Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 27 | 35 | 44.20 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| LDFHHHAM_67 | 19474 | 20343 | rfbA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | WP_011681286 |
| LDFHHHAM_67 | 20343 | 20936 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | WP_011226149 |
| LDFHHHAM_33 | 6419 | 7228 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 99.88 | 100.00 | WP_002948020 |
| LDFHHHAM_67 | 20343 | 20936 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | WP_011226149 |
| LDFHHHAM_33 | 7212 | 8168 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 99.79 | 100.00 | WP_011226328 |
| LDFHHHAM_33 | 8165 | 9313 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 99.74 | 100.00 | WP_041828290 |
| LDFHHHAM_67 | 20343 | 20936 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | WP_011226149 |
| LDFHHHAM_33 | 12809 | 13660 | rfbD | 0.0 | Capsule | Immune modulation | 99.65 | 100.00 | WP_014621820 |
| LDFHHHAM_30 | 13055 | 14713 | fbp54 | 0.0 | FBPs | Adherence | 99.58 | 100.00 | WP_011227179 |
| LDFHHHAM_33 | 5214 | 6419 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | WP_011226326 |
| LDFHHHAM_101 | 2499 | 3642 | cshA | 0.0 | Cell surface hydrophobicity proteins | Adherence | 99.56 | 100.00 | - |
| LDFHHHAM_44 | 15993 | 16592 | STR_RS05245 | 0.0 | Capsule | Immune modulation | 99.50 | 100.00 | WP_196767671 |
| LDFHHHAM_33 | 9422 | 10432 | STU_RS16260 | 0.0 | Capsule | Immune modulation | 99.50 | 100.00 | WP_011226330 |
| LDFHHHAM_33 | 2358 | 4142 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 99.44 | 100.00 | WP_011226325 |
| LDFHHHAM_33 | 4139 | 5194 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 99.43 | 100.00 | WP_002948022 |
| LDFHHHAM_107 | 318 | 1733 | STER_RS05250 | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | WP_011681165 |
| LDFHHHAM_44 | 15106 | 15841 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 98.91 | 99.33 | WP_011681174 |
| LDFHHHAM_49 | 59036 | 60004 | cbpD | 0.0 | Autolysin | Exoenzyme | 98.86 | 100.00 | WP_082302295 |
| LDFHHHAM_15 | 25559 | 26320 | srtA | 0.0 | Sortase A | Exoenzyme | 98.82 | 100.00 | - |
| LDFHHHAM_44 | 13664 | 14395 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 98.77 | 100.00 | WP_011681176 |
| LDFHHHAM_44 | 12209 | 13663 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 98.76 | 100.00 | WP_041827043 |
| LDFHHHAM_44 | 16757 | 17716 | STR_RS05240 | 0.0 | Capsule | Immune modulation | 98.54 | 100.00 | WP_041827042 |
| LDFHHHAM_44 | 13664 | 14395 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 98.50 | 100.00 | WP_011226048 |
| LDFHHHAM_44 | 13664 | 14395 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 98.36 | 100.00 | WP_011227248 |
| LDFHHHAM_44 | 15106 | 15855 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 98.27 | 100.00 | WP_011227246 |
| LDFHHHAM_44 | 12209 | 13663 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 98.21 | 100.00 | WP_011226049 |
| LDFHHHAM_44 | 15106 | 15841 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 98.10 | 99.33 | WP_011226046 |
| LDFHHHAM_33 | 10435 | 11706 | STU_RS16265 | 0.0 | Capsule | Immune modulation | 97.48 | 99.76 | WP_011226331 |
| LDFHHHAM_44 | 12209 | 13663 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 96.65 | 99.79 | WP_011681177 |
| LDFHHHAM_86 | 33277 | 38171 | SAG_RS09105 | 0.0 | Agglutinin receptor | Adherence | 92.87 | 99.98 | WP_000167699 |
| LDFHHHAM_86 | 33277 | 38219 | SSU98_0978 | 0.0 | Agglutinin receptor | Adherence | 92.82 | 99.78 | YP_001200536 |
| LDFHHHAM_86 | 33277 | 38219 | SSU05_0965 | 0.0 | Agglutinin receptor | Adherence | 92.80 | 99.78 | YP_001198331 |
| LDFHHHAM_44 | 14404 | 15096 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.90 | 100.00 | WP_011681175 |
| LDFHHHAM_44 | 14404 | 15096 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 89.75 | 100.00 | WP_011226047 |
| LDFHHHAM_44 | 14404 | 15096 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.47 | 100.00 | WP_011227247 |
| LDFHHHAM_39 | 96831 | 98134 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.10 | 99.46 | WP_000022832 |
| LDFHHHAM_82 | 14329 | 15339 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 86.54 | 99.41 | WP_002986042 |
| LDFHHHAM_64 | 4783 | 6066 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.73 | 99.77 | WP_000107753 |
| LDFHHHAM_67 | 21365 | 22411 | rfbB | 0.0 | Capsule | Immune modulation | 80.61 | 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 |
|---|---|---|---|---|---|---|---|---|
| LDFHHHAM_15 | 22872 | 21889 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 94.82 | 100.00 | AAK75326 |
| LDFHHHAM_89 | 13750 | 12677 | MntE | 0.0 | manganese homeostasis | 94.41 | 99.72 | ABF32167 |
| LDFHHHAM_86 | 38192 | 33282 | B9H01_RS04765 | 0.0 | glucan-binding protein | 93.40 | 99.63 | AUS90958 |
| LDFHHHAM_39 | 13145 | 14113 | spr0084 | 0.0 | pathogenitcity related | 93.19 | 98.48 | AAK98888 |
| LDFHHHAM_77 | 40785 | 43088 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 92.97 | 99.22 | AAK74619 |
| LDFHHHAM_76 | 13138 | 11657 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 92.31 | 100.00 | ABJ54480 |
| LDFHHHAM_74 | 6142 | 8388 | metE | 0.0 | methionine biosynthesis enzymes | 91.72 | 100.00 | AAK74738 |
| LDFHHHAM_80 | 12607 | 13605 | recA | 0.0 | DNA recombination and repair | 90.99 | 85.82 | AAL00560 |
| LDFHHHAM_25 | 3364 | 4335 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 90.12 | 100.00 | ABF36968 |
| LDFHHHAM_62 | 73031 | 74182 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.32 | 99.74 | AAL00050 |
| LDFHHHAM_33 | 28630 | 26642 | uvrB | 0.0 | excinuclease ABC, B subunit | 88.99 | 100.00 | AE014259_2 |
| LDFHHHAM_15 | 39071 | 40801 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 88.04 | 100.00 | AAK34199 |
| LDFHHHAM_78 | 26990 | 28468 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.22 | 100.00 | ADE32434 |
| LDFHHHAM_39 | 96831 | 98132 | Eno | 0.0 | enolase | 86.21 | 99.77 | ABP90468 |
| LDFHHHAM_78 | 42179 | 44071 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 86.05 | 98.90 | ABP91129 |
| LDFHHHAM_74 | 11313 | 9604 | PGM | 0.0 | phosphoglucomutase | 83.71 | 99.65 | ACH87041 |
| LDFHHHAM_98 | 2068 | 1058 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| LDFHHHAM_38 | 24209 | 22848 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.24 | 99.56 | ABP90420 |
