Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   EQG56_RS05905 Genome accession   NZ_CP035055
Coordinates   1112969..1114342 (-) Length   457 a.a.
NCBI ID   WP_057194461.1    Uniprot ID   A0AAJ6A204
Organism   Limosilactobacillus fermentum strain SRCM 103290     
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 1078615..1121338 1112969..1114342 within 0


Gene organization within MGE regions


Location: 1078615..1121338
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  EQG56_RS05730 (EQG56_05730) holB 1078615..1079655 (-) 1041 WP_107759814.1 DNA polymerase III subunit delta' -
  EQG56_RS05735 (EQG56_05735) - 1079673..1079993 (-) 321 WP_004562765.1 cyclic-di-AMP receptor -
  EQG56_RS05740 (EQG56_05740) tmk 1080006..1080650 (-) 645 WP_057194441.1 dTMP kinase -
  EQG56_RS05745 (EQG56_05745) - 1080670..1080918 (-) 249 WP_107759812.1 YaaL family protein -
  EQG56_RS05750 (EQG56_05750) recR 1080920..1081519 (-) 600 WP_004562762.1 recombination mediator RecR -
  EQG56_RS05755 (EQG56_05755) - 1081535..1081843 (-) 309 WP_004562761.1 YbaB/EbfC family nucleoid-associated protein -
  EQG56_RS05760 (EQG56_05760) dnaX 1081866..1083557 (-) 1692 WP_107759810.1 DNA polymerase III subunit gamma/tau -
  EQG56_RS05770 (EQG56_05770) tadA 1083852..1084337 (-) 486 WP_107759808.1 tRNA adenosine(34) deaminase TadA -
  EQG56_RS05775 (EQG56_05775) nrdH 1084594..1084815 (+) 222 WP_107759807.1 glutaredoxin-like protein NrdH -
  EQG56_RS05780 (EQG56_05780) nrdE 1084915..1087086 (+) 2172 WP_107759805.1 class 1b ribonucleoside-diphosphate reductase subunit alpha -
  EQG56_RS05785 (EQG56_05785) nrdF 1087148..1088149 (+) 1002 WP_102116036.1 class 1b ribonucleoside-diphosphate reductase subunit beta -
  EQG56_RS05790 (EQG56_05790) brnQ 1088224..1089603 (-) 1380 WP_104877848.1 branched-chain amino acid transport system II carrier protein -
  EQG56_RS05795 (EQG56_05795) adhE 1090129..1092732 (-) 2604 WP_104877847.1 bifunctional acetaldehyde-CoA/alcohol dehydrogenase -
  EQG56_RS05800 (EQG56_05800) cydC 1093210..1094961 (-) 1752 WP_104877846.1 thiol reductant ABC exporter subunit CydC -
  EQG56_RS05805 (EQG56_05805) cydD 1094951..1096681 (-) 1731 WP_107759803.1 thiol reductant ABC exporter subunit CydD -
  EQG56_RS05810 (EQG56_05810) cydB 1096681..1097697 (-) 1017 WP_107759801.1 cytochrome d ubiquinol oxidase subunit II -
  EQG56_RS05815 (EQG56_05815) - 1097699..1099135 (-) 1437 WP_107759799.1 cytochrome ubiquinol oxidase subunit I -
  EQG56_RS05820 (EQG56_05820) rplL 1099579..1099944 (-) 366 WP_004562749.1 50S ribosomal protein L7/L12 -
  EQG56_RS05825 (EQG56_05825) rplJ 1100013..1100516 (-) 504 WP_057194453.1 50S ribosomal protein L10 -
  EQG56_RS05830 (EQG56_05830) - 1100893..1102221 (+) 1329 WP_107759797.1 APC family permease -
  EQG56_RS05840 (EQG56_05840) - 1102415..1103401 (+) 987 WP_187346373.1 IS30 family transposase -
  EQG56_RS05845 (EQG56_05845) rplA 1103466..1104158 (-) 693 WP_057194454.1 50S ribosomal protein L1 -
  EQG56_RS05850 (EQG56_05850) rplK 1104252..1104677 (-) 426 WP_004562745.1 50S ribosomal protein L11 -
  EQG56_RS05855 (EQG56_05855) nusG 1104797..1105342 (-) 546 WP_021349745.1 transcription termination/antitermination protein NusG -
  EQG56_RS05860 (EQG56_05860) secE 1105451..1105627 (-) 177 WP_057194456.1 preprotein translocase subunit SecE -
  EQG56_RS05865 (EQG56_05865) rpmG 1105642..1105788 (-) 147 WP_004562742.1 50S ribosomal protein L33 -
  EQG56_RS05870 (EQG56_05870) - 1105853..1106431 (-) 579 WP_107760363.1 RNA polymerase sigma factor -
  EQG56_RS05875 (EQG56_05875) rlmB 1106669..1107424 (-) 756 WP_062813453.1 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB -
  EQG56_RS05880 (EQG56_05880) - 1107414..1107827 (-) 414 WP_107760365.1 Mini-ribonuclease 3 -
  EQG56_RS05885 (EQG56_05885) cysS 1107834..1109252 (-) 1419 WP_104877841.1 cysteine--tRNA ligase -
  EQG56_RS05890 (EQG56_05890) - 1109600..1110169 (-) 570 WP_107760367.1 TIGR01440 family protein -
  EQG56_RS05895 (EQG56_05895) gltX 1110237..1111733 (-) 1497 WP_104877840.1 glutamate--tRNA ligase -
  EQG56_RS05900 (EQG56_05900) - 1111804..1112937 (-) 1134 WP_104877839.1 PIN/TRAM domain-containing protein -
  EQG56_RS05905 (EQG56_05905) radA 1112969..1114342 (-) 1374 WP_057194461.1 DNA repair protein RadA Machinery gene
  EQG56_RS05910 (EQG56_05910) - 1114355..1114894 (-) 540 WP_057194477.1 dUTP diphosphatase -
  EQG56_RS05915 (EQG56_05915) - 1115095..1115406 (+) 312 WP_049182693.1 GNAT family N-acetyltransferase -
  EQG56_RS05920 (EQG56_05920) - 1115609..1116859 (-) 1251 WP_128492883.1 RNA-guided endonuclease TnpB family protein -
  EQG56_RS05925 (EQG56_05925) tnpA 1116934..1117383 (+) 450 Protein_1144 IS200/IS605 family transposase -
  EQG56_RS05930 (EQG56_05930) rpiA 1117418..1118104 (+) 687 WP_107760318.1 ribose-5-phosphate isomerase RpiA -
  EQG56_RS05935 (EQG56_05935) - 1118132..1118746 (+) 615 WP_057194463.1 sugar O-acetyltransferase -
  EQG56_RS05940 (EQG56_05940) - 1118810..1120147 (+) 1338 WP_004562729.1 aminopeptidase C -
  EQG56_RS11150 - 1120463..1121338 (-) 876 WP_187344770.1 alpha/beta hydrolase -

