Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   ABGT35_RS06040 Genome accession   NZ_OZ006975
Coordinates   1252861..1254237 (-) Length   458 a.a.
NCBI ID   WP_346682308.1    Uniprot ID   -
Organism   MAG: Megasphaera stantonii isolate     
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 1255186..1302508 1252861..1254237 flank 949


Gene organization within MGE regions


Location: 1252861..1302508
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABGT35_RS06040 radA 1252861..1254237 (-) 1377 WP_346682308.1 DNA repair protein RadA Machinery gene
  ABGT35_RS06045 - 1254248..1254937 (-) 690 WP_346682310.1 HAD family hydrolase -
  ABGT35_RS06050 - 1255079..1256275 (-) 1197 WP_087476938.1 acetate/propionate family kinase -
  ABGT35_RS06055 - 1256304..1256843 (-) 540 WP_346682312.1 hypothetical protein -
  ABGT35_RS06060 - 1257066..1258283 (+) 1218 WP_087476936.1 nucleotidyltransferase family protein -
  ABGT35_RS06065 gltS 1258421..1259689 (+) 1269 WP_239386275.1 sodium/glutamate symporter -
  ABGT35_RS06070 - 1259835..1260641 (-) 807 WP_346682315.1 tetratricopeptide repeat protein -
  ABGT35_RS06075 clpB 1260836..1263427 (+) 2592 WP_087476934.1 ATP-dependent chaperone ClpB -
  ABGT35_RS06080 - 1263551..1264126 (+) 576 WP_267312829.1 PepSY domain-containing protein -
  ABGT35_RS06085 nadC 1264192..1265052 (-) 861 WP_346682318.1 carboxylating nicotinate-nucleotide diphosphorylase -
  ABGT35_RS06090 - 1265049..1266359 (-) 1311 WP_087476932.1 L-aspartate oxidase -
  ABGT35_RS06095 nadA 1266386..1267294 (-) 909 WP_087476931.1 quinolinate synthase NadA -
  ABGT35_RS06100 - 1267604..1268110 (+) 507 WP_346682320.1 S-adenosylmethionine decarboxylase -
  ABGT35_RS06105 - 1268140..1268748 (+) 609 WP_095629935.1 HD-GYP domain-containing protein -
  ABGT35_RS06110 - 1268743..1269384 (-) 642 WP_346682322.1 ComF family protein -
  ABGT35_RS06115 - 1269378..1271540 (-) 2163 WP_346682324.1 ATP-dependent RecD-like DNA helicase -
  ABGT35_RS06120 - 1271542..1271811 (-) 270 WP_087476926.1 chorismate mutase -
  ABGT35_RS06125 - 1271959..1272867 (-) 909 WP_346682326.1 thiamine pyrophosphate-dependent enzyme -
  ABGT35_RS06130 porA 1272880..1274061 (-) 1182 WP_346682328.1 pyruvate ferredoxin oxidoreductase -
  ABGT35_RS06135 - 1274065..1274331 (-) 267 WP_346682330.1 4Fe-4S binding protein -
  ABGT35_RS06140 - 1274344..1274880 (-) 537 WP_346682332.1 2-oxoacid:acceptor oxidoreductase family protein -
  ABGT35_RS06145 - 1275123..1275893 (+) 771 WP_346682334.1 IclR family transcriptional regulator -
  ABGT35_RS06150 - 1276032..1277483 (+) 1452 WP_346682335.1 amino acid permease -
  ABGT35_RS06155 - 1277545..1278006 (-) 462 WP_346682337.1 hypothetical protein -
  ABGT35_RS06160 - 1278273..1279397 (-) 1125 WP_346682339.1 DUF362 domain-containing protein -
  ABGT35_RS06165 - 1279521..1280696 (-) 1176 WP_346682341.1 phosphoribosylaminoimidazolecarboxamide formyltransferase -
  ABGT35_RS06170 - 1280916..1281539 (-) 624 WP_346682342.1 DUF1847 domain-containing protein -
  ABGT35_RS06175 - 1281563..1281916 (-) 354 WP_087476915.1 hypothetical protein -
  ABGT35_RS06180 - 1281954..1282772 (-) 819 WP_346682344.1 MBL fold metallo-hydrolase -
  ABGT35_RS06185 - 1282786..1283610 (-) 825 WP_087476988.1 hypothetical protein -
  ABGT35_RS06190 - 1283620..1284426 (-) 807 WP_346682347.1 PHP domain-containing protein -
  ABGT35_RS06195 - 1284423..1285874 (-) 1452 WP_346682349.1 leucyl aminopeptidase family protein -
  ABGT35_RS06200 - 1286183..1286479 (-) 297 WP_346682351.1 hypothetical protein -
  ABGT35_RS06205 - 1286486..1286692 (-) 207 WP_346682353.1 hypothetical protein -
  ABGT35_RS06210 - 1286737..1287282 (-) 546 WP_346682355.1 N-acetylmuramoyl-L-alanine amidase -
  ABGT35_RS06215 - 1287279..1287704 (-) 426 WP_346682357.1 phage holin family protein -
  ABGT35_RS06220 - 1287869..1288282 (-) 414 WP_346682359.1 hypothetical protein -
  ABGT35_RS06225 - 1288327..1289352 (+) 1026 WP_346682361.1 tyrosine-type recombinase/integrase -
  ABGT35_RS06230 - 1290786..1291148 (+) 363 WP_346682363.1 hypothetical protein -
  ABGT35_RS06235 - 1291337..1292365 (-) 1029 WP_346682365.1 hypothetical protein -
  ABGT35_RS06240 - 1292370..1293005 (-) 636 WP_346682367.1 putative phage tail protein -
  ABGT35_RS06245 - 1293002..1294093 (-) 1092 WP_346682369.1 baseplate J/gp47 family protein -
  ABGT35_RS06250 - 1294096..1294524 (-) 429 WP_346682370.1 DUF2634 domain-containing protein -
  ABGT35_RS06255 - 1294526..1294933 (-) 408 WP_346682372.1 DUF2577 family protein -
  ABGT35_RS06260 - 1294938..1296470 (-) 1533 WP_346682374.1 hypothetical protein -
  ABGT35_RS06265 - 1296479..1297234 (-) 756 WP_346682376.1 phage baseplate protein -
  ABGT35_RS06270 - 1297235..1299532 (-) 2298 WP_346682378.1 phage tail tape measure protein -
  ABGT35_RS06275 - 1299719..1300135 (-) 417 WP_346682380.1 phage tail assembly chaperone -
  ABGT35_RS06280 - 1300147..1300581 (-) 435 WP_346682382.1 phage tail tube protein -
  ABGT35_RS06285 - 1300596..1301762 (-) 1167 WP_346682383.1 phage tail sheath subtilisin-like domain-containing protein -
  ABGT35_RS06290 - 1301774..1302280 (-) 507 WP_346682384.1 DUF6838 family protein -

