Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 4 | 19 | 35 | 40.02 |
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. |
|---|---|---|---|---|---|---|---|---|
| PHFGABPO_11 | 344068 | 345987 | tet(M) | ARO:3000186 | tet(M) | 96.87 | 100.00 | AB039845.1 |
| PHFGABPO_11 | 329474 | 330952 | lsaC | ARO:3003112 | lsaC | 99.39 | 100.00 | HM990671.1 |
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. |
|---|---|---|---|---|---|---|---|
| PHFGABPO_23 | 57431 | 58648 | mef(A) | Erythromycin, Azithromycin | 100.00 | 100.00 | U83667 |
| PHFGABPO_23 | 55848 | 57311 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | AF274302 |
| PHFGABPO_11 | 329474 | 330952 | lsa(C) | Lincomycin, Clindamycin, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 99.80 | 100.00 | HM990671 |
| PHFGABPO_11 | 344068 | 345987 | tet(M) | Doxycycline, Tetracycline, Minocycline | 99.79 | 100.00 | FR671418 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PHFGABPO_23 | 57434 | 58648 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| PHFGABPO_23 | 55851 | 57311 | msr(D) | ABC-F type ribosomal protection protein Msr(D) | EXACTX | 100.00 | 100.00 | WP_000420313.1 |
| PHFGABPO_11 | 344068 | 345984 | tet(M) | tetracycline resistance ribosomal protection protein Tet(M) | EXACTX | 100.00 | 100.00 | WP_000691743.1 |
| PHFGABPO_11 | 329477 | 330952 | lsa(C) | ABC-F type ribosomal protection protein Lsa(C) | BLASTX | 99.39 | 100.00 | WP_063851347.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PHFGABPO_2 | 134879 | 135847 | STER_RS07090 | 0.0 | Capsule | Immune modulation | 98.14 | 100.00 | WP_011681443 |
| PHFGABPO_2 | 134162 | 134877 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 96.79 | 99.86 | WP_011681442 |
| PHFGABPO_2 | 136815 | 138068 | STER_RS07100 | 0.0 | Capsule | Immune modulation | 96.49 | 99.52 | WP_011681445 |
| PHFGABPO_5 | 92387 | 93127 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 95.01 | 100.00 | WP_011681174 |
| PHFGABPO_26 | 88483 | 89076 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 94.61 | 100.00 | WP_011226149 |
| PHFGABPO_26 | 88483 | 89076 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 94.44 | 100.00 | WP_011226149 |
| PHFGABPO_26 | 88483 | 89076 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 94.44 | 100.00 | WP_011226149 |
| PHFGABPO_5 | 92387 | 93127 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 94.33 | 100.00 | WP_011226046 |
| PHFGABPO_2 | 138187 | 139038 | rfbD | 0.0 | Capsule | Immune modulation | 94.25 | 100.00 | WP_014621820 |
| PHFGABPO_5 | 89484 | 90944 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 94.11 | 100.14 | WP_011226049 |
| PHFGABPO_5 | 89484 | 90944 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 94.05 | 99.93 | WP_011681177 |
| PHFGABPO_5 | 93184 | 94551 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.01 | 100.00 | WP_011226045 |
| PHFGABPO_5 | 92387 | 93122 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 93.75 | 98.13 | WP_011227246 |
| PHFGABPO_5 | 93184 | 94549 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 93.70 | 99.85 | WP_011681173 |
| PHFGABPO_5 | 89484 | 90944 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.22 | 100.14 | WP_041827043 |
| PHFGABPO_2 | 133046 | 133816 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 93.14 | 99.10 | WP_011681440 |
| PHFGABPO_5 | 90945 | 91676 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 91.53 | 100.00 | WP_011226048 |
| PHFGABPO_26 | 89076 | 89945 | rfbA | 0.0 | Capsule | Immune modulation | 91.26 | 100.00 | WP_011681286 |
| PHFGABPO_5 | 90945 | 91676 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.12 | 100.00 | WP_011681176 |
| PHFGABPO_5 | 90945 | 91676 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 90.57 | 100.00 | WP_011227248 |
| PHFGABPO_11 | 77641 | 79299 | fbp54 | 0.0 | FBPs | Adherence | 90.36 | 99.94 | WP_011227179 |
| PHFGABPO_1 | 41802 | 42641 | cbpD | 0.0 | Autolysin | Exoenzyme | 90.12 | 100.00 | WP_011226733 |
| PHFGABPO_27 | 59162 | 60172 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.45 | 99.80 | WP_002986042 |
| PHFGABPO_23 | 82624 | 83927 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.40 | 99.54 | WP_000022832 |
| PHFGABPO_5 | 91685 | 92377 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.04 | 99.86 | WP_011227247 |
| PHFGABPO_5 | 91685 | 92377 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.04 | 99.86 | WP_011226047 |
| PHFGABPO_5 | 91685 | 92377 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 87.46 | 99.86 | WP_011681175 |
| PHFGABPO_11 | 221486 | 222247 | srtA | 0.0 | Sortase A | Exoenzyme | 83.90 | 99.74 | - |
| PHFGABPO_26 | 87172 | 88218 | rfbB | 0.0 | Capsule | Immune modulation | 81.57 | 100.00 | WP_009659423 |
| PHFGABPO_25 | 213809 | 215092 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.76 | 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 |
|---|---|---|---|---|---|---|---|---|
| PHFGABPO_11 | 224936 | 225910 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.31 | 99.09 | AAK75326 |
