Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 22 | 33 | 39.71 |
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. |
|---|---|---|---|---|---|---|---|
| APPLDMEG_8 | 825 | 2042 | mef(A) | Erythromycin, Azithromycin | 100.00 | 100.00 | U83667 |
| APPLDMEG_8 | 2162 | 3625 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | AF274302 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| APPLDMEG_8 | 825 | 2039 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| APPLDMEG_8 | 2162 | 3622 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| APPLDMEG_1 | 48654 | 50114 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 96.92 | 100.21 | WP_011226049 |
| APPLDMEG_1 | 48654 | 50114 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 96.85 | 100.00 | WP_011681177 |
| APPLDMEG_1 | 48654 | 50114 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 96.03 | 100.21 | WP_041827043 |
| APPLDMEG_19 | 77169 | 77978 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 95.31 | 100.00 | WP_002948020 |
| APPLDMEG_1 | 45049 | 46414 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 95.09 | 99.85 | WP_011681173 |
| APPLDMEG_19 | 85116 | 85967 | rfbD | 0.0 | Capsule | Immune modulation | 95.07 | 100.00 | WP_014621820 |
| APPLDMEG_1 | 46471 | 47211 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 94.87 | 100.00 | WP_011681174 |
| APPLDMEG_1 | 45047 | 46414 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.59 | 100.00 | WP_011226045 |
| APPLDMEG_1 | 46471 | 47211 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 94.33 | 100.00 | WP_011226046 |
| APPLDMEG_16 | 2648 | 3931 | tig/ropA | 0.0 | Trigger factor | Stress survival | 94.08 | 100.00 | WP_011225339 |
| APPLDMEG_1 | 46476 | 47211 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 93.89 | 98.13 | WP_011227246 |
| APPLDMEG_1 | 47922 | 48653 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 93.85 | 100.00 | WP_011681176 |
| APPLDMEG_1 | 47922 | 48653 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.72 | 100.00 | WP_011226048 |
| APPLDMEG_19 | 82744 | 84015 | STU_RS16265 | 0.0 | Capsule | Immune modulation | 93.71 | 99.76 | WP_011226331 |
| APPLDMEG_19 | 75964 | 77169 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 93.53 | 100.00 | WP_011226326 |
| APPLDMEG_1 | 47922 | 48653 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 93.17 | 100.00 | WP_011227248 |
| APPLDMEG_19 | 73129 | 74913 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.94 | 100.00 | WP_011226325 |
| APPLDMEG_19 | 78915 | 80063 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 92.17 | 100.00 | WP_041828290 |
| APPLDMEG_18 | 80441 | 81034 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.92 | 100.00 | WP_011226149 |
| APPLDMEG_18 | 80441 | 81034 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 91.75 | 100.00 | WP_011226149 |
| APPLDMEG_18 | 80441 | 81034 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 91.75 | 100.00 | WP_011226149 |
| APPLDMEG_19 | 74910 | 75944 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.39 | 99.05 | WP_002948022 |
| APPLDMEG_19 | 77962 | 78918 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 91.33 | 100.00 | WP_011226328 |
| APPLDMEG_18 | 81034 | 81903 | rfbA | 0.0 | Capsule | Immune modulation | 91.03 | 100.00 | WP_011681286 |
| APPLDMEG_11 | 18537 | 20195 | fbp54 | 0.0 | FBPs | Adherence | 90.36 | 99.94 | WP_011227179 |
| APPLDMEG_22 | 60689 | 61699 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.65 | 99.80 | WP_002986042 |
| APPLDMEG_1 | 47221 | 47913 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.47 | 99.86 | WP_011227247 |
| APPLDMEG_1 | 47221 | 47913 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.47 | 99.86 | WP_011226047 |
| APPLDMEG_15 | 18791 | 20094 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.47 | 99.54 | WP_000022832 |
| APPLDMEG_20 | 6834 | 7739 | cbpD | 0.0 | Autolysin | Exoenzyme | 88.41 | 93.50 | WP_082302295 |
| APPLDMEG_1 | 47221 | 47913 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 88.18 | 99.86 | WP_011681175 |
| APPLDMEG_11 | 174680 | 175441 | srtA | 0.0 | Sortase A | Exoenzyme | 84.03 | 99.74 | - |
| APPLDMEG_18 | 79192 | 80238 | rfbB | 0.0 | Capsule | Immune modulation | 80.42 | 100.00 | WP_009659423 |
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 |
|---|---|---|---|---|---|---|---|---|
| APPLDMEG_11 | 178131 | 179105 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.92 | 99.09 | AAK75326 |
| APPLDMEG_11 | 166550 | 165477 | MntE | 0.0 | manganese homeostasis | 95.25 | 99.72 | ABF32167 |
