Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 24 | 30 | 38.42 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PDOKEKDG_1 | 1603078 | 1603929 | rfbD | 0.0 | Capsule | Immune modulation | 95.19 | 100.00 | WP_014621820 |
| PDOKEKDG_1 | 983403 | 984143 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 95.01 | 100.00 | WP_011681174 |
| PDOKEKDG_1 | 983403 | 984143 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 94.33 | 100.00 | WP_011226046 |
| PDOKEKDG_1 | 980500 | 981960 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 94.11 | 100.14 | WP_011226049 |
| PDOKEKDG_1 | 980500 | 981960 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 94.05 | 99.93 | WP_011681177 |
| PDOKEKDG_1 | 984200 | 985567 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.01 | 100.00 | WP_011226045 |
| PDOKEKDG_1 | 983403 | 984138 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 93.75 | 98.13 | WP_011227246 |
| PDOKEKDG_1 | 1600706 | 1601977 | STU_RS16265 | 0.0 | Capsule | Immune modulation | 93.71 | 99.76 | WP_011226331 |
| PDOKEKDG_1 | 984200 | 985565 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 93.70 | 99.85 | WP_011681173 |
| PDOKEKDG_1 | 1599748 | 1600703 | STU_RS16260 | 0.0 | Capsule | Immune modulation | 93.41 | 94.56 | WP_011226330 |
| PDOKEKDG_1 | 980500 | 981960 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.22 | 100.14 | WP_041827043 |
| PDOKEKDG_1 | 1591096 | 1592880 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.61 | 99.94 | WP_011226325 |
| PDOKEKDG_1 | 1595930 | 1596886 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 92.48 | 100.00 | WP_011226328 |
| PDOKEKDG_1 | 1596883 | 1598031 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 92.34 | 100.00 | WP_041828290 |
| PDOKEKDG_1 | 1595137 | 1595946 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 92.23 | 99.88 | WP_002948020 |
| PDOKEKDG_1 | 1593932 | 1595137 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 92.12 | 100.00 | WP_011226326 |
| PDOKEKDG_1 | 981961 | 982692 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 91.53 | 100.00 | WP_011226048 |
| PDOKEKDG_1 | 1592877 | 1593911 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.29 | 99.15 | WP_002948022 |
| PDOKEKDG_1 | 981961 | 982692 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.12 | 100.00 | WP_011681176 |
| PDOKEKDG_1 | 635715 | 636308 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| PDOKEKDG_1 | 2160720 | 2161559 | cbpD | 0.0 | Autolysin | Exoenzyme | 90.95 | 100.00 | WP_011226733 |
| PDOKEKDG_1 | 635715 | 636308 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| PDOKEKDG_1 | 635715 | 636308 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| PDOKEKDG_1 | 1089596 | 1091254 | fbp54 | 0.0 | FBPs | Adherence | 90.84 | 99.94 | WP_011227179 |
| PDOKEKDG_1 | 981961 | 982692 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 90.57 | 100.00 | WP_011227248 |
| PDOKEKDG_1 | 636308 | 637177 | rfbA | 0.0 | Capsule | Immune modulation | 90.46 | 100.00 | WP_011681286 |
| PDOKEKDG_1 | 1906808 | 1907818 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.55 | 99.80 | WP_002986042 |
| PDOKEKDG_1 | 847346 | 848649 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| PDOKEKDG_1 | 982701 | 983393 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.04 | 99.86 | WP_011227247 |
| PDOKEKDG_1 | 982701 | 983393 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.04 | 99.86 | WP_011226047 |
| PDOKEKDG_1 | 982701 | 983393 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 87.46 | 99.86 | WP_011681175 |
| PDOKEKDG_1 | 1228146 | 1228907 | srtA | 0.0 | Sortase A | Exoenzyme | 84.40 | 99.87 | - |
| PDOKEKDG_1 | 634398 | 635444 | rfbB | 0.0 | Capsule | Immune modulation | 83.98 | 99.81 | WP_002263087 |
| PDOKEKDG_1 | 135612 | 136895 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.84 | 99.61 | WP_000107753 |
| PDOKEKDG_1 | 994706 | 995291 | SPD_RS01775 | 2.18e-139 | Capsule | Immune modulation | 82.28 | 96.53 | 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 |
