Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 16 | 36 | 39.40 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| JOHDHDGE_11 | 181294 | 182025 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 94.54 | 100.00 | WP_011227248 |
| JOHDHDGE_44 | 23795 | 24511 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 94.42 | 100.00 | WP_011681442 |
| JOHDHDGE_44 | 20219 | 21070 | rfbD | 0.0 | Capsule | Immune modulation | 94.37 | 100.00 | WP_014621820 |
| JOHDHDGE_11 | 181294 | 182025 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.85 | 100.00 | WP_011226048 |
| JOHDHDGE_11 | 181294 | 182025 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 93.58 | 100.00 | WP_011681176 |
| JOHDHDGE_44 | 24857 | 25627 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 92.35 | 99.23 | WP_011681440 |
| JOHDHDGE_11 | 182026 | 183486 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 91.26 | 99.86 | WP_011681177 |
| JOHDHDGE_6 | 7699 | 8292 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| JOHDHDGE_6 | 7699 | 8292 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| JOHDHDGE_6 | 7699 | 8292 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| JOHDHDGE_11 | 182026 | 183486 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.65 | 100.00 | WP_011226049 |
| JOHDHDGE_11 | 79117 | 80774 | fbp54 | 0.0 | FBPs | Adherence | 90.30 | 99.88 | WP_011227179 |
| JOHDHDGE_11 | 182026 | 183486 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 89.97 | 100.00 | WP_041827043 |
| JOHDHDGE_11 | 180593 | 181285 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 89.90 | 100.00 | WP_011226047 |
| JOHDHDGE_11 | 180593 | 181285 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011227247 |
| JOHDHDGE_11 | 180593 | 181285 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.47 | 100.00 | WP_011681175 |
| JOHDHDGE_4 | 38085 | 39388 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| JOHDHDGE_88 | 12513 | 13352 | cbpD | 0.0 | Autolysin | Exoenzyme | 87.87 | 99.88 | WP_011226733 |
| JOHDHDGE_13 | 16189 | 17202 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| JOHDHDGE_22 | 80693 | 81454 | srtA | 0.0 | Sortase A | Exoenzyme | 84.40 | 99.87 | - |
| JOHDHDGE_6 | 6383 | 7429 | rfbB | 0.0 | Capsule | Immune modulation | 83.59 | 99.90 | WP_002263087 |
| JOHDHDGE_20 | 8443 | 9726 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.76 | 99.61 | WP_000107753 |
| JOHDHDGE_6 | 8292 | 9161 | rfbA | 0.0 | Capsule | Immune modulation | 80.28 | 99.77 | WP_002904719 |
| JOHDHDGE_11 | 179913 | 180583 | STU_RS14635 | 2.96e-149 | Capsule | Immune modulation | 81.13 | 90.28 | WP_011226046 |
| JOHDHDGE_11 | 179913 | 180583 | STER_RS05305 | 1.38e-147 | Capsule | Immune modulation | 80.98 | 90.28 | WP_011681174 |
| JOHDHDGE_11 | 179913 | 180583 | STR_RS05250 | 1.40e-137 | 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 |
|---|---|---|---|---|---|---|---|---|
| JOHDHDGE_22 | 84143 | 85126 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| JOHDHDGE_22 | 72555 | 71482 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| JOHDHDGE_55 | 119137 | 121443 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| JOHDHDGE_3 | 26876 | 27844 | spr0084 | 0.0 | pathogenitcity related | 93.19 | 98.48 | AAK98888 |
| JOHDHDGE_77 | 5782 | 7263 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 92.92 | 100.00 | ABJ54480 |
| JOHDHDGE_22 | 53495 | 51249 | metE | 0.0 | methionine biosynthesis enzymes | 92.66 | 100.00 | AAK74738 |
| JOHDHDGE_22 | 133096 | 126623 | PrtA | 0.0 | serine protease | 91.48 | 100.61 | ABJ55268 |
| JOHDHDGE_9 | 4974 | 5945 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.36 | 100.00 | ABF36968 |
| JOHDHDGE_6 | 34537 | 32807 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| JOHDHDGE_44 | 5086 | 7074 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.74 | 100.00 | AE014259_2 |
| JOHDHDGE_5 | 25708 | 24557 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| JOHDHDGE_10 | 29517 | 28039 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| JOHDHDGE_4 | 39388 | 38087 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| JOHDHDGE_10 | 14176 | 12284 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| JOHDHDGE_22 | 48331 | 50040 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| JOHDHDGE_9 | 38060 | 39151 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| JOHDHDGE_11 | 94536 | 93175 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.89 | 99.56 | ABP90420 |
