Table 2 Details of MGEs detected from the human oral metagenome by IPCR
Sample name (Accession number) | Primer pair | Size (bp) | BlastN | BlastX | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Closest homologue | Percentage identity (%) | Coverage (%) | Accession number of the homologous DNA (BlastN) | Closest homologue | ORF size (bp) | Percentage identity (%) | Coverage (%) | Position on sample | Accession number of the homologous proteins (BlastX) | |||
Flip-MARS-3 (OL695865) | MARS2-MARS5 | 1824 | Uncultured bacterium clone MMU-PRO-6 gene cassette | 91 | 38 | MH536761.1 | Restriction endonuclease [Treponema sp.] | 852 | 55 | 99.6 | 211–1062 | MBO6220054.1 |
Flip-MARS-4 (OL695866) | MARS2-MARS5 | 2355 | Treponema sp. OMZ 804 chromosome, complete genome | 91.9 | 42 | CP048020.1 | No significant similarity found | 387 | – | – | 67–453 | – |
Type II toxin-antitoxin system RelE/ParE family toxin [Treponema succinifaciens] | 360 | 95 | 100 | 611–970 | WP_162664812.1 | |||||||
Helix-turn-helix transcriptional regulator [Treponema sp.] | 288 | 96 | 100 | 960–1247 | MBP5436565.1 | |||||||
HNH endonuclease [Treponema sp. OMZ 804] | 348 | 91 | 100 | 1357–1704 | WP_162663704.1 | |||||||
DUF697 domain-containing protein [Treponema sp. OMZ 804] | 585 | 95 | 100 | 1744–2328 | WP_162664812.1 | |||||||
Flip-MARS-5 (OL695867) | MARS2-MARS5 | 1704 | Treponema sp. OMZ 838, complete genome | 95 | 45 | CP009227.1 | Hypothetical protein [Treponema pedis] | 609 | 91 | 100 | 116–724 | WP_024468093.1 |
Type II toxin-antitoxin system prevent-host-death family antitoxin [Treponema] | 246 | 96 | 98.8 | 1110–1355 | WP_002690260.1 | |||||||
Type II toxin-antitoxin system RelE/ParE family toxin [Treponema medium] | 321 | 95 | 100 | 1355–1675 | WP_016522547.1 | |||||||
Flip-MARS-9 (OL695868) | MARS2-MARS5 | 1912 | Treponema denticola ATCC 35,405, complete genome | 94.4 | 53 | AE017226.1 | Hypothetical protein [Treponema sp. OMZ 804] | 774 | 91 | 100 | 75–848 | WP_162662615.1 |
Carbon–nitrogen hydrolase family protein [Treponema denticola] | 894 | 98 | 100 | 998–1891 | WP_187115772.1 | |||||||
Flip-MARS-11 (OL695869) | MARS2-MARS5 | 2890 | Uncultured bacterium clone SSU24 gene cassette SSU24.1 genomic sequence | 99 | 33 | KT921490.1 | Vicinal oxygen chelate (VOC) family protein [Treponema denticola] | 393 | 100 | 100 | 68–460 | WP_002683256.1 |
Competence protein TfoX [uncultured bacterium] | 222 | 100 | 100 | 629–850 | ANC55521.1 | |||||||
IS4 family transposase [Treponema sp.] | 909 | 66 | 99 | 1630–2538 | MBR1911588.1 | |||||||
IS431-5 (OL695870) | IS431-Inverse-F-IS431-inverse-R | 1735 | Staphylococcus capitis strain FDAARGOS_753 chromosome | 91 | 100 | CP053957.1 | No significant similarity found | 345 | – | – | 591–247 | – |
Hypothetical protein [Staphylococcus epidermidis] | 465 | 89 | 100 | 1299–835 | MBE0334850.1 | |||||||