|---|---|---|---|---|---|---|---|---|
| PDOKEKDG_1 | 1231597 | 1232580 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.65 | 100.00 | AAK75326 |
| PDOKEKDG_1 | 1220010 | 1218937 | MntE | 0.0 | manganese homeostasis | 95.53 | 99.72 | ABF32167 |
| PDOKEKDG_1 | 1742107 | 1739801 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| PDOKEKDG_1 | 1377192 | 1375711 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.32 | 100.00 | ABJ54480 |
| PDOKEKDG_1 | 449964 | 448996 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| PDOKEKDG_1 | 1200950 | 1198704 | metE | 0.0 | methionine biosynthesis enzymes | 92.52 | 100.00 | AAK74738 |
| PDOKEKDG_1 | 2146297 | 2147268 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| PDOKEKDG_1 | 662554 | 660824 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| PDOKEKDG_1 | 1616143 | 1614155 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.44 | 100.00 | AE014259_2 |
| PDOKEKDG_1 | 1698084 | 1699235 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.32 | 99.74 | AAL00050 |
| PDOKEKDG_1 | 2030770 | 2032248 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| PDOKEKDG_1 | 848649 | 847348 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| PDOKEKDG_1 | 2046103 | 2047995 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| PDOKEKDG_1 | 1195785 | 1197494 | PGM | 0.0 | phosphoglucomutase | 85.11 | 99.65 | ACH87041 |
| PDOKEKDG_1 | 2183049 | 2184140 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| PDOKEKDG_1 | 1960404 | 1961414 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| PDOKEKDG_1 | 1075833 | 1077194 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.46 | 99.56 | ABP90420 |
| PDOKEKDG_1 | 863068 | 862178 | bglB | 2.38e-176 | putative phospho--glucosidase | 87.20 | 99.66 | AAK33487 |
| PDOKEKDG_1 | 1156518 | 1157468 | SP_0676 | 3.11e-169 | transcription facot | 81.39 | 98.45 | AAK74821 |
| PDOKEKDG_1 | 1198517 | 1197660 | metF | 5.53e-168 | methionine biosynthesis enzymes | 87.76 | 99.31 | AAK74739 |
| PDOKEKDG_1 | 1107094 | 1106309 | pnuC | 7.09e-149 | NAD salvage pathway importer | 87.02 | 97.40 | AAK75931 |
| PDOKEKDG_1 | 1303039 | 1302368 | rr01 | 4.71e-126 | response regulator | 84.82 | 99.56 | CAB54566 |
| PDOKEKDG_1 | 934839 | 935543 | covR | 9.77e-126 | responder protein | 85.53 | 100.00 | AAK71319 |
| PDOKEKDG_1 | 1191818 | 1191147 | ciaR | 2.10e-124 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| PDOKEKDG_1 | 1191818 | 1191150 | CiaR | 3.88e-124 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| PDOKEKDG_1 | 934839 | 935543 | walR | 2.22e-119 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| PDOKEKDG_1 | 280091 | 280777 | CovR | 4.79e-119 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| PDOKEKDG_1 | 2184314 | 2184709 | SpxA2 | 2.16e-74 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| PDOKEKDG_1 | 1064368 | 1063967 | SpxA1 | 4.49e-69 | transcriptional regulator | 82.84 | 100.00 | ERL19273 |
| PDOKEKDG_1 | 121991 | 122404 | GrpE | 1.71e-66 | protein grpE | 81.88 | 80.59 | ABP89267 |
| PDOKEKDG_1 | 137062 | 137553 | RopE (M5005_Spy_1611) | 1.06e-71 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| PDOKEKDG_1 | 1742107 | 1739807 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| PDOKEKDG_1 | 1996838 | 1995819 | 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 |
|---|---|---|---|
| PDOKEKDG_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PDOKEKDG_1 | 808804 | 844616 | False | Siphoviridae | VOG4025, VOG7557, VOG5034, VOG0054, VOG0641, VOG4828, VOG4633, VOG3636, VOG0701, VOG8357, VOG0698, VOG0697, VOG0696, VOG0695, VOG5872, VOG4711, VOG4555, VOG0692, VOG0691, VOG4544, VOG0796, VOG4987, VOG0658, VOG0044, VOG0657, VOG0152, VOG0656, VOG3468, VOG0655, VOG7265, VOG4693, VOG7264, VOG4548, VOG7263, VOG0322, VOG0083, VOG0651, VOG3478, VOG3622 |
Phigaro v2.4.0 (Database: Jan. 2024 release)