Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 19 | 33 | 38.13 |
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. |
|---|---|---|---|---|---|---|---|
| JJPAMAED_11 | 221442 | 222905 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | AF274302 |
| JJPAMAED_11 | 223025 | 224242 | mef(A) | Erythromycin, Azithromycin | 99.92 | 100.00 | U83667 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| JJPAMAED_11 | 223028 | 224242 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| JJPAMAED_11 | 221445 | 222905 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| JJPAMAED_30 | 147401 | 148369 | STER_RS07090 | 0.0 | Capsule | Immune modulation | 98.14 | 100.00 | WP_011681443 |
| JJPAMAED_30 | 148371 | 149086 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 96.79 | 99.86 | WP_011681442 |
| JJPAMAED_30 | 145180 | 146433 | STER_RS07100 | 0.0 | Capsule | Immune modulation | 96.49 | 99.52 | WP_011681445 |
| JJPAMAED_30 | 144210 | 145061 | rfbD | 0.0 | Capsule | Immune modulation | 94.25 | 100.00 | WP_014621820 |
| JJPAMAED_22 | 176705 | 178165 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 93.98 | 100.14 | WP_011226049 |
| JJPAMAED_22 | 176705 | 178165 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 93.98 | 100.00 | WP_011681177 |
| JJPAMAED_22 | 173097 | 174464 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 93.20 | 100.00 | WP_011226045 |
| JJPAMAED_11 | 80572 | 81165 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 93.10 | 100.00 | WP_011226149 |
| JJPAMAED_22 | 176705 | 178165 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.09 | 100.14 | WP_041827043 |
| JJPAMAED_22 | 173099 | 174464 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 93.05 | 99.85 | WP_011681173 |
| JJPAMAED_30 | 149432 | 150201 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 93.00 | 98.97 | WP_011681440 |
| JJPAMAED_11 | 80572 | 81165 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 92.93 | 100.00 | WP_011226149 |
| JJPAMAED_11 | 80572 | 81165 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 92.93 | 100.00 | WP_011226149 |
| JJPAMAED_22 | 175973 | 176704 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 91.94 | 100.00 | WP_011226048 |
| JJPAMAED_22 | 175973 | 176704 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.53 | 100.00 | WP_011681176 |
| JJPAMAED_22 | 174522 | 175262 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 91.51 | 99.87 | WP_011681174 |
| JJPAMAED_11 | 81165 | 82034 | rfbA | 0.0 | Capsule | Immune modulation | 91.49 | 100.00 | WP_011681286 |
| JJPAMAED_22 | 175973 | 176704 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 90.98 | 100.00 | WP_011227248 |
| JJPAMAED_22 | 72039 | 73697 | fbp54 | 0.0 | FBPs | Adherence | 90.60 | 99.94 | WP_011227179 |
| JJPAMAED_22 | 174522 | 175262 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 90.57 | 99.87 | WP_011226046 |
| JJPAMAED_22 | 174527 | 175262 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 90.23 | 98.00 | WP_011227246 |
| JJPAMAED_11 | 286973 | 288276 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| JJPAMAED_11 | 416208 | 417101 | cbpD | 0.0 | Autolysin | Exoenzyme | 88.08 | 93.40 | WP_082302295 |
| JJPAMAED_34 | 14391 | 15401 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 87.56 | 99.80 | WP_002986042 |
| JJPAMAED_36 | 84786 | 85547 | srtA | 0.0 | Sortase A | Exoenzyme | 86.52 | 99.74 | - |
| JJPAMAED_22 | 175272 | 175964 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 85.45 | 99.86 | WP_011226047 |
| JJPAMAED_22 | 175272 | 175964 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 85.16 | 99.86 | WP_011227247 |
| JJPAMAED_22 | 175272 | 175964 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 84.87 | 99.86 | WP_011681175 |
| JJPAMAED_31 | 2693 | 3976 | tig/ropA | 0.0 | Trigger factor | Stress survival | 81.07 | 99.61 | WP_000107753 |
| JJPAMAED_11 | 79261 | 80307 | rfbB | 0.0 | Capsule | Immune modulation | 80.71 | 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 |
|---|---|---|---|---|---|---|---|---|
| JJPAMAED_36 | 76655 | 75582 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| JJPAMAED_36 | 88236 | 89210 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.00 | 99.09 | AAK75326 |
| JJPAMAED_1 | 55465 | 57771 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| JJPAMAED_32 | 132740 | 134221 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| JJPAMAED_36 | 57558 | 55312 | metE | 0.0 | methionine biosynthesis enzymes | 93.06 | 100.00 | AAK74738 |
| JJPAMAED_11 | 378045 | 377077 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| JJPAMAED_3 | 38691 | 37720 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| JJPAMAED_32 | 20575 | 14027 | PrtA | 0.0 | serine protease | 90.07 | 101.68 | ABJ55268 |
| JJPAMAED_11 | 107414 | 105684 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.78 | 100.00 | AAK34199 |
| JJPAMAED_30 | 102388 | 103539 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| JJPAMAED_30 | 130766 | 132754 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.44 | 100.00 | AE014259_2 |