| PHFGABPO_11 | 213353 | 212280 | MntE | 0.0 | manganese homeostasis | 95.53 | 99.72 | ABF32167 |
| PHFGABPO_8 | 40176 | 37870 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.54 | 99.22 | AAK74619 |
| PHFGABPO_11 | 378032 | 379513 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| PHFGABPO_3 | 26732 | 25764 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| PHFGABPO_11 | 185296 | 183050 | metE | 0.0 | methionine biosynthesis enzymes | 92.52 | 100.00 | AAK74738 |
| PHFGABPO_1 | 24568 | 25539 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.36 | 100.00 | ABF36968 |
| PHFGABPO_26 | 115327 | 113597 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.78 | 100.00 | AAK34199 |
| PHFGABPO_2 | 181088 | 179937 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| PHFGABPO_2 | 152479 | 150491 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.44 | 100.00 | AE014259_2 |
| PHFGABPO_12 | 27076 | 28554 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.63 | 100.00 | ADE32434 |
| PHFGABPO_23 | 83927 | 82626 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| PHFGABPO_12 | 42400 | 44292 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.26 | 98.90 | ABP91129 |
| PHFGABPO_11 | 180129 | 181838 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| PHFGABPO_1 | 13467 | 14558 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| PHFGABPO_12 | 185970 | 184960 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| PHFGABPO_11 | 61775 | 63136 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.46 | 99.56 | ABP90420 |
| PHFGABPO_23 | 98337 | 97447 | bglB | 1.86e-178 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| PHFGABPO_11 | 139338 | 140288 | SP_0676 | 1.20e-169 | transcription facot | 81.07 | 98.45 | AAK74821 |
| PHFGABPO_11 | 182860 | 182003 | metF | 2.09e-168 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| PHFGABPO_29 | 38766 | 38086 | NisR | 6.65e-133 | two-component signal-transduction systems | 94.71 | 100.00 | ABP89873 |
| PHFGABPO_29 | 38098 | 37394 | NisK | 2.87e-131 | two-component signal-transduction systems | 91.06 | 100.00 | ABP89872 |
| PHFGABPO_5 | 43083 | 43787 | covR | 1.69e-126 | responder protein | 85.11 | 100.00 | AAK71319 |
| PHFGABPO_11 | 294700 | 294029 | rr01 | 3.36e-126 | response regulator | 84.38 | 99.56 | CAB54566 |
| PHFGABPO_11 | 176161 | 175490 | ciaR | 2.15e-124 | two component system response regulator | 85.71 | 99.12 | AIK75708 |
| PHFGABPO_11 | 176161 | 175493 | CiaR | 2.67e-124 | two-component response regulator | 87.00 | 99.55 | AAK74935 |
| PHFGABPO_5 | 43083 | 43787 | walR | 3.10e-120 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| PHFGABPO_25 | 54896 | 54210 | CovR | 4.78e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| PHFGABPO_1 | 14734 | 15108 | SpxA2 | 1.52e-71 | transcriptional regulator | 92.00 | 94.70 | ERL21461 |
| PHFGABPO_11 | 50305 | 49904 | SpxA1 | 5.33e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| PHFGABPO_28 | 6669 | 6256 | GrpE | 1.15e-67 | protein grpE | 81.16 | 80.59 | ABP89267 |
| PHFGABPO_25 | 31688 | 31401 | spr0479 | 4.63e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| PHFGABPO_3 | 69210 | 68956 | spr1327 | 6.54e-45 | essential gene | 91.77 | 100.00 | AAL00131 |
| PHFGABPO_12 | 73391 | 73128 | spr0175 | 1.12e-42 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| PHFGABPO_12 | 72565 | 72299 | spr0177 | 1.56e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| PHFGABPO_25 | 213642 | 213151 | RopE (M5005_Spy_1611) | 1.06e-72 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| PHFGABPO_8 | 40176 | 37876 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.36 | 98.08 | MYN69560 |
| PHFGABPO_12 | 149529 | 150548 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 97.65 | 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. |
|---|---|---|---|---|---|---|
| PHFGABPO_11 | 334589 | 335794 | repUS43 | 1206 / 1206 | 99.83 | CP003584 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| PHFGABPO_1 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_2 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_3 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_4 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_5 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_6 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_7 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_8 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_9 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_10 | 1.0 | 0.0 | 1.0 |
| PHFGABPO_11 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_12 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_16 | 1.0 | 0.0 | 1.0 |
| PHFGABPO_23 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_25 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_26 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_27 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_28 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_29 | 0.0 | 1.0 | 0.0 |
| PHFGABPO_30 | 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)