Sequence

Protein


Download         Length: 457 a.a.        Molecular weight: 49415.82 Da        Isoelectric Point: 8.7358

>NTDB_id=334313 EQG56_RS05905 WP_057194461.1 1112969..1114342(-) (radA) [Limosilactobacillus fermentum strain SRCM 103290]
MAKAKTHFVCQNCGYNSPRYLGRCPNCGQWSTLVEEVEQASTPAAKNATATLTGIVARPQRIQEIDTKKTPRVKTRLNEL
NRVLGGGIVPGSLVLIGGDPGIGKSTMLLQVSGQLSVEHHKVLYVSGEESASQIKLRAQRLDVSGEDFYIYPETNMEAIR
ATIDSIQPEFVIIDSVQTMQAADVTSAIGSVSQIRAVTAQLMQIAKGQNITVFVVGHVTKGGVLAGPKILEHMVDTVLYF
EGDLHHTYRILRSVKNRFGSTNELGIFEMNTRGLTEVANPSEIFLEERLKDATGSAVVVSLEGTRPILVEIQALITPTVF
GNAQRTATGLNRNRVSLIMAVLEKRANLLLQNQDAYLKAAGGVKLDEPAIDLAIAVAIASSYRDKGTRPTDAFVGEVGLT
GEIRRVSRIEQRVAEAAKLGFKRILVPKNNLAGWNPPQDIEVVGVTTLGEALKISLG

