Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 15 | 34 | 37.22 |
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. |
|---|---|---|---|---|---|---|---|
| JFAFKPKF_9 | 11389 | 12606 | mef(A) | Erythromycin, Azithromycin | 100.00 | 100.00 | U83667 |
| JFAFKPKF_9 | 9806 | 11269 | 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. |
|---|---|---|---|---|---|---|---|---|
| JFAFKPKF_9 | 11392 | 12606 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| JFAFKPKF_9 | 9809 | 11269 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| JFAFKPKF_22 | 80363 | 81214 | rfbD | 0.0 | Capsule | Immune modulation | 94.95 | 100.00 | WP_014621820 |
| JFAFKPKF_3 | 46807 | 48267 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 93.98 | 100.14 | WP_011226049 |
| JFAFKPKF_3 | 46807 | 48267 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 93.98 | 100.00 | WP_011681177 |
| JFAFKPKF_3 | 46807 | 48267 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.22 | 100.14 | WP_041827043 |
| JFAFKPKF_3 | 43199 | 44566 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 93.13 | 100.00 | WP_011226045 |
| JFAFKPKF_3 | 43201 | 44566 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 92.97 | 99.85 | WP_011681173 |
| JFAFKPKF_11 | 82622 | 83215 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 92.42 | 100.00 | WP_011226149 |
| JFAFKPKF_11 | 82622 | 83215 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 92.26 | 100.00 | WP_011226149 |
| JFAFKPKF_11 | 82622 | 83215 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 92.26 | 100.00 | WP_011226149 |
| JFAFKPKF_3 | 46075 | 46806 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 91.94 | 100.00 | WP_011226048 |
| JFAFKPKF_11 | 83215 | 84084 | rfbA | 0.0 | Capsule | Immune modulation | 91.61 | 100.00 | WP_011681286 |
| JFAFKPKF_3 | 46075 | 46806 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.53 | 100.00 | WP_011681176 |
| JFAFKPKF_3 | 46075 | 46806 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 90.98 | 100.00 | WP_011227248 |
| JFAFKPKF_3 | 44624 | 45364 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 90.84 | 99.87 | WP_011681174 |
| JFAFKPKF_33 | 49600 | 51254 | fbp54 | 0.0 | FBPs | Adherence | 90.52 | 99.70 | WP_011227179 |
| JFAFKPKF_3 | 44624 | 45364 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 89.89 | 99.87 | WP_011226046 |
| JFAFKPKF_3 | 44629 | 45364 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 89.55 | 98.00 | WP_011227246 |
| JFAFKPKF_11 | 244891 | 246194 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.17 | 99.54 | WP_000022832 |
| JFAFKPKF_11 | 425575 | 426480 | cbpD | 0.0 | Autolysin | Exoenzyme | 88.08 | 93.50 | WP_082302295 |
| JFAFKPKF_13 | 5867 | 6877 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 87.36 | 99.80 | WP_002986042 |
| JFAFKPKF_3 | 45374 | 46066 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 85.45 | 99.86 | WP_011226047 |
| JFAFKPKF_3 | 45374 | 46066 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 85.16 | 99.86 | WP_011227247 |
| JFAFKPKF_3 | 45374 | 46066 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 84.87 | 99.86 | WP_011681175 |
| JFAFKPKF_11 | 81373 | 82419 | rfbB | 0.0 | Capsule | Immune modulation | 84.54 | 99.90 | WP_002263087 |
| JFAFKPKF_34 | 33239 | 34000 | srtA | 0.0 | Sortase A | Exoenzyme | 84.40 | 99.87 | - |
| JFAFKPKF_7 | 1900 | 3183 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.68 | 99.61 | WP_000107753 |
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 |
|---|---|---|---|---|---|---|---|---|
| JFAFKPKF_34 | 30550 | 29567 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| JFAFKPKF_34 | 42138 | 43211 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| JFAFKPKF_31 | 107714 | 110020 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.54 | 99.22 | AAK74619 |
| JFAFKPKF_34 | 61195 | 63441 | metE | 0.0 | methionine biosynthesis enzymes | 93.19 | 100.00 | AAK74738 |
| JFAFKPKF_32 | 37773 | 36292 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 92.92 | 100.00 | ABJ54480 |
| JFAFKPKF_11 | 336670 | 335702 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| JFAFKPKF_8 | 4326 | 5297 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.36 | 100.00 | ABF36968 |
| JFAFKPKF_6 | 19018 | 12470 | PrtA | 0.0 | serine protease | 90.35 | 101.73 | ABJ55268 |
| JFAFKPKF_11 | 109466 | 107736 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 90.12 | 100.00 | AAK34199 |
| JFAFKPKF_22 | 66631 | 68619 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.59 | 100.00 | AE014259_2 |
| JFAFKPKF_22 | 38225 | 39376 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| JFAFKPKF_4 | 25875 | 27353 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| JFAFKPKF_11 | 246194 | 244893 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| JFAFKPKF_4 | 41223 | 43115 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.42 | 98.90 | ABP91129 |
| JFAFKPKF_34 | 66363 | 64654 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| JFAFKPKF_8 | 38211 | 39302 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| JFAFKPKF_36 | 28510 | 29520 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| JFAFKPKF_33 | 67103 | 65742 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.67 | 99.56 | ABP90420 |
