Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 20 | 33 | 38.59 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PCHDJPAE_26 | 1815 | 2546 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 94.40 | 100.00 | WP_011227248 |
| PCHDJPAE_33 | 87002 | 87853 | rfbD | 0.0 | Capsule | Immune modulation | 94.25 | 100.00 | WP_014621820 |
| PCHDJPAE_26 | 1815 | 2546 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.72 | 100.00 | WP_011226048 |
| PCHDJPAE_26 | 1815 | 2546 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 93.44 | 100.00 | WP_011681176 |
| PCHDJPAE_33 | 83931 | 84740 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 92.85 | 99.88 | WP_002948020 |
| PCHDJPAE_33 | 79918 | 81674 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.60 | 98.43 | WP_011226325 |
| PCHDJPAE_33 | 82726 | 83931 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 92.37 | 100.00 | WP_011226326 |
| PCHDJPAE_33 | 84724 | 85680 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 91.85 | 100.00 | WP_011226328 |
| PCHDJPAE_33 | 85677 | 86825 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 91.57 | 99.83 | WP_041828290 |
| PCHDJPAE_53 | 82560 | 84218 | fbp54 | 0.0 | FBPs | Adherence | 91.14 | 99.94 | WP_011227179 |
| PCHDJPAE_26 | 354 | 1814 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 91.13 | 99.86 | WP_011681177 |
| PCHDJPAE_55 | 78581 | 79174 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| PCHDJPAE_33 | 81671 | 82705 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.00 | 99.15 | WP_002948022 |
| PCHDJPAE_55 | 78581 | 79174 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| PCHDJPAE_55 | 78581 | 79174 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| PCHDJPAE_26 | 354 | 1814 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.51 | 100.00 | WP_011226049 |
| PCHDJPAE_33 | 139951 | 140856 | cbpD | 0.0 | Autolysin | Exoenzyme | 89.96 | 93.50 | WP_082302295 |
| PCHDJPAE_26 | 2555 | 3247 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 89.90 | 100.00 | WP_011226047 |
| PCHDJPAE_26 | 354 | 1814 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 89.83 | 100.00 | WP_041827043 |
| PCHDJPAE_26 | 2555 | 3247 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011227247 |
| PCHDJPAE_26 | 2555 | 3247 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.47 | 100.00 | WP_011681175 |
| PCHDJPAE_57 | 33686 | 34989 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.47 | 99.54 | WP_000022832 |
| PCHDJPAE_44 | 14381 | 15394 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| PCHDJPAE_58 | 11255 | 12016 | srtA | 0.0 | Sortase A | Exoenzyme | 84.40 | 99.87 | - |
| PCHDJPAE_55 | 79444 | 80490 | rfbB | 0.0 | Capsule | Immune modulation | 83.49 | 99.90 | WP_002263087 |
| PCHDJPAE_16 | 27490 | 28773 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.84 | 99.61 | WP_000107753 |
| PCHDJPAE_55 | 77712 | 78581 | rfbA | 0.0 | Capsule | Immune modulation | 80.28 | 99.77 | WP_002904719 |
| PCHDJPAE_26 | 3257 | 3927 | STU_RS14635 | 1.17e-150 | Capsule | Immune modulation | 81.13 | 90.28 | WP_011226046 |
| PCHDJPAE_26 | 3257 | 3927 | STER_RS05305 | 5.45e-149 | Capsule | Immune modulation | 80.98 | 90.28 | WP_011681174 |
| PCHDJPAE_26 | 3257 | 3927 | STR_RS05250 | 5.53e-139 | Capsule | Immune modulation | 80.09 | 89.20 | WP_011227246 |
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 |
|---|---|---|---|---|---|---|---|---|
| PCHDJPAE_58 | 8566 | 7583 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| PCHDJPAE_58 | 20152 | 21225 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| PCHDJPAE_44 | 147584 | 145278 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.28 | 99.22 | AAK74619 |
| PCHDJPAE_22 | 88987 | 90468 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| PCHDJPAE_58 | 39213 | 41459 | metE | 0.0 | methionine biosynthesis enzymes | 92.66 | 100.00 | AAK74738 |
| PCHDJPAE_7 | 30858 | 31826 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| PCHDJPAE_9 | 922 | 1893 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| PCHDJPAE_55 | 52339 | 54069 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 90.12 | 100.00 | AAK34199 |
| PCHDJPAE_33 | 100029 | 98041 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.44 | 100.00 | AE014259_2 |
| PCHDJPAE_5 | 30011 | 31162 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.32 | 99.74 | AAL00050 |
| PCHDJPAE_10 | 29766 | 28288 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.63 | 100.00 | ADE32434 |
| PCHDJPAE_57 | 33686 | 34987 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| PCHDJPAE_10 | 14420 | 12528 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| PCHDJPAE_58 | 44381 | 42672 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| PCHDJPAE_9 | 35360 | 36451 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| PCHDJPAE_3 | 19783 | 20793 | pdh | 0.0 | pyruvate dehydrogenase | 83.38 | 99.70 | ABP91006 |
| PCHDJPAE_53 | 69044 | 70405 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.67 | 99.56 | ABP90420 |
| PCHDJPAE_57 | 19278 | 20168 | bglB | 7.91e-178 | putative phospho--glucosidase | 87.20 | 99.66 | AAK33487 |