Sequence

Protein


Download         Length: 458 a.a.        Molecular weight: 49303.08 Da        Isoelectric Point: 8.4739

>NTDB_id=1162669 ABGT35_RS06040 WP_346682308.1 1252861..1254237(-) (radA) [MAG: Megasphaera stantonii isolate]
MAKTKIRYVCANCGSVSSRWLGRCPQCGEWNTMMEEQAVPEPPKGVGARQGKGAKPALLQDIAMEQMSRVRTGIGELDRV
LGGGIVPGALILLSGDPGIGKSTLVLQIADAVCRHAGAVLYGSGEESAGQIKVRAERLGITASNLIIQADTSLDAVLQEA
KRRRPVLLIIDSIQTMYSSDADGMPGSMTQIRESTRRLMEFAKTESISVIVIGHVTKEGAIAGPRMMEHMVDVVLYFEGE
RNYQFRVLRGIKNRFGSTNETGLFTMEETGLSELTNPSQMLLAERSANQAGSAVAAVMDGMRPLLGEIQALTTHSVFAVP
RRTASGMDYNRLIILLAVLEKRVGLSLGTQDVYINSVGGLRVTETAADLAVVLAVFSSLRDVPMDSRTVVMGEVGLTGDI
RRVPHALRRIKEGAKMGFQTFIIPKGNLDEIKEGAFPQCRIIGAATLRDAIQAAFTAT