| JFAFKPKF_11 | 260602 | 259712 | bglB | 6.49e-178 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| JFAFKPKF_34 | 63631 | 64488 | metF | 1.98e-170 | methionine biosynthesis enzymes | 88.11 | 99.31 | AAK74739 |
| JFAFKPKF_34 | 106375 | 105413 | SP_0676 | 3.76e-170 | transcription facot | 80.69 | 99.69 | AAK74821 |
| JFAFKPKF_14 | 439 | 1143 | covR | 9.42e-128 | responder protein | 85.53 | 100.00 | AAK71319 |
| JFAFKPKF_6 | 56201 | 55530 | rr01 | 1.43e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| JFAFKPKF_34 | 71030 | 71701 | ciaR | 1.73e-124 | two component system response regulator | 85.71 | 99.12 | AIK75708 |
| JFAFKPKF_34 | 71030 | 71698 | CiaR | 4.88e-124 | two-component response regulator | 86.55 | 99.55 | AAK74935 |
| JFAFKPKF_14 | 439 | 1143 | walR | 2.14e-121 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| JFAFKPKF_35 | 55414 | 54728 | CovR | 1.94e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| JFAFKPKF_8 | 39476 | 39871 | SpxA2 | 3.95e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| JFAFKPKF_33 | 78577 | 78978 | SpxA1 | 1.79e-70 | transcriptional regulator | 82.84 | 100.00 | ERL19273 |
| JFAFKPKF_2 | 5975 | 5562 | GrpE | 5.67e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| JFAFKPKF_35 | 32197 | 31910 | spr0479 | 1.88e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| JFAFKPKF_11 | 373284 | 373030 | spr1327 | 2.37e-44 | essential gene | 92.94 | 100.00 | AAL00131 |
| JFAFKPKF_4 | 84907 | 84644 | spr0175 | 6.64e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| JFAFKPKF_4 | 84081 | 83815 | spr0177 | 9.26e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| JFAFKPKF_7 | 3350 | 3841 | RopE (M5005_Spy_1611) | 2.35e-73 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| JFAFKPKF_31 | 107714 | 110014 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.22 | 98.08 | MYN69560 |
| JFAFKPKF_36 | 103423 | 102404 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 85.88 | 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 |
|---|---|---|---|
| JFAFKPKF_1 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_2 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_3 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_4 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_5 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_6 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_7 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_8 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_9 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_10 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_11 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_12 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_13 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_14 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_15 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_16 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_17 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_18 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_19 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_20 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_21 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_22 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_23 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_24 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_25 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_26 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_27 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_28 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_30 | 1.0 | 0.0 | 1.0 |
| JFAFKPKF_31 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_32 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_33 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_34 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_35 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_36 | 0.0 | 1.0 | 0.0 |
| JFAFKPKF_37 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JFAFKPKF_5 | 16387 | 60013 | False | Siphoviridae | VOG0275, VOG0682, VOG4602, VOG0743, VOG3622, VOG8337, VOG1563, VOG0650, VOG0651, VOG5996, VOG0321, VOG0322, VOG4548, VOG6545, VOG4632, VOG4606, VOG0327, VOG0655, VOG0656, VOG0152, VOG0657, VOG0044, VOG0658, VOG0198, VOG4841, VOG4581, VOG1886, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG0204, VOG0205, VOG0207, VOG4586, VOG0209, VOG6163, VOG4605, VOG4599, VOG0647, VOG0648, VOG7888, VOG0054, VOG5034, VOG7557, VOG3631, VOG10230, VOG3299, VOG0866 |
| JFAFKPKF_36 | 49087 | 90207 | False | Siphoviridae | VOG3946, VOG4649, VOG3614, VOG7557, VOG5034, VOG0054, VOG0641, VOG4684, VOG0429, VOG4763, VOG0727, VOG9762, VOG0800, VOG0725, VOG0799, VOG0724, VOG5660, VOG0723, VOG4713, VOG3649, VOG4553, VOG7049, VOG4564, VOG0720, VOG10227, VOG0796, VOG0198, VOG0658, VOG0044, VOG5439, VOG0657, VOG4567, VOG0292, VOG0152, VOG0656, VOG0655, VOG4693, VOG0226, VOG0685, VOG0283, VOG8355, VOG5996, VOG0651, VOG2246, VOG4908, VOG7236, VOG6495, VOG0743, VOG4602, VOG3304, VOG0221 |
Phigaro v2.4.0 (Database: Jan. 2024 release)