Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 24 | 34 | 41.62 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| LLMEOKLN_2 | 129811 | 130662 | rfbD | 0.0 | Capsule | Immune modulation | 95.19 | 100.00 | WP_014621820 |
| LLMEOKLN_1 | 444571 | 445311 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 95.01 | 100.00 | WP_011681174 |
| LLMEOKLN_1 | 444571 | 445311 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 94.33 | 100.00 | WP_011226046 |
| LLMEOKLN_1 | 446754 | 448214 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 94.11 | 100.14 | WP_011226049 |
| LLMEOKLN_1 | 446754 | 448214 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 94.05 | 99.93 | WP_011681177 |
| LLMEOKLN_1 | 443147 | 444514 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.01 | 100.00 | WP_011226045 |
| LLMEOKLN_1 | 444576 | 445311 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 93.75 | 98.13 | WP_011227246 |
| LLMEOKLN_2 | 127439 | 128710 | STU_RS16265 | 0.0 | Capsule | Immune modulation | 93.71 | 99.76 | WP_011226331 |
| LLMEOKLN_1 | 443149 | 444514 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 93.70 | 99.85 | WP_011681173 |
| LLMEOKLN_2 | 126481 | 127436 | STU_RS16260 | 0.0 | Capsule | Immune modulation | 93.41 | 94.56 | WP_011226330 |
| LLMEOKLN_1 | 446754 | 448214 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.22 | 100.14 | WP_041827043 |
| LLMEOKLN_2 | 117829 | 119613 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.61 | 99.94 | WP_011226325 |
| LLMEOKLN_2 | 122663 | 123619 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 92.48 | 100.00 | WP_011226328 |
| LLMEOKLN_2 | 123616 | 124764 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 92.34 | 100.00 | WP_041828290 |
| LLMEOKLN_2 | 121870 | 122679 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 92.23 | 99.88 | WP_002948020 |
| LLMEOKLN_2 | 120665 | 121870 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 92.12 | 100.00 | WP_011226326 |
| LLMEOKLN_1 | 446022 | 446753 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 91.53 | 100.00 | WP_011226048 |
| LLMEOKLN_2 | 119610 | 120644 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.29 | 99.15 | WP_002948022 |
| LLMEOKLN_1 | 446022 | 446753 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.12 | 100.00 | WP_011681176 |
| LLMEOKLN_1 | 615300 | 615893 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| LLMEOKLN_10 | 18035 | 18874 | cbpD | 0.0 | Autolysin | Exoenzyme | 90.95 | 100.00 | WP_011226733 |
| LLMEOKLN_1 | 615300 | 615893 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| LLMEOKLN_1 | 615300 | 615893 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| LLMEOKLN_1 | 337460 | 339118 | fbp54 | 0.0 | FBPs | Adherence | 90.84 | 99.94 | WP_011227179 |
| LLMEOKLN_1 | 446022 | 446753 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 90.57 | 100.00 | WP_011227248 |
| LLMEOKLN_1 | 615893 | 616762 | rfbA | 0.0 | Capsule | Immune modulation | 90.46 | 100.00 | WP_011681286 |
| LLMEOKLN_2 | 437333 | 438343 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.55 | 99.80 | WP_002986042 |
| LLMEOKLN_5 | 180491 | 181794 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| LLMEOKLN_1 | 445321 | 446013 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.04 | 99.86 | WP_011227247 |
| LLMEOKLN_1 | 445321 | 446013 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.04 | 99.86 | WP_011226047 |
| LLMEOKLN_1 | 445321 | 446013 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 87.46 | 99.86 | WP_011681175 |
| LLMEOKLN_1 | 199933 | 200694 | srtA | 0.0 | Sortase A | Exoenzyme | 84.40 | 99.87 | - |
| LLMEOKLN_1 | 613983 | 615029 | rfbB | 0.0 | Capsule | Immune modulation | 83.98 | 99.81 | WP_002263087 |
| LLMEOKLN_4 | 197071 | 198354 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.84 | 99.61 | WP_000107753 |
| LLMEOKLN_1 | 433423 | 434008 | SPD_RS01775 | 6.49e-140 | Capsule | Immune modulation | 82.28 | 96.53 | WP_001819836 |
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 |
|---|---|---|---|---|---|---|---|---|
| LLMEOKLN_1 | 197243 | 196260 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.65 | 100.00 | AAK75326 |
| LLMEOKLN_1 | 208830 | 209903 | MntE | 0.0 | manganese homeostasis | 95.53 | 99.72 | ABF32167 |
| LLMEOKLN_2 | 313132 | 315438 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| LLMEOKLN_1 | 56222 | 54741 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.32 | 100.00 | ABJ54480 |
| LLMEOKLN_5 | 91660 | 92628 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| LLMEOKLN_1 | 227890 | 230136 | metE | 0.0 | methionine biosynthesis enzymes | 92.52 | 100.00 | AAK74738 |
