Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 18 | 34 | 38.52 |
PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).
Antibiotic resistance genes
Comprehensive Antibiotic Resistance Database (CARD)
| Query ID | Begin | End | ARO name | ARO accession | CARD name | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)
ResFinder
| Query ID | Begin | End | Resistance gene | Phenotype | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|
| LJOLFEFE_211 | 8860 | 10323 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | AF274302 |
| LJOLFEFE_211 | 10443 | 11660 | mef(A) | Erythromycin, Azithromycin | 99.92 | 100.00 | U83667 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| LJOLFEFE_211 | 10446 | 11660 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| LJOLFEFE_211 | 8863 | 10323 | msr(D) | ABC-F type ribosomal protection protein Msr(D) | EXACTX | 100.00 | 100.00 | WP_000420313.1 |
AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)
Virulence factors
Virulence Factor Database (VFDB)
| Query ID | qstart | qend | Gene name | e-value | VF name | VF category | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|---|
| LJOLFEFE_1 | 183207 | 184667 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 97.06 | 100.00 | WP_011681177 |
| LJOLFEFE_1 | 183207 | 184667 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 96.72 | 100.21 | WP_011226049 |
| LJOLFEFE_255 | 65682 | 66397 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 96.37 | 99.86 | WP_011681442 |
| LJOLFEFE_1 | 183207 | 184667 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 96.17 | 100.21 | WP_041827043 |
| LJOLFEFE_1 | 179602 | 180967 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 95.24 | 99.85 | WP_011681173 |
| LJOLFEFE_255 | 68821 | 69672 | rfbD | 0.0 | Capsule | Immune modulation | 95.07 | 100.00 | WP_014621820 |
| LJOLFEFE_1 | 179600 | 180967 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.30 | 100.00 | WP_011226045 |
| LJOLFEFE_365 | 73952 | 74545 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 94.11 | 100.00 | WP_011226149 |
| LJOLFEFE_365 | 73952 | 74545 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 93.94 | 100.00 | WP_011226149 |
| LJOLFEFE_365 | 73952 | 74545 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 93.94 | 100.00 | WP_011226149 |
| LJOLFEFE_1 | 181024 | 181764 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 93.79 | 100.00 | WP_011681174 |
| LJOLFEFE_1 | 181024 | 181764 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 93.12 | 100.00 | WP_011226046 |
| LJOLFEFE_255 | 64566 | 65336 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 93.00 | 99.10 | WP_011681440 |
| LJOLFEFE_1 | 181029 | 181764 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 92.53 | 98.13 | WP_011227246 |
| LJOLFEFE_255 | 67444 | 68702 | STER_RS07100 | 0.0 | Capsule | Immune modulation | 92.22 | 99.92 | WP_011681445 |
| LJOLFEFE_1 | 182475 | 183206 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 92.08 | 100.00 | WP_011226048 |
| LJOLFEFE_1 | 182475 | 183206 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.67 | 100.00 | WP_011681176 |
| LJOLFEFE_1 | 65642 | 67300 | fbp54 | 0.0 | FBPs | Adherence | 91.20 | 99.94 | WP_011227179 |
| LJOLFEFE_1 | 182475 | 183206 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 91.12 | 100.00 | WP_011227248 |
| LJOLFEFE_365 | 73083 | 73952 | rfbA | 0.0 | Capsule | Immune modulation | 90.92 | 100.00 | WP_011681286 |
| LJOLFEFE_1 | 181774 | 182466 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.92 | 99.71 | WP_011227247 |
| LJOLFEFE_1 | 181774 | 182466 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.92 | 99.71 | WP_011226047 |
| LJOLFEFE_388 | 14267 | 15277 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.45 | 99.80 | WP_002986042 |
| LJOLFEFE_256 | 19024 | 19863 | cbpD | 0.0 | Autolysin | Exoenzyme | 88.35 | 99.88 | WP_011226733 |
| LJOLFEFE_211 | 31198 | 32501 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.17 | 99.54 | WP_000022832 |
| LJOLFEFE_1 | 181774 | 182466 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 87.05 | 99.71 | WP_011681175 |
| LJOLFEFE_1027 | 3804 | 4565 | srtA | 0.0 | Sortase A | Exoenzyme | 83.90 | 99.74 | - |
| LJOLFEFE_365 | 74817 | 75863 | rfbB | 0.0 | Capsule | Immune modulation | 81.51 | 99.90 | WP_009659423 |
| LJOLFEFE_476 | 131038 | 132321 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.92 | 99.61 | WP_000107753 |
BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)
VirulenceFinder
| Query ID | Begin | End | Database | Virulence factor | Protein function | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)
Pathogenic genes
PHI-base
| Query ID | qstart | qend | Gene name | e-value | Function | Identity | Coverage | Gene ID |
|---|---|---|---|---|---|---|---|---|
| LJOLFEFE_1027 | 12696 | 13769 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| LJOLFEFE_1027 | 1115 | 141 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.00 | 99.09 | AAK75326 |
| LJOLFEFE_696 | 87728 | 85422 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.54 | 99.22 | AAK74619 |
| LJOLFEFE_586 | 84679 | 83198 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 92.92 | 100.00 | ABJ54480 |
| LJOLFEFE_366 | 12652 | 11684 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| LJOLFEFE_1027 | 31755 | 34001 | metE | 0.0 | methionine biosynthesis enzymes | 92.12 | 100.00 | AAK74738 |
| LJOLFEFE_488 | 2 | 6214 | PrtA | 0.0 | serine protease | 91.51 | 96.55 | ABJ55268 |
| LJOLFEFE_256 | 4322 | 5293 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.36 | 100.00 | ABF36968 |
| LJOLFEFE_365 | 42183 | 43913 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.78 | 100.00 | AAK34199 |
