Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 22 | 33 | 39.66 |
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. |
|---|---|---|---|---|---|---|---|
| No hit found | |||||||
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
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. |
|---|---|---|---|---|---|---|---|---|---|
| PCLDDPFM_7 | 73589 | 74398 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 95.68 | 100.00 | WP_002948020 |
| PCLDDPFM_2 | 1015185 | 1016550 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 95.61 | 99.85 | WP_011681173 |
| PCLDDPFM_2 | 1015185 | 1016552 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 95.10 | 100.00 | WP_011226045 |
| PCLDDPFM_7 | 77744 | 78595 | rfbD | 0.0 | Capsule | Immune modulation | 94.48 | 100.00 | WP_014621820 |
| PCLDDPFM_2 | 1014388 | 1015128 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 94.20 | 100.00 | WP_011681174 |
| PCLDDPFM_2 | 1011485 | 1012945 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 93.98 | 100.00 | WP_011681177 |
| PCLDDPFM_2 | 1011485 | 1012945 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 93.84 | 100.14 | WP_011226049 |
| PCLDDPFM_2 | 1014388 | 1015128 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 93.66 | 100.00 | WP_011226046 |
| PCLDDPFM_2 | 1011485 | 1012945 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.22 | 100.14 | WP_041827043 |
| PCLDDPFM_2 | 1014388 | 1015123 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 93.21 | 98.13 | WP_011227246 |
| PCLDDPFM_7 | 69548 | 71332 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.94 | 100.00 | WP_011226325 |
| PCLDDPFM_2 | 1012946 | 1013677 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 92.35 | 100.00 | WP_011226048 |
| PCLDDPFM_7 | 72384 | 73589 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 92.21 | 100.00 | WP_011226326 |
| PCLDDPFM_2 | 844453 | 845046 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.92 | 100.00 | WP_011226149 |
| PCLDDPFM_7 | 75335 | 76483 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 91.91 | 100.00 | WP_041828290 |
| PCLDDPFM_2 | 844453 | 845046 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 91.75 | 100.00 | WP_011226149 |
| PCLDDPFM_2 | 844453 | 845046 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 91.75 | 100.00 | WP_011226149 |
| PCLDDPFM_2 | 1012946 | 1013677 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.67 | 100.00 | WP_011681176 |
| PCLDDPFM_7 | 71329 | 72363 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.67 | 99.05 | WP_002948022 |
| PCLDDPFM_7 | 74382 | 75338 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 91.64 | 100.00 | WP_011226328 |
| PCLDDPFM_2 | 843584 | 844453 | rfbA | 0.0 | Capsule | Immune modulation | 91.49 | 100.00 | WP_011681286 |
| PCLDDPFM_2 | 1012946 | 1013677 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 91.39 | 100.00 | WP_011227248 |
| PCLDDPFM_2 | 1133455 | 1135113 | fbp54 | 0.0 | FBPs | Adherence | 91.08 | 99.94 | WP_011227179 |
| PCLDDPFM_2 | 1013686 | 1014378 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.91 | 99.86 | WP_011227247 |
| PCLDDPFM_2 | 1013686 | 1014378 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.91 | 99.86 | WP_011226047 |
| PCLDDPFM_7 | 416551 | 417561 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.65 | 99.80 | WP_002986042 |
| PCLDDPFM_2 | 658121 | 659424 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.40 | 99.54 | WP_000022832 |
| PCLDDPFM_2 | 38630 | 39469 | cbpD | 0.0 | Autolysin | Exoenzyme | 87.87 | 99.88 | WP_011226733 |
| PCLDDPFM_2 | 1013686 | 1014378 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 87.18 | 99.86 | WP_011681175 |
| PCLDDPFM_2 | 845248 | 846294 | rfbB | 0.0 | Capsule | Immune modulation | 84.06 | 99.90 | WP_002263087 |
| PCLDDPFM_2 | 1277863 | 1278624 | srtA | 0.0 | Sortase A | Exoenzyme | 83.77 | 99.74 | - |
| PCLDDPFM_2 | 154837 | 156120 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.76 | 99.61 | WP_000107753 |
| PCLDDPFM_2 | 1027382 | 1027965 | SPD_RS01775 | 4.06e-150 | Capsule | Immune modulation | 83.42 | 96.20 | WP_001819836 |
