.662
  radA Streptococcus pneumoniae TIGR4

66.594

99.349

0.662
  radA Streptococcus mitis SK321

66.594

99.349

0.662
  radA Streptococcus mitis NCTC 12261

66.376

99.349

0.659
  radA Bacillus subtilis subsp. subtilis str. 168

59.471

98.482

0.586