Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   LA161_RS07060 Genome accession   NZ_CP083725
Coordinates   1421847..1423217 (-) Length   456 a.a.
NCBI ID   WP_224428800.1    Uniprot ID   -
Organism   Pediococcus acidilactici strain MT25     
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)
ICE 1378068..1432560 1421847..1423217 within 0


Gene organization within MGE regions


Location: 1378068..1432560
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LA161_RS06810 - 1379168..1379581 (-) 414 WP_005918087.1 hypothetical protein -
  LA161_RS06815 - 1379635..1380513 (-) 879 WP_005918084.1 RluA family pseudouridine synthase -
  LA161_RS06820 - 1380803..1381357 (+) 555 WP_008841857.1 folate family ECF transporter S component -
  LA161_RS06825 - 1381430..1381576 (+) 147 WP_002832310.1 hypothetical protein -
  LA161_RS06830 - 1381702..1383030 (-) 1329 WP_070366350.1 nucleobase:cation symporter-2 family protein -
  LA161_RS06835 - 1383230..1384636 (+) 1407 WP_004165537.1 C69 family dipeptidase -
  LA161_RS06840 - 1384798..1386036 (-) 1239 WP_070366352.1 ABC transporter permease -
  LA161_RS06845 - 1386038..1386928 (-) 891 WP_128475091.1 ABC transporter ATP-binding protein -
  LA161_RS06850 - 1387131..1387475 (-) 345 WP_004165540.1 helix-turn-helix domain-containing protein -
  LA161_RS06855 - 1387838..1389943 (-) 2106 WP_224428789.1 BspA family leucine-rich repeat surface protein -
  LA161_RS06860 - 1390588..1391040 (+) 453 WP_224428790.1 hypothetical protein -
  LA161_RS06865 - 1391056..1391640 (+) 585 WP_224428791.1 hypothetical protein -
  LA161_RS06870 - 1391847..1392248 (+) 402 WP_224428792.1 hypothetical protein -
  LA161_RS06875 - 1392415..1392741 (+) 327 WP_224428793.1 hypothetical protein -
  LA161_RS06880 - 1392680..1393063 (+) 384 WP_224428794.1 zinc ribbon domain-containing protein -
  LA161_RS06885 - 1393358..1394002 (-) 645 WP_002832321.1 redox-sensing transcriptional repressor Rex -
  LA161_RS06890 - 1394017..1394994 (-) 978 WP_002832322.1 serine hydrolase -
  LA161_RS06895 tsaD 1395010..1396047 (-) 1038 WP_005918059.1 tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD -
  LA161_RS06900 rimI 1396034..1396630 (-) 597 WP_005918056.1 ribosomal protein S18-alanine N-acetyltransferase -
  LA161_RS06905 tsaB 1396611..1397339 (-) 729 WP_008841867.1 tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB -
  LA161_RS06910 galE 1397502..1398494 (-) 993 WP_224428795.1 UDP-glucose 4-epimerase GalE -
  LA161_RS06915 - 1398539..1399276 (-) 738 WP_193223298.1 acyl-[acyl-carrier-protein] thioesterase -
  LA161_RS06920 rsmI 1399310..1400182 (-) 873 WP_070366356.1 16S rRNA (cytidine(1402)-2'-O)-methyltransferase -
  LA161_RS06925 - 1400184..1400531 (-) 348 WP_002832330.1 DNA replication initiation control protein YabA -
  LA161_RS06930 holB 1400536..1401546 (-) 1011 WP_056985082.1 DNA polymerase III subunit delta' -
  LA161_RS06935 - 1401553..1401888 (-) 336 WP_002832332.1 cyclic-di-AMP receptor -
  LA161_RS06940 tmk 1401904..1402533 (-) 630 WP_024862963.1 dTMP kinase -
  LA161_RS06945 recR 1402960..1403559 (-) 600 WP_002832336.1 recombination mediator RecR -
  LA161_RS06950 - 1403583..1403897 (-) 315 WP_002832337.1 YbaB/EbfC family nucleoid-associated protein -
  LA161_RS06955 dnaX 1403913..1405649 (-) 1737 WP_224428796.1 DNA polymerase III subunit gamma/tau -
  LA161_RS06965 tadA 1405864..1406349 (-) 486 WP_005916020.1 tRNA adenosine(34) deaminase TadA -
  LA161_RS06970 - 1406342..1406947 (-) 606 WP_002832340.1 class I SAM-dependent methyltransferase -
  LA161_RS06975 nrdH 1407169..1407399 (+) 231 WP_224428797.1 glutaredoxin-like protein NrdH -
  LA161_RS06980 nrdE 1407492..1409657 (+) 2166 WP_008841876.1 class 1b ribonucleoside-diphosphate reductase subunit alpha -
  LA161_RS06985 nrdF 1409676..1410629 (+) 954 WP_224428798.1 class 1b ribonucleoside-diphosphate reductase subunit beta -
  LA161_RS06990 rplL 1410971..1411336 (-) 366 WP_002832345.1 50S ribosomal protein L7/L12 -
  LA161_RS06995 rplJ 1411382..1411888 (-) 507 WP_002832346.1 50S ribosomal protein L10 -
  LA161_RS07000 rplA 1412088..1412777 (-) 690 WP_224428799.1 50S ribosomal protein L1 -
  LA161_RS07005 rplK 1412869..1413294 (-) 426 WP_002832348.1 50S ribosomal protein L11 -
  LA161_RS07010 nusG 1413423..1413971 (-) 549 WP_024862957.1 transcription termination/antitermination protein NusG -
  LA161_RS07015 secE 1414062..1414232 (-) 171 WP_002832350.1 preprotein translocase subunit SecE -
  LA161_RS07020 rpmG 1414245..1414394 (-) 150 WP_002832352.1 50S ribosomal protein L33 -
  LA161_RS07025 - 1414448..1415029 (-) 582 WP_193223300.1 RNA polymerase sigma factor -
  LA161_RS07030 - 1415137..1416102 (-) 966 WP_016526705.1 IS30 family transposase -
  LA161_RS07035 rlmB 1416241..1416996 (-) 756 WP_002832356.1 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB -
  LA161_RS07040 - 1416989..1417402 (-) 414 WP_004165556.1 Mini-ribonuclease 3 -
  LA161_RS07045 cysS 1417395..1418813 (-) 1419 WP_024862956.1 cysteine--tRNA ligase -
  LA161_RS07050 gltX 1418970..1420457 (-) 1488 WP_002832359.1 glutamate--tRNA ligase -
  LA161_RS07055 - 1420583..1421731 (-) 1149 WP_002832360.1 PIN/TRAM domain-containing protein -
  LA161_RS07060 radA 1421847..1423217 (-) 1371 WP_224428800.1 DNA repair protein RadA Machinery gene
  LA161_RS07065 - 1423311..1423847 (-) 537 WP_224428801.1 dUTP diphosphatase -
  LA161_RS07070 - 1423976..1424299 (+) 324 WP_224428802.1 GNAT family N-acetyltransferase -
  LA161_RS07075 rpiA 1424310..1424996 (+) 687 WP_224428803.1 ribose-5-phosphate isomerase RpiA -
  LA161_RS07080 - 1425045..1426391 (+) 1347 WP_002832366.1 aminopeptidase C -
  LA161_RS07085 - 1426737..1427408 (-) 672 WP_070366360.1 2,3-diphosphoglycerate-dependent phosphoglycerate mutase -
  LA161_RS07090 - 1427488..1428189 (-) 702 WP_224428804.1 carboxyl transferase domain-containing protein -
  LA161_RS07095 - 1428191..1428973 (-) 783 WP_159211320.1 acetyl-CoA carboxylase carboxyltransferase subunit beta -
  LA161_RS07100 - 1428976..1430271 (-) 1296 WP_224428805.1 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha -
  LA161_RS07105 - 1430273..1430656 (-) 384 WP_224428806.1 biotin/lipoyl-containing protein -
  LA161_RS07110 - 1430666..1431634 (-) 969 WP_159211322.1 beta-ketoacyl-ACP synthase III -
  LA161_RS07115 - 1431863..1432324 (+) 462 WP_159211323.1 hypothetical protein -