tet(M)-1 (OL695871) | tet(M)-inverse-F- tet(M)-inverse-R | 5054 | Neisseria sicca ATCC 29,256 chromosome | 98 | 100 | CP079820.1 | Murein transglycosylase A [unclassified Neisseria] | 1323 | 99 | 100 | 901–2223 | WP_070606572.1 |
Hypothetical protein | 711 | 100 | 100 | 3456–2746 | WP_070606574.1 | |||||||
Holliday junction branch migration protein RuvA [unclassified Neisseria] | 585 | 100 | 100 | 4342–3758 | WP_070606583.1 | |||||||
tet(M)-2 (OL695872) | tet(M)-inverse-F- tet(M)-inverse-R | 2456 | Streptococcus agalactiae strain GBS6 | 99.6 | 85 | CP007572.1 | Hypothetical protein [Streptococcus pneumoniae] | 195 | 98 | 100 | 901–1095 | CDO19408.1 |
Hypothetical protein AZK08_11845, partial [Streptococcus pneumoniae] | 180 | 100 | 98.3 | 1629–1450 | TXL69036.1 | |||||||
IS21-like element helper ATPase IstB [Streptococcus parasanguinis] | 315 | 100 | 39.8 | 2009–1695 | WP_101770904.1 | |||||||
tet(M)-6 (OL695873) | tet(M)-inverse-F- tet(M)-inverse-R | 4683 | Streptococcus pneumoniae integrative and conjugative element ICESpnIC1, isolate 9611 + 04,103 | 100 | 100 | HG799494.1 | Hypothetical protein [Streptococcus pneumoniae] | 195 | 98 | 100 | 901–1095 | CDO19408.1 |
Hypothetical protein HMPREF1885_00780 [Streptococcus agalactiae] | 364 | 99 | 100 | 1815–1450 | KXA59032.1 | |||||||
23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) [Streptococcus] | 738 | 100 | 100 | 1916–2653 | AYK27796.1 | |||||||
Resolvase [Streptococcus pneumoniae] | 555 | 99 | 100 | 3008–3562 | VSD99176.1 | |||||||
Tn3 family transposase [Enterococcus faecalis] | 671 | 99 | 74.8 | 3566–4236 | EGO7700322.1 | |||||||
tet(M)-9 (OL695874) | tet(M)-inverse-F- tet(M)-inverse-R | 2329 | Streptococcus pneumoniae integrative and conjugative element ICE6BST90, isolate IC161 | 99.8 | 100 | HG799499.1 | Conjugal transfer protein [Streptococcus agalactiae] | 186 | 95 | 100 | 910–1095 | KAF1190941.1 |
Helix-turn-helix transcriptional regulator [Bacteria] (orf9 Tn916) | 354 | 100 | 100 | 1508–1155 | WP_001227347.1 | |||||||
xis-int-9 (OL695875) | xis-int-inverse-F-xis-int-inverse-R | 3704 | Streptococcus pneumoniae strain 080,217 transposon Tn6822 | 90 | 100 | MT489699.1 | MFS transporter [Streptococcus sp. ZB199] | 230 | 95 | 40.3 | 1134–905 | QWL83132.1 |
Cysteine-rich KTR domain-containing protein [Bacteria] | 192 | 98 | 100 | 1258–1449 | WP_001860868.1 | |||||||
Helix-turn-helix transcriptional regulator [Bacteria] (orf9 Tn916) | 354 | 100 | 100 | 1862–1509 | WP_001227347.1 | |||||||
Conserved hypothetical protein [Streptococcus pneumoniae] (orf10 Tn916) | 147 | 100 | 100 | 1992–2138 | ACA36714.1 | |||||||
Sigma-70 family RNA polymerase sigma factor [Streptococcus] (orf7 Tn916) | 423 | 99 | 100 | 2367–2789 | WP_196313264.1 | |||||||
Helix-turn-helix domain [Bacteria] (orf8 Tn916) | 231 | 100 | 100 | 2786–3016 | WP_000857133.1 | |||||||
Hypothetical protein [Firmicutes] (orf5 Tn916) | 252 | 100 | 100 | 3493–3242 | WP_001845478.1 | |||||||