| JJPAMAED_33 | 25882 | 27360 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.63 | 100.00 | ADE32434 |
| JJPAMAED_11 | 288276 | 286975 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| JJPAMAED_33 | 41223 | 43115 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.42 | 98.90 | ABP91129 |
| JJPAMAED_36 | 52390 | 54099 | PGM | 0.0 | phosphoglucomutase | 84.94 | 99.65 | ACH87041 |
| JJPAMAED_3 | 2042 | 951 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| JJPAMAED_33 | 157033 | 156023 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| JJPAMAED_22 | 87468 | 86107 | mnmE | 0.0 | central tRNA-modifying GTPase | 81.80 | 99.56 | ABP90420 |
| JJPAMAED_11 | 302682 | 301792 | bglB | 3.43e-177 | putative phospho--glucosidase | 87.54 | 99.66 | AAK33487 |
| JJPAMAED_36 | 10901 | 11839 | SP_0676 | 7.61e-170 | transcription facot | 81.79 | 97.20 | AAK74821 |
| JJPAMAED_36 | 55122 | 54265 | metF | 3.85e-169 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| JJPAMAED_22 | 223770 | 223066 | covR | 4.10e-126 | responder protein | 85.11 | 100.00 | AAK71319 |
| JJPAMAED_32 | 57771 | 57100 | rr01 | 4.69e-126 | response regulator | 84.38 | 99.56 | CAB54566 |
| JJPAMAED_36 | 47725 | 47054 | ciaR | 8.53e-126 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| JJPAMAED_36 | 47725 | 47057 | CiaR | 1.58e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| JJPAMAED_31 | 161548 | 162234 | CovR | 4.74e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| JJPAMAED_22 | 223770 | 223066 | walR | 7.53e-120 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| JJPAMAED_3 | 776 | 381 | SpxA2 | 4.22e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| JJPAMAED_22 | 98935 | 99336 | SpxA1 | 2.87e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| JJPAMAED_2 | 46366 | 46779 | GrpE | 3.41e-67 | protein grpE | 80.44 | 80.59 | ABP89267 |
| JJPAMAED_31 | 184759 | 185046 | spr0479 | 5.74e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| JJPAMAED_11 | 451862 | 451608 | spr1327 | 2.73e-44 | essential gene | 92.94 | 100.00 | AAL00131 |
| JJPAMAED_33 | 72228 | 71965 | spr0175 | 9.60e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| JJPAMAED_31 | 4143 | 4634 | RopE (M5005_Spy_1611) | 1.05e-72 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| JJPAMAED_1 | 55465 | 57765 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| JJPAMAED_33 | 120346 | 121365 | 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. |
|---|---|---|---|---|---|---|
| JJPAMAED_12 | 566 | 1245 | repUS2 | 682 / 681 | 98.53 | BFU30316 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| JJPAMAED_1 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_2 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_3 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_4 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_5 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_6 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_7 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_8 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_9 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_10 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_11 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_12 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_13 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_14 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_15 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_16 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_17 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_18 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_19 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_20 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_21 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_22 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_23 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_24 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_25 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_27 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_28 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_29 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_30 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_31 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_32 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_33 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_34 | 0.0 | 1.0 | 0.0 |
| JJPAMAED_35 | 1.0 | 0.0 | 1.0 |
| JJPAMAED_36 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JJPAMAED_11 | 245207 | 284645 | False | Siphoviridae | VOG10230, VOG3631, VOG7557, VOG5034, VOG0054, VOG0641, VOG0648, VOG0647, VOG4599, VOG4605, VOG4545, VOG0209, VOG4586, VOG0207, VOG0205, VOG0204, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841, VOG0198, VOG0658, VOG0657, VOG0152, VOG3468, VOG0655, VOG4693, VOG0226, VOG0685, VOG1309, VOG3430, VOG0189, VOG4566, VOG5996, VOG0651, VOG3478, VOG4552, VOG2338, VOG8520 |
Phigaro v2.4.0 (Database: Jan. 2024 release)