| LJOLFEFE_255 | 82079 | 80091 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.59 | 100.00 | AE014259_2 |
| LJOLFEFE_255 | 110485 | 109334 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| LJOLFEFE_189 | 36974 | 35496 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.42 | 100.00 | ADE32434 |
| LJOLFEFE_211 | 32501 | 31200 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| LJOLFEFE_189 | 21630 | 19738 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.26 | 98.90 | ABP91129 |
| LJOLFEFE_1027 | 36923 | 35214 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| LJOLFEFE_256 | 41841 | 42932 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| LJOLFEFE_178 | 28548 | 29558 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| LJOLFEFE_1 | 92523 | 91162 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.67 | 99.56 | ABP90420 |
| LJOLFEFE_211 | 46910 | 46020 | bglB | 3.11e-178 | putative phospho--glucosidase | 87.54 | 99.66 | AAK33487 |
| LJOLFEFE_1 | 3486 | 2536 | SP_0676 | 3.21e-170 | transcription facot | 81.39 | 98.45 | AAK74821 |
| LJOLFEFE_1027 | 34191 | 35048 | metF | 3.16e-169 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| LJOLFEFE_300 | 403 | 1107 | covR | 1.26e-127 | responder protein | 85.53 | 100.00 | AAK71319 |
| LJOLFEFE_289 | 15405 | 16076 | rr01 | 2.36e-127 | response regulator | 84.38 | 99.56 | CAB54566 |
| LJOLFEFE_1027 | 41587 | 42255 | CiaR | 2.53e-125 | two-component response regulator | 87.00 | 99.55 | AAK74935 |
| LJOLFEFE_1027 | 41587 | 42258 | ciaR | 2.51e-124 | two component system response regulator | 85.27 | 99.12 | AIK75708 |
| LJOLFEFE_300 | 403 | 1107 | walR | 2.87e-121 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| LJOLFEFE_807 | 53782 | 53096 | CovR | 1.77e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| LJOLFEFE_256 | 43108 | 43503 | SpxA2 | 4.30e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| LJOLFEFE_1 | 103991 | 104392 | SpxA1 | 4.14e-70 | transcriptional regulator | 82.84 | 100.00 | ERL19273 |
| LJOLFEFE_432 | 6266 | 5853 | GrpE | 1.24e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| LJOLFEFE_807 | 30575 | 30288 | spr0479 | 2.02e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| LJOLFEFE_113 | 30382 | 30636 | spr1327 | 2.97e-45 | essential gene | 92.94 | 100.00 | AAL00131 |
| LJOLFEFE_916 | 53764 | 54027 | spr0175 | 3.81e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| LJOLFEFE_916 | 54590 | 54856 | spr0177 | 6.63e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| LJOLFEFE_476 | 130871 | 130380 | RopE (M5005_Spy_1611) | 6.51e-73 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| LJOLFEFE_696 | 87728 | 85428 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.22 | 98.08 | MYN69560 |
| LJOLFEFE_916 | 1216 | 197 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 97.35 | 100.00 | ABJ55451 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LJOLFEFE_1 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_2 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_113 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_167 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_178 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_189 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_200 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_211 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_222 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_233 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_244 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_255 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_256 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_267 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_278 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_289 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_300 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_311 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_322 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_332 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_343 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_354 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_365 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_366 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_377 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_388 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_399 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_410 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_421 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_432 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_443 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_454 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_476 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_477 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_488 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_499 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_520 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_531 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_542 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_553 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_564 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_575 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_586 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_587 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_598 | 1.0 | 0.0 | 1.0 |
| LJOLFEFE_696 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_807 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_916 | 0.0 | 1.0 | 0.0 |
| LJOLFEFE_1027 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| No hit found | |||||
Phigaro v2.4.0 (Database: Jan. 2024 release)