| LLMEOKLN_10 | 3612 | 4583 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| LLMEOKLN_1 | 642139 | 640409 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| LLMEOKLN_2 | 142876 | 140888 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.44 | 100.00 | AE014259_2 |
| LLMEOKLN_2 | 171229 | 170078 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.32 | 99.74 | AAL00050 |
| LLMEOKLN_3 | 175477 | 173999 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| LLMEOKLN_5 | 180491 | 181792 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| LLMEOKLN_3 | 160144 | 158252 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| LLMEOKLN_1 | 233055 | 231346 | PGM | 0.0 | phosphoglucomutase | 85.11 | 99.65 | ACH87041 |
| LLMEOKLN_10 | 40364 | 41455 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| LLMEOKLN_3 | 27307 | 28317 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| LLMEOKLN_1 | 352881 | 351520 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.46 | 99.56 | ABP90420 |
| LLMEOKLN_5 | 166072 | 166962 | bglB | 1.97e-177 | putative phospho--glucosidase | 87.20 | 99.66 | AAK33487 |
| LLMEOKLN_1 | 272196 | 271246 | SP_0676 | 5.58e-169 | transcription facot | 81.39 | 98.45 | AAK74821 |
| LLMEOKLN_1 | 230323 | 231180 | metF | 1.64e-168 | methionine biosynthesis enzymes | 87.76 | 99.31 | AAK74739 |
| LLMEOKLN_1 | 321620 | 322405 | pnuC | 4.70e-149 | NAD salvage pathway importer | 87.02 | 97.40 | AAK75931 |
| LLMEOKLN_1 | 125801 | 126472 | rr01 | 1.40e-126 | response regulator | 84.82 | 99.56 | CAB54566 |
| LLMEOKLN_1 | 493875 | 493171 | covR | 2.91e-126 | responder protein | 85.53 | 100.00 | AAK71319 |
| LLMEOKLN_1 | 237022 | 237693 | ciaR | 6.25e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| LLMEOKLN_1 | 237022 | 237690 | CiaR | 1.15e-124 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| LLMEOKLN_4 | 53874 | 53188 | CovR | 4.37e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| LLMEOKLN_1 | 493875 | 493171 | walR | 6.60e-120 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| LLMEOKLN_10 | 41629 | 42024 | SpxA2 | 4.16e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| LLMEOKLN_1 | 364346 | 364747 | SpxA1 | 1.34e-69 | transcriptional regulator | 82.84 | 100.00 | ERL19273 |
| LLMEOKLN_13 | 6644 | 6231 | GrpE | 1.51e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| LLMEOKLN_4 | 30665 | 30378 | spr0479 | 5.30e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| LLMEOKLN_5 | 57905 | 58159 | spr1327 | 8.27e-45 | essential gene | 92.94 | 100.00 | AAL00131 |
| LLMEOKLN_3 | 118344 | 118607 | spr0175 | 1.04e-42 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| LLMEOKLN_3 | 119168 | 119434 | spr0177 | 2.31e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| LLMEOKLN_4 | 196904 | 196413 | RopE (M5005_Spy_1611) | 9.69e-73 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| LLMEOKLN_2 | 313132 | 315432 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| LLMEOKLN_3 | 63741 | 62722 | 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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LLMEOKLN_1 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_2 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_3 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_4 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_5 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_6 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_7 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_8 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_9 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_10 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_11 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_12 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_13 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_14 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_15 | 1.0 | 0.0 | 1.0 |
| LLMEOKLN_17 | 1.0 | 0.0 | 1.0 |
| LLMEOKLN_18 | 1.0 | 0.0 | 1.0 |
| LLMEOKLN_19 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_20 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_21 | 0.0 | 1.0 | 0.0 |
| LLMEOKLN_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 |
|---|---|---|---|---|---|
| LLMEOKLN_11 | 2675 | 37388 | False | Siphoviridae | VOG7557, VOG5034, VOG0054, VOG0641, VOG4828, VOG4633, VOG3636, VOG0701, VOG8357, VOG0698, VOG0697, VOG0696, VOG0695, VOG5872, VOG4711, VOG4555, VOG0692, VOG0691, VOG4544, VOG0796, VOG4987, VOG0658, VOG0044, VOG0657, VOG0152, VOG0656, VOG3468, VOG0655, VOG7265, VOG4693, VOG7264, VOG4548, VOG7263, VOG0322, VOG0083, VOG0651, VOG3478 |
Phigaro v2.4.0 (Database: Jan. 2024 release)