| PCHDJPAE_8 | 13534 | 12584 | SP_0676 | 5.43e-171 | transcription facot | 81.39 | 98.45 | AAK74821 |
| PCHDJPAE_58 | 41649 | 42506 | metF | 3.09e-169 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| PCHDJPAE_13 | 1845 | 2549 | covR | 1.49e-127 | responder protein | 85.53 | 100.00 | AAK71319 |
| PCHDJPAE_22 | 22440 | 21769 | rr01 | 3.66e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| PCHDJPAE_58 | 48351 | 49022 | ciaR | 6.84e-126 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| PCHDJPAE_58 | 48351 | 49019 | CiaR | 1.26e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| PCHDJPAE_13 | 1845 | 2549 | walR | 3.38e-121 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| PCHDJPAE_11 | 137762 | 138448 | CovR | 4.19e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| PCHDJPAE_9 | 36624 | 37019 | SpxA2 | 3.68e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| PCHDJPAE_53 | 57587 | 57186 | SpxA1 | 8.14e-70 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| PCHDJPAE_56 | 86021 | 85608 | GrpE | 6.48e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| PCHDJPAE_11 | 160971 | 161258 | spr0479 | 5.07e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| PCHDJPAE_17 | 20954 | 21208 | spr1327 | 1.08e-44 | essential gene | 90.59 | 100.00 | AAL00131 |
| PCHDJPAE_15 | 1215 | 952 | spr0175 | 1.60e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| PCHDJPAE_15 | 390 | 124 | spr0177 | 3.56e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| PCHDJPAE_16 | 27323 | 26832 | RopE (M5005_Spy_1611) | 1.43e-73 | probable DNA-directed RNA polymerase subunit delta | 83.54 | 85.86 | AAK34603 |
| PCHDJPAE_44 | 147584 | 145284 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 82.97 | 98.08 | MYN69560 |
| PCHDJPAE_24 | 9484 | 10503 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 85.88 | 100.00 | ABJ55451 |
| PCHDJPAE_53 | 98046 | 97507 | pnuC | 1.67e-94 | NAD salvage pathway importer | 83.89 | 66.91 | AAK75931 |
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 |
|---|---|---|---|
| PCHDJPAE_1 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_2 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_3 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_4 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_5 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_6 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_7 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_8 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_9 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_10 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_11 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_12 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_13 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_14 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_15 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_16 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_17 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_18 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_19 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_20 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_21 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_22 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_23 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_24 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_25 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_26 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_27 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_28 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_29 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_30 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_31 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_32 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_33 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_34 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_35 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_36 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_37 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_39 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_40 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_41 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_42 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_44 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_45 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_46 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_47 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_48 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_49 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_50 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_51 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_52 | 1.0 | 0.0 | 1.0 |
| PCHDJPAE_53 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_54 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_55 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_56 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_57 | 0.0 | 1.0 | 0.0 |
| PCHDJPAE_58 | 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)