| LDFHHHAM_60 | 48543 | 46651 | PepO | 0.0 | endopeptidase | 80.19 | 100.00 | ABF32980 |
| LDFHHHAM_39 | 82396 | 83286 | bglB | 1.06e-179 | putative phospho--glucosidase | 88.89 | 99.66 | AAK33487 |
| LDFHHHAM_75 | 3941 | 3003 | SP_0676 | 5.99e-169 | transcription facot | 81.15 | 97.20 | AAK74821 |
| LDFHHHAM_74 | 8580 | 9437 | metF | 1.40e-166 | methionine biosynthesis enzymes | 86.36 | 99.31 | AAK74739 |
| LDFHHHAM_90 | 24438 | 23734 | covR | 1.26e-132 | responder protein | 85.53 | 100.00 | AAK71319 |
| LDFHHHAM_12 | 19723 | 19052 | rr01 | 6.85e-126 | response regulator | 83.93 | 99.56 | CAB54566 |
| LDFHHHAM_90 | 24438 | 23734 | walR | 5.31e-123 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| LDFHHHAM_61 | 7737 | 7051 | CovR | 1.29e-119 | serves to repress GAS virulence factor-encoding genes | 80.79 | 100.00 | ACE75886 |
| LDFHHHAM_74 | 15267 | 15935 | CiaR | 1.86e-119 | two-component response regulator | 84.31 | 99.55 | AAK74935 |
| LDFHHHAM_74 | 15267 | 15938 | ciaR | 1.83e-117 | two component system response regulator | 82.14 | 99.12 | AIK75708 |
| LDFHHHAM_80 | 13881 | 14255 | SpxA2 | 8.91e-72 | transcriptional regulator | 91.20 | 94.70 | ERL21461 |
| LDFHHHAM_38 | 35568 | 35969 | SpxA1 | 1.10e-67 | transcriptional regulator | 80.60 | 100.00 | ERL19273 |
| LDFHHHAM_28 | 13128 | 13415 | spr0479 | 1.31e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| LDFHHHAM_49 | 18146 | 17892 | spr1327 | 1.11e-45 | essential gene | 95.29 | 100.00 | AAL00131 |
| LDFHHHAM_78 | 86731 | 86468 | spr0175 | 4.62e-42 | pathogenitcity related | 84.09 | 100.00 | AAK98979 |
| LDFHHHAM_78 | 85904 | 85638 | spr0177 | 8.16e-34 | essential gene | 84.27 | 88.12 | AAK98981 |
| LDFHHHAM_64 | 6224 | 6724 | RopE (M5005_Spy_1611) | 1.82e-76 | probable DNA-directed RNA polymerase subunit delta | 81.44 | 87.43 | AAK34603 |
| LDFHHHAM_77 | 40785 | 43082 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 82.94 | 98.08 | MYN69560 |
| LDFHHHAM_86 | 3569 | 2373 | AUS90997 (B9H01_RS07385) | 0.0 | site-specific integrase | 97.74 | 100.00 | AUS90997 |
| LDFHHHAM_60 | 34071 | 33052 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 96.47 | 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 |
|---|---|---|---|
| LDFHHHAM_1 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_3 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_8 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_12 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_13 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_14 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_15 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_18 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_19 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_22 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_23 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_25 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_28 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_30 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_33 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_38 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_39 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_44 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_46 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_48 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_49 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_50 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_56 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_57 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_59 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_60 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_61 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_62 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_63 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_64 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_65 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_67 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_70 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_72 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_73 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_74 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_75 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_76 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_77 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_78 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_79 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_80 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_81 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_82 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_84 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_85 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_86 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_87 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_88 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_89 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_90 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_91 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_92 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_93 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_94 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_95 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_96 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_97 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_98 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_100 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_101 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_102 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_103 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_104 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_105 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_106 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_107 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_108 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_109 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_110 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_112 | 1.0 | 0.0 | 1.0 |
| LDFHHHAM_115 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_119 | 0.0 | 1.0 | 0.0 |
| LDFHHHAM_121 | 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)