Nucleotide


Download         Length: 1377 bp        

>NTDB_id=1162669 ABGT35_RS06040 WP_346682308.1 1252861..1254237(-) (radA) [MAG: Megasphaera stantonii isolate]
ATGGCTAAAACGAAGATCCGATACGTATGCGCTAACTGCGGCAGCGTGTCCAGCCGCTGGCTGGGCCGGTGCCCCCAGTG
CGGAGAATGGAATACGATGATGGAAGAACAGGCTGTGCCTGAACCGCCTAAAGGCGTCGGCGCGCGGCAGGGCAAGGGGG
CGAAGCCGGCCTTGCTGCAGGATATCGCCATGGAACAGATGAGCCGCGTCCGGACGGGCATCGGCGAATTGGACCGCGTG
CTGGGCGGCGGCATCGTGCCGGGAGCGCTGATCTTGCTGAGCGGCGACCCCGGTATCGGCAAATCGACCTTGGTGCTGCA
GATTGCCGATGCCGTGTGCCGCCATGCCGGCGCGGTGCTGTACGGCTCCGGCGAAGAATCGGCCGGACAGATTAAGGTGC
GGGCGGAACGATTGGGAATTACGGCTTCCAATCTCATCATACAGGCCGATACGTCTCTCGACGCCGTACTGCAGGAAGCA
AAGCGACGCCGTCCGGTGCTGCTGATCATCGATTCTATCCAGACGATGTACAGCAGCGACGCCGACGGCATGCCGGGCAG
CATGACTCAGATACGGGAAAGCACGCGGCGTCTCATGGAATTTGCCAAGACGGAGTCCATTTCGGTCATCGTCATAGGCC
ATGTCACGAAGGAAGGGGCGATTGCCGGACCGCGCATGATGGAACATATGGTAGACGTCGTCCTGTATTTTGAAGGCGAG
CGGAATTATCAGTTCCGCGTGTTGCGGGGAATCAAAAATCGCTTTGGGTCGACGAACGAAACGGGATTGTTTACGATGGA
AGAAACGGGGTTGTCCGAATTGACTAATCCGTCGCAAATGCTCCTGGCCGAGCGGTCGGCAAATCAAGCCGGCTCGGCTG
TCGCCGCCGTCATGGACGGCATGCGGCCCCTTTTAGGGGAGATTCAAGCCCTGACAACGCATTCCGTTTTTGCCGTCCCG
CGCCGCACGGCGTCGGGCATGGACTATAACCGGCTGATTATTCTGCTGGCCGTGCTGGAAAAGCGCGTCGGCCTGTCTTT
GGGCACGCAGGACGTGTATATCAACAGCGTCGGCGGCCTGCGCGTCACGGAAACTGCCGCCGATTTAGCCGTCGTGCTGG
CCGTTTTTTCCAGCCTGCGCGACGTGCCGATGGACAGCCGAACCGTCGTCATGGGTGAAGTAGGCCTGACCGGCGACATA
CGGCGCGTGCCCCATGCCTTGCGGCGCATCAAGGAAGGCGCGAAGATGGGGTTCCAGACCTTTATCATTCCCAAGGGAAA
TCTGGATGAAATCAAGGAAGGAGCTTTCCCGCAATGCCGGATTATCGGGGCGGCGACGCTGCGCGACGCGATACAGGCGG
CGTTTACAGCGACGTAG

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(350-427)

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

AAA domain (AAA_25)

(66-219)


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 Bacillus subtilis subsp. subtilis str. 168

48.802

100

0.489
  radA Streptococcus pneumoniae Rx1

48.684

99.563

0.485
  radA Streptococcus pneumoniae D39

48.684

99.563

0.485
  radA Streptococcus pneumoniae R6

48.684

99.563

0.485
  radA Streptococcus pneumoniae TIGR4

48.684

99.563

0.485
  radA Streptococcus mitis NCTC 12261

48.571

99.345

0.483
  radA Streptococcus mitis SK321

48.571

99.345

0.483

Multiple sequence alignment