Sequence

Protein


Download         Length: 456 a.a.        Molecular weight: 50183.68 Da        Isoelectric Point: 7.1014

>NTDB_id=607482 LA161_RS07060 WP_224428800.1 1421847..1423217(-) (radA) [Pediococcus acidilactici strain MT25]
MAKVKTQFVCNNCGYASPKFLGRCPNCGKWNTLVEERMSDPKAERKSRVSFDGKHTQPQLISDVAMHEEPRVKTGMEELN
RVLGGGVVDGSLVLIGGDPGIGKSTLLLQLSGQLAETQSKVLYVSGEESASQIKMRAERLKVNSERFYLYPETDMSSVRA
VIEELHPEYVIIDSVQTMQEPDIESAVGSVSQIREITAELMQIAKTNNITIFIVGHVTKGGAIAGPKILEHMVDTVLYFE
GDLHHTYRILRAVKNRFGSTNELGIFEMREEGLREVANPSEIFLEERLKDASGSAIVVSMEGTRPILVEIQALITPTIFG
NAQRTASGLDRNRVSLIMAVLEKRAKLTLQNQDAYLKAAGGVKLDEPAIDLALAISIVSSFKNQGTRPTDSFVGEIGLTG
EIRRVNRIEQRVAEAQKLGFKRILIPKNNLKGWQPPEGIEVVGVATIADAIRRAFN