Nucleotide


Download         Length: 1374 bp        

>NTDB_id=334313 EQG56_RS05905 WP_057194461.1 1112969..1114342(-) (radA) [Limosilactobacillus fermentum strain SRCM 103290]
ATGGCAAAAGCCAAAACACACTTTGTCTGCCAAAACTGCGGTTATAATTCACCGCGCTATTTAGGGCGGTGTCCCAATTG
TGGCCAGTGGAGTACCTTAGTTGAAGAAGTCGAGCAGGCAAGTACCCCGGCGGCTAAAAACGCTACGGCAACCTTAACCG
GGATTGTGGCCCGGCCCCAGCGAATCCAAGAAATTGACACCAAAAAAACGCCCCGGGTTAAGACCCGCTTAAATGAGTTA
AACCGGGTGCTAGGTGGCGGAATTGTACCCGGCTCGTTGGTCTTAATTGGTGGGGATCCCGGGATCGGGAAGTCCACCAT
GCTCTTACAAGTGTCGGGGCAACTGAGCGTGGAACACCACAAGGTTCTTTACGTTTCCGGGGAAGAATCGGCCTCCCAAA
TTAAATTACGGGCCCAACGCTTAGACGTTTCCGGCGAGGACTTTTATATCTACCCGGAAACCAACATGGAAGCCATCCGT
GCGACGATTGATTCCATTCAGCCCGAGTTTGTAATCATTGACTCGGTTCAGACGATGCAGGCGGCCGACGTGACCTCGGC
GATTGGGTCGGTCTCCCAAATCCGGGCGGTCACCGCCCAGTTGATGCAGATTGCCAAGGGGCAAAACATCACGGTCTTCG
TGGTTGGTCACGTCACCAAGGGTGGGGTCTTAGCCGGTCCCAAGATCTTGGAACACATGGTTGACACGGTGCTGTACTTT
GAAGGGGACCTCCACCACACCTACCGGATTTTACGGTCGGTCAAAAACCGGTTTGGGTCCACCAATGAGTTAGGGATCTT
CGAAATGAATACCCGCGGTTTGACCGAGGTCGCAAACCCCTCGGAAATCTTTTTGGAAGAGCGGCTTAAGGATGCCACCG
GGTCGGCCGTGGTCGTATCCCTGGAGGGAACCCGACCGATCCTGGTTGAAATCCAGGCCTTGATCACGCCAACCGTCTTT
GGAAACGCCCAAAGAACGGCGACGGGTTTAAACCGCAACCGGGTTTCCTTGATCATGGCGGTCCTAGAAAAACGGGCGAA
CCTGCTCTTACAAAACCAGGATGCCTACTTGAAGGCGGCCGGGGGCGTTAAGTTAGACGAGCCGGCCATCGACCTTGCGA
TCGCGGTGGCAATTGCTTCTTCTTACCGGGATAAGGGGACCCGGCCGACCGACGCCTTCGTCGGTGAAGTTGGCTTAACC
GGGGAGATCCGTCGGGTGAGCCGAATTGAACAGCGGGTGGCCGAAGCCGCTAAACTAGGCTTTAAGCGGATTTTAGTGCC
CAAAAACAATTTAGCGGGTTGGAACCCGCCGCAAGACATCGAAGTCGTGGGGGTAACGACCCTTGGCGAAGCACTTAAAA
TTTCCCTTGGATAG

Domains

Predicted by InterproScan.

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

Subunit ChlI of Mg-chelatase (ChlI)

(364-430)

AAA domain (AAA_25)

(64-222)


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

67.991

99.125

0.674
  radA Streptococcus mitis NCTC 12261

67.77

99.125

0.672
  radA Streptococcus pneumoniae Rx1

67.77

99.125

0.672
  radA Streptococcus pneumoniae D39

67.77

99.125

0.672
  radA Streptococcus pneumoniae R6

67.77

99.125

0.672
  radA Streptococcus pneumoniae TIGR4

67.77

99.125

0.672
  radA Bacillus subtilis subsp. subtilis str. 168

63.676

100

0.637

Multiple sequence alignment