| APPLDMEG_15 | 198363 | 196057 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| APPLDMEG_11 | 333476 | 334957 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| APPLDMEG_15 | 109893 | 108925 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| APPLDMEG_11 | 138495 | 136249 | metE | 0.0 | methionine biosynthesis enzymes | 92.39 | 100.00 | AAK74738 |
| APPLDMEG_5 | 35936 | 34965 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.36 | 100.00 | ABF36968 |
| APPLDMEG_15 | 348899 | 350047 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 90.08 | 99.48 | AAL00050 |
| APPLDMEG_18 | 107288 | 105558 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| APPLDMEG_19 | 99363 | 97375 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.59 | 100.00 | AE014259_2 |
| APPLDMEG_17 | 163544 | 162066 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.63 | 100.00 | ADE32434 |
| APPLDMEG_15 | 20094 | 18793 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| APPLDMEG_17 | 148221 | 146329 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.26 | 98.90 | ABP91129 |
| APPLDMEG_11 | 133330 | 135039 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| APPLDMEG_5 | 2042 | 951 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| APPLDMEG_17 | 28753 | 29763 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| APPLDMEG_11 | 5016 | 6377 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.46 | 99.56 | ABP90420 |
| APPLDMEG_15 | 34504 | 33614 | bglB | 4.63e-178 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| APPLDMEG_11 | 92681 | 93631 | SP_0676 | 1.13e-169 | transcription facot | 81.39 | 98.45 | AAK74821 |
| APPLDMEG_11 | 136062 | 135205 | metF | 9.29e-168 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| APPLDMEG_7 | 426 | 1130 | covR | 3.37e-127 | responder protein | 85.11 | 100.00 | AAK71319 |
| APPLDMEG_11 | 261361 | 260690 | rr01 | 8.08e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| APPLDMEG_11 | 129362 | 128691 | ciaR | 1.89e-124 | two component system response regulator | 85.71 | 99.12 | AIK75708 |
| APPLDMEG_11 | 129362 | 128694 | CiaR | 2.34e-124 | two-component response regulator | 87.00 | 99.55 | AAK74935 |
| APPLDMEG_7 | 426 | 1130 | walR | 6.19e-121 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| APPLDMEG_16 | 162188 | 162874 | CovR | 4.80e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| APPLDMEG_5 | 777 | 382 | SpxA2 | 3.95e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| APPLDMEG_4 | 6454 | 6855 | SpxA1 | 4.48e-70 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| APPLDMEG_2 | 6355 | 5942 | GrpE | 9.69e-68 | protein grpE | 81.16 | 80.59 | ABP89267 |
| APPLDMEG_16 | 185967 | 186254 | spr0479 | 5.81e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| APPLDMEG_20 | 59740 | 59994 | spr1327 | 4.75e-45 | essential gene | 92.94 | 100.00 | AAL00131 |
| APPLDMEG_17 | 117225 | 117488 | spr0175 | 9.79e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| APPLDMEG_17 | 118051 | 118317 | spr0177 | 1.36e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| APPLDMEG_16 | 4098 | 4589 | RopE (M5005_Spy_1611) | 1.06e-72 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| APPLDMEG_15 | 198363 | 196063 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| APPLDMEG_17 | 65475 | 64456 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 96.77 | 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 |
|---|---|---|---|
| APPLDMEG_1 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_2 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_3 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_4 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_5 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_6 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_7 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_8 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_9 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_11 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_12 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_13 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_14 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_15 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_16 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_17 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_18 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_19 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_20 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_21 | 0.0 | 1.0 | 0.0 |
| APPLDMEG_22 | 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)