Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   SSU16085_RS09775 Genome accession   NZ_CP058740
Coordinates   2021132..2022502 (-) Length   456 a.a.
NCBI ID   WP_004298358.1    Uniprot ID   A0A126UJP8
Organism   Streptococcus suis strain 16085/3b     
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 2023049..2046307 2021132..2022502 flank 547


Gene organization within MGE regions


Location: 2021132..2046307
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SSU16085_RS09775 (SSU16085_01990) radA 2021132..2022502 (-) 1371 WP_004298358.1 DNA repair protein RadA Machinery gene
  SSU16085_RS09780 (SSU16085_01991) - 2022509..2023042 (-) 534 WP_004298356.1 histidine phosphatase family protein -
  SSU16085_RS09785 (SSU16085_01992) - 2023049..2023492 (-) 444 WP_004298354.1 dUTP diphosphatase -
  SSU16085_RS09790 (SSU16085_01993) - 2023591..2024736 (-) 1146 WP_043032909.1 site-specific integrase -
  SSU16085_RS09795 (SSU16085_01994) - 2025163..2025747 (-) 585 WP_024417296.1 helix-turn-helix transcriptional regulator -
  SSU16085_RS09800 (SSU16085_01995) - 2025910..2026107 (+) 198 WP_024417295.1 helix-turn-helix transcriptional regulator -
  SSU16085_RS09805 (SSU16085_01996) - 2026125..2026283 (+) 159 Protein_1910 helix-turn-helix domain-containing protein -
  SSU16085_RS09810 (SSU16085_01997) - 2026344..2026973 (+) 630 WP_043032905.1 Rha family transcriptional regulator -
  SSU16085_RS09815 (SSU16085_01998) - 2027437..2027838 (+) 402 WP_014637233.1 hypothetical protein -
  SSU16085_RS09820 (SSU16085_01999) - 2027826..2028029 (+) 204 WP_014637232.1 hypothetical protein -
  SSU16085_RS09825 (SSU16085_02000) - 2028041..2028190 (+) 150 WP_014637231.1 hypothetical protein -
  SSU16085_RS09830 (SSU16085_02001) - 2028187..2028525 (+) 339 WP_014637230.1 hypothetical protein -
  SSU16085_RS09835 (SSU16085_02002) - 2028515..2028790 (+) 276 WP_024394567.1 hypothetical protein -
  SSU16085_RS09840 (SSU16085_02003) - 2028787..2028939 (+) 153 WP_162841229.1 hypothetical protein -
  SSU16085_RS09845 (SSU16085_02005) - 2029035..2029910 (+) 876 WP_043033044.1 primase alpha helix C-terminal domain-containing protein -
  SSU16085_RS09850 (SSU16085_02006) - 2029928..2031400 (+) 1473 WP_024394565.1 phage/plasmid primase, P4 family -
  SSU16085_RS09855 (SSU16085_02007) - 2031634..2031807 (+) 174 WP_162841090.1 hypothetical protein -
  SSU16085_RS09860 (SSU16085_02008) - 2031828..2032403 (+) 576 WP_024394564.1 hypothetical protein -
  SSU16085_RS09865 (SSU16085_02009) - 2032453..2032854 (+) 402 WP_024394563.1 hypothetical protein -
  SSU16085_RS10700 (SSU16085_02010) - 2032906..2033409 (+) 504 WP_024394562.1 hypothetical protein -
  SSU16085_RS09870 (SSU16085_02011) - 2033540..2033959 (+) 420 WP_024394561.1 hypothetical protein -
  SSU16085_RS09875 (SSU16085_02012) - 2034018..2034329 (+) 312 WP_153055172.1 DUF1492 domain-containing protein -
  SSU16085_RS09880 (SSU16085_02013) - 2034861..2036645 (-) 1785 WP_024394879.1 ABC transporter ATP-binding protein -
  SSU16085_RS09885 (SSU16085_02014) - 2036646..2038352 (-) 1707 WP_024394878.1 ABC transporter ATP-binding protein -
  SSU16085_RS09890 (SSU16085_02015) - 2038345..2038794 (-) 450 WP_024387360.1 MarR family winged helix-turn-helix transcriptional regulator -
  SSU16085_RS09895 (SSU16085_02016) - 2039016..2040032 (+) 1017 WP_012027922.1 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase -
  SSU16085_RS09900 (SSU16085_02017) galU 2040077..2040976 (+) 900 WP_004298345.1 UTP--glucose-1-phosphate uridylyltransferase GalU -
  SSU16085_RS09905 (SSU16085_02018) - 2040994..2041671 (-) 678 WP_043033090.1 rhomboid family intramembrane serine protease -
  SSU16085_RS09910 (SSU16085_02019) - 2041655..2042197 (-) 543 WP_024387358.1 5-formyltetrahydrofolate cyclo-ligase -
  SSU16085_RS09915 (SSU16085_02020) - 2042238..2043365 (-) 1128 WP_192062987.1 N-acetyldiaminopimelate deacetylase -
  SSU16085_RS09920 (SSU16085_02021) dapD 2043375..2044073 (-) 699 WP_024376132.1 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase -
  SSU16085_RS09925 (SSU16085_02022) - 2044149..2044889 (-) 741 WP_024387356.1 metallophosphoesterase -
  SSU16085_RS09930 (SSU16085_02023) - 2045051..2046307 (+) 1257 WP_192062988.1 ISL3 family transposase -