| JOHDHDGE_66 | 19904 | 20914 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| JOHDHDGE_4 | 53794 | 52904 | bglB | 7.62e-179 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| JOHDHDGE_22 | 8362 | 9312 | SP_0676 | 2.74e-170 | transcription facot | 81.39 | 98.45 | AAK74821 |
| JOHDHDGE_22 | 51059 | 50202 | metF | 8.05e-169 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| JOHDHDGE_87 | 18644 | 19501 | mtsA | 2.56e-152 | substrate-binding lipoprotein of manganese transporter | 80.49 | 92.86 | AIK76191 |
| JOHDHDGE_44 | 20219 | 21040 | GacA | 2.97e-147 | dTDP-4-dehydrorhamnose reductas | 80.29 | 96.48 | AAZ51220 |
| JOHDHDGE_22 | 150951 | 150280 | rr01 | 3.99e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| JOHDHDGE_11 | 215794 | 215090 | covR | 1.47e-126 | responder protein | 85.53 | 100.00 | AAK71319 |
| JOHDHDGE_22 | 43666 | 42995 | ciaR | 1.78e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| JOHDHDGE_22 | 43666 | 42998 | CiaR | 3.29e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| JOHDHDGE_33 | 53873 | 53187 | CovR | 1.48e-120 | serves to repress GAS virulence factor-encoding genes | 82.10 | 100.00 | ACE75886 |
| JOHDHDGE_11 | 215794 | 215090 | walR | 1.31e-119 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| JOHDHDGE_9 | 39324 | 39719 | SpxA2 | 3.92e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| JOHDHDGE_11 | 105993 | 106394 | SpxA1 | 1.48e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| JOHDHDGE_7 | 45912 | 46325 | GrpE | 4.07e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| JOHDHDGE_33 | 30666 | 30379 | spr0479 | 4.69e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| JOHDHDGE_15 | 4876 | 4622 | spr1327 | 1.52e-45 | essential gene | 91.77 | 100.00 | AAL00131 |
| JOHDHDGE_66 | 110688 | 110951 | spr0175 | 5.78e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| JOHDHDGE_66 | 111513 | 111779 | spr0177 | 1.28e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| JOHDHDGE_20 | 8276 | 7785 | RopE (M5005_Spy_1611) | 5.08e-74 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| JOHDHDGE_55 | 119137 | 121437 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.22 | 98.08 | MYN69560 |
| JOHDHDGE_66 | 56044 | 55025 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 85.88 | 100.00 | ABJ55451 |
| JOHDHDGE_11 | 66131 | 66670 | pnuC | 1.28e-98 | NAD salvage pathway importer | 88.89 | 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 |
|---|---|---|---|
| JOHDHDGE_1 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_2 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_3 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_4 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_5 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_6 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_7 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_8 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_9 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_10 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_11 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_12 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_13 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_14 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_15 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_16 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_17 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_18 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_19 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_20 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_21 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_22 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_24 | 1.0 | 0.0 | 1.0 |
| JOHDHDGE_26 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_28 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_30 | 1.0 | 0.0 | 1.0 |
| JOHDHDGE_31 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_33 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_44 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_55 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_66 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_77 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_87 | 0.0 | 1.0 | 0.0 |
| JOHDHDGE_88 | 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)