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 |
|---|---|---|---|---|---|---|---|---|
| PCLDDPFM_2 | 1281311 | 1282294 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| PCLDDPFM_2 | 1269733 | 1268660 | MntE | 0.0 | manganese homeostasis | 95.53 | 99.72 | ABF32167 |
| PCLDDPFM_7 | 287977 | 290283 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| PCLDDPFM_2 | 1387595 | 1389076 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| PCLDDPFM_2 | 1250677 | 1248431 | metE | 0.0 | methionine biosynthesis enzymes | 92.66 | 100.00 | AAK74738 |
| PCLDDPFM_2 | 551761 | 552729 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| PCLDDPFM_2 | 23440 | 24411 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| PCLDDPFM_2 | 818202 | 819932 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| PCLDDPFM_7 | 92031 | 90043 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.74 | 100.00 | AE014259_2 |
| PCLDDPFM_7 | 128064 | 126913 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.32 | 99.74 | AAL00050 |
| PCLDDPFM_7 | 605082 | 603604 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.63 | 100.00 | ADE32434 |
| PCLDDPFM_2 | 658121 | 659422 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| PCLDDPFM_7 | 589762 | 587870 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.10 | 98.90 | ABP91129 |
| PCLDDPFM_2 | 1245510 | 1247219 | PGM | 0.0 | phosphoglucomutase | 84.94 | 99.65 | ACH87041 |
| PCLDDPFM_2 | 61920 | 63011 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| PCLDDPFM_7 | 468953 | 469963 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| PCLDDPFM_2 | 1108132 | 1109493 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.24 | 99.56 | ABP90420 |
| PCLDDPFM_2 | 643711 | 644601 | bglB | 1.53e-177 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| PCLDDPFM_2 | 1204611 | 1205561 | SP_0676 | 2.38e-169 | transcription facot | 81.39 | 98.45 | AAK74821 |
| PCLDDPFM_2 | 1248241 | 1247384 | metF | 1.18e-167 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| PCLDDPFM_2 | 968427 | 969131 | covR | 3.39e-131 | responder protein | 85.53 | 100.00 | AAK71319 |
| PCLDDPFM_2 | 1344200 | 1343529 | rr01 | 1.01e-126 | response regulator | 85.27 | 99.56 | CAB54566 |
| PCLDDPFM_2 | 1241542 | 1240871 | ciaR | 1.43e-124 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| PCLDDPFM_2 | 1241542 | 1240874 | CiaR | 2.64e-124 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| PCLDDPFM_2 | 968427 | 969131 | walR | 2.12e-121 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| PCLDDPFM_2 | 313920 | 314606 | CovR | 3.26e-119 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| PCLDDPFM_2 | 63187 | 63582 | SpxA2 | 1.47e-74 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| PCLDDPFM_2 | 1096663 | 1096262 | SpxA1 | 1.65e-68 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| PCLDDPFM_2 | 134993 | 135406 | GrpE | 2.74e-66 | protein grpE | 81.16 | 80.59 | ABP89267 |
| PCLDDPFM_2 | 337132 | 337419 | spr0479 | 3.94e-47 | essential gene | 85.42 | 98.97 | AAK99283 |
| PCLDDPFM_2 | 517660 | 517914 | spr1327 | 7.61e-44 | essential gene | 92.94 | 100.00 | AAL00131 |
| PCLDDPFM_7 | 557342 | 557605 | spr0175 | 3.48e-42 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| PCLDDPFM_7 | 558168 | 558434 | spr0177 | 4.86e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| PCLDDPFM_2 | 156287 | 156778 | RopE (M5005_Spy_1611) | 7.21e-72 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| PCLDDPFM_7 | 287977 | 290277 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| PCLDDPFM_7 | 504073 | 503054 | 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 |
|---|---|---|---|
| PCLDDPFM_1 | 1.0 | 0.0 | 1.0 |
| PCLDDPFM_2 | 0.0 | 1.0 | 0.0 |
| PCLDDPFM_3 | 1.0 | 0.0 | 1.0 |
| PCLDDPFM_4 | 0.0 | 1.0 | 0.0 |
| PCLDDPFM_5 | 1.0 | 0.0 | 1.0 |
| PCLDDPFM_6 | 1.0 | 0.0 | 1.0 |
| PCLDDPFM_7 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PCLDDPFM_2 | 634140 | 637438 | False | Unknown | VOG0198, VOG0189, VOG4566, VOG8336, VOG8353 |
Phigaro v2.4.0 (Database: Jan. 2024 release)