Sequence

Protein


Download         Length: 456 a.a.        Molecular weight: 50002.51 Da        Isoelectric Point: 6.1911

>NTDB_id=465168 SSU16085_RS09775 WP_004298358.1 2021132..2022502(-) (radA) [Streptococcus suis strain 16085/3b]
MTIAKKKTTFVCQSCEYHSPKYLGRCPNCGSWSSFVEEVEVAEVKNERVSLTGEKTRPMKLNEVSSIQVARTKTNMEEFN
RVLGGGVVPGSLVLIGGDPGIGKSTLLLQVSTQLSTIGTVLYVSGEESAQQIKLRAERLGDIDSEFYLYAETNMQSIRTE
IEKIKPDFLIIDSIQTIMSPDISSVQGSVSQVREVTNELMQIAKTNNIATFIVGHMTKEGTLAGPRTLEHMVDTVLYFEG
ERQHTFRILRAVKNRFGSTNEIGIFEMQSQGLVEVLNPSEVFLEERLDGATGSAIVVTMEGTRPILAEVQALVTPTMFGN
AKRTTTGLDFNRASLIMAVLEKRAGLLLQNQDAYLKSAGGVKLDEPAIDLAVAVALASSYKDKPTNPQECFIGEIGLTGE
IRRVNRIEQRINEAAKLGFTKVYAPKNSLTGIKVPKEITVISVTTIGEVLQKVFNL

Nucleotide


Download         Length: 1371 bp        

>NTDB_id=465168 SSU16085_RS09775 WP_004298358.1 2021132..2022502(-) (radA) [Streptococcus suis strain 16085/3b]
ATGACCATCGCTAAGAAAAAAACAACCTTTGTCTGTCAATCCTGCGAGTACCACTCGCCCAAGTATCTGGGCCGTTGCCC
CAACTGTGGCTCCTGGTCTAGCTTTGTCGAGGAAGTGGAAGTCGCTGAAGTCAAGAACGAGCGGGTCAGTCTGACAGGTG
AGAAGACCCGTCCTATGAAGCTCAATGAAGTGTCGTCCATTCAAGTGGCCCGCACCAAGACCAATATGGAAGAGTTTAAC
CGTGTCCTTGGTGGCGGCGTGGTGCCGGGCAGTCTGGTCCTGATTGGAGGCGATCCAGGGATTGGCAAATCGACCTTGCT
CCTGCAAGTATCGACCCAACTTTCGACTATTGGCACCGTCCTCTATGTGTCGGGGGAAGAGTCTGCCCAGCAGATTAAGT
TGCGAGCGGAGCGTTTGGGCGACATTGACAGCGAGTTCTATCTCTATGCGGAGACCAATATGCAGAGCATTCGGACTGAG
ATTGAGAAAATCAAGCCAGATTTCCTGATTATCGACTCTATCCAGACCATTATGAGCCCTGACATTTCTAGCGTGCAAGG
TTCTGTCAGTCAGGTCCGTGAAGTGACCAATGAGCTTATGCAGATTGCCAAGACCAACAATATCGCAACCTTTATCGTCG
GCCACATGACCAAGGAAGGCACCCTGGCTGGACCGCGGACCTTGGAGCACATGGTAGACACCGTTCTCTATTTTGAGGGC
GAGCGTCAACACACCTTCCGTATCTTGAGGGCGGTCAAAAATCGCTTTGGCTCCACCAACGAAATCGGTATTTTTGAAAT
GCAGTCGCAGGGCTTGGTCGAAGTTCTCAATCCAAGTGAGGTCTTTCTGGAAGAGCGTCTGGACGGAGCGACTGGCTCGG
CTATTGTCGTGACCATGGAGGGCACCCGCCCTATCCTTGCCGAAGTGCAGGCTCTGGTGACCCCGACCATGTTTGGCAAT
GCCAAGCGGACCACGACAGGCTTGGATTTCAACCGTGCCAGCTTGATTATGGCGGTTTTGGAAAAACGGGCCGGTCTGCT
CCTCCAAAACCAAGATGCCTACCTTAAGTCAGCAGGCGGTGTCAAACTGGATGAGCCAGCTATTGACCTAGCGGTCGCAG
TTGCCCTTGCCTCCAGTTACAAGGACAAGCCAACCAACCCACAAGAGTGCTTTATAGGCGAGATTGGCCTGACAGGGGAA
ATCCGCCGCGTCAATCGGATTGAACAACGGATTAACGAAGCCGCCAAATTGGGCTTTACCAAGGTCTATGCCCCAAAAAA
TTCCCTGACAGGTATCAAGGTGCCCAAGGAAATCACCGTTATCAGCGTGACCACCATTGGCGAAGTCTTGCAGAAAGTAT
TCAACTTATGA

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(363-427)

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(10-37)

AAA domain (AAA_25)

(64-220)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A126UJP8

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 NCTC 12261

91.15

99.123

0.904
  radA Streptococcus pneumoniae D39

90.929

99.123

0.901
  radA Streptococcus pneumoniae R6

90.929

99.123

0.901
  radA Streptococcus pneumoniae Rx1

90.929

99.123

0.901
  radA Streptococcus pneumoniae TIGR4

90.929

99.123

0.901
  radA Streptococcus mitis SK321

90.708

99.123

0.899
  radA Bacillus subtilis subsp. subtilis str. 168

62.472

99.342

0.621