Nucleotide


Download         Length: 1371 bp        

>NTDB_id=607482 LA161_RS07060 WP_224428800.1 1421847..1423217(-) (radA) [Pediococcus acidilactici strain MT25]
ATGGCAAAAGTTAAGACCCAGTTTGTATGCAATAATTGCGGATACGCCTCCCCTAAATTTTTAGGACGCTGTCCCAATTG
TGGTAAGTGGAACACTTTAGTTGAAGAACGGATGAGCGATCCAAAGGCTGAACGAAAAAGTCGGGTGAGCTTTGACGGCA
AACATACGCAACCACAGCTGATTTCGGACGTCGCGATGCACGAAGAACCCCGGGTAAAAACCGGGATGGAAGAACTTAAC
CGCGTGCTTGGTGGCGGGGTGGTTGACGGCTCCCTAGTCTTAATTGGTGGGGATCCTGGAATCGGAAAATCAACCCTGTT
GTTACAGCTATCAGGACAGTTGGCAGAGACGCAAAGCAAGGTACTTTACGTTTCTGGTGAAGAAAGTGCTTCCCAGATTA
AGATGCGTGCCGAACGATTGAAAGTCAATAGTGAACGCTTCTATTTGTATCCAGAGACCGATATGTCTAGCGTGCGGGCG
GTGATTGAGGAGTTACACCCCGAATACGTGATCATTGATTCGGTTCAGACCATGCAGGAACCGGATATTGAATCGGCGGT
GGGGAGCGTTTCTCAAATTCGAGAAATTACCGCAGAATTAATGCAAATCGCGAAAACCAATAACATTACCATCTTCATCG
TTGGTCACGTGACCAAGGGCGGTGCAATTGCGGGGCCGAAGATTTTGGAACACATGGTGGATACGGTGCTTTACTTTGAA
GGTGATCTGCACCACACTTACCGGATCCTGCGAGCGGTGAAGAACCGGTTTGGTTCCACGAACGAATTAGGAATCTTTGA
GATGCGCGAAGAAGGGTTACGCGAGGTGGCTAACCCGTCAGAAATTTTCTTAGAAGAGCGGCTAAAAGATGCTTCGGGAT
CGGCAATTGTAGTTTCAATGGAAGGAACTCGGCCGATTTTAGTTGAAATACAAGCCTTGATTACGCCCACCATCTTCGGC
AATGCGCAGCGCACGGCGAGCGGGTTGGACCGCAACCGGGTTTCGCTGATCATGGCGGTGCTCGAAAAACGGGCAAAGCT
TACTTTGCAAAACCAAGACGCCTATTTAAAGGCGGCGGGCGGCGTCAAGCTTGACGAACCCGCAATTGACTTAGCGTTGG
CGATTAGTATTGTTTCAAGTTTTAAAAATCAGGGAACCCGGCCGACCGATAGTTTTGTTGGTGAAATCGGCTTAACTGGT
GAAATTCGGCGGGTTAACCGAATTGAACAACGGGTCGCTGAAGCACAAAAGCTTGGTTTTAAGCGGATTTTGATTCCGAA
GAATAATTTGAAGGGGTGGCAGCCCCCCGAAGGAATTGAAGTTGTAGGGGTAGCTACGATTGCCGACGCGATTCGGCGGG
CATTTAATTAA

Domains

Predicted by InterproScan.

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

AAA domain (AAA_25)

(72-221)

Subunit ChlI of Mg-chelatase (ChlI)

(362-429)


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 mitis SK321

67.033

99.781

0.669
  radA Streptococcus mitis NCTC 12261

66.813

99.781

0.667
  radA Streptococcus pneumoniae Rx1

66.813

99.781

0.667
  radA Streptococcus pneumoniae TIGR4

66.813

99.781

0.667
  radA Streptococcus pneumoniae D39

66.813

99.781

0.667
  radA Streptococcus pneumoniae R6

66.813

99.781

0.667
  radA Bacillus subtilis subsp. subtilis str. 168

65.351

100

0.654