Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 16 | 33 | 36.67 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| HMPMLPCN_20 | 17372 | 18103 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 94.81 | 100.00 | WP_011681176 |
| HMPMLPCN_20 | 17372 | 18103 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 94.54 | 100.00 | WP_011226048 |
| HMPMLPCN_12 | 12055 | 12906 | rfbD | 0.0 | Capsule | Immune modulation | 94.48 | 100.00 | WP_014621820 |
| HMPMLPCN_12 | 8614 | 9330 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 94.42 | 100.00 | WP_011681442 |
| HMPMLPCN_20 | 17372 | 18103 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 94.13 | 100.00 | WP_011227248 |
| HMPMLPCN_12 | 7498 | 8268 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 92.35 | 99.23 | WP_011681440 |
| HMPMLPCN_14 | 1184 | 1777 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| HMPMLPCN_20 | 18104 | 19564 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 90.92 | 99.86 | WP_011681177 |
| HMPMLPCN_14 | 1184 | 1777 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| HMPMLPCN_14 | 1184 | 1777 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| HMPMLPCN_20 | 18104 | 19564 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.78 | 100.00 | WP_011226049 |
| HMPMLPCN_9 | 3441 | 5098 | fbp54 | 0.0 | FBPs | Adherence | 90.36 | 99.88 | WP_011227179 |
| HMPMLPCN_20 | 18104 | 19564 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 89.97 | 100.00 | WP_041827043 |
| HMPMLPCN_20 | 16671 | 17363 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 89.90 | 100.00 | WP_011226047 |
| HMPMLPCN_20 | 16671 | 17363 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011227247 |
| HMPMLPCN_20 | 16671 | 17363 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.47 | 100.00 | WP_011681175 |
| HMPMLPCN_3 | 34490 | 35793 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| HMPMLPCN_33 | 72419 | 73258 | cbpD | 0.0 | Autolysin | Exoenzyme | 87.87 | 99.88 | WP_011226733 |
| HMPMLPCN_11 | 64519 | 65280 | srtA | 0.0 | Sortase A | Exoenzyme | 86.65 | 99.74 | - |
| HMPMLPCN_25 | 13638 | 14651 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| HMPMLPCN_14 | 3 | 914 | rfbB | 0.0 | Capsule | Immune modulation | 84.34 | 87.01 | WP_002263087 |
| HMPMLPCN_10 | 41383 | 42666 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.68 | 99.61 | WP_000107753 |
| HMPMLPCN_14 | 1777 | 2646 | rfbA | 0.0 | Capsule | Immune modulation | 80.28 | 99.77 | WP_002904719 |
| HMPMLPCN_20 | 15991 | 16661 | STU_RS14635 | 1.17e-148 | Capsule | Immune modulation | 80.98 | 90.28 | WP_011226046 |
| HMPMLPCN_20 | 15991 | 16661 | STER_RS05305 | 5.46e-147 | Capsule | Immune modulation | 80.83 | 90.28 | WP_011681174 |
| HMPMLPCN_20 | 16059 | 16661 | STR_RS05250 | 5.54e-137 | Capsule | Immune modulation | 81.46 | 80.13 | WP_011227246 |
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 |
|---|---|---|---|---|---|---|---|---|
| HMPMLPCN_11 | 61830 | 60847 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| HMPMLPCN_11 | 73412 | 74485 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| HMPMLPCN_58 | 96760 | 99066 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| HMPMLPCN_55 | 36426 | 37907 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.32 | 100.00 | ABJ54480 |
| HMPMLPCN_11 | 92953 | 95199 | metE | 0.0 | methionine biosynthesis enzymes | 92.92 | 100.00 | AAK74738 |
| HMPMLPCN_44 | 13648 | 12680 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| HMPMLPCN_13 | 23827 | 22856 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| HMPMLPCN_11 | 133 | 6606 | PrtA | 0.0 | serine protease | 91.35 | 100.61 | ABJ55268 |
| HMPMLPCN_28 | 1936 | 206 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| HMPMLPCN_12 | 26586 | 24598 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.59 | 100.00 | AE014259_2 |
| HMPMLPCN_44 | 89781 | 88630 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| HMPMLPCN_5 | 7293 | 8771 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| HMPMLPCN_3 | 34490 | 35791 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| HMPMLPCN_5 | 23073 | 24965 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| HMPMLPCN_26 | 12594 | 13685 | recA | 0.0 | DNA recombination and repair | 84.91 | 95.36 | AAL00560 |
| HMPMLPCN_11 | 98117 | 96408 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| HMPMLPCN_9 | 18859 | 17498 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.89 | 99.56 | ABP90420 |
| HMPMLPCN_1 | 20178 | 21188 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| HMPMLPCN_3 | 20080 | 20970 | bglB | 8.51e-178 | putative phospho--glucosidase | 87.20 | 99.66 | AAK33487 |
| HMPMLPCN_11 | 95389 | 96246 | metF | 4.68e-170 | methionine biosynthesis enzymes | 87.76 | 99.31 | AAK74739 |
| HMPMLPCN_11 | 139668 | 138730 | SP_0676 | 9.66e-169 | transcription facot | 81.47 | 97.20 | AAK74821 |
| HMPMLPCN_18 | 1815 | 2519 | covR | 1.87e-128 | responder protein | 85.96 | 100.00 | AAK71319 |
| HMPMLPCN_7 | 23818 | 23147 | rr01 | 5.10e-127 | response regulator | 84.38 | 99.56 | CAB54566 |
| HMPMLPCN_11 | 102782 | 103453 | ciaR | 1.78e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| HMPMLPCN_11 | 102782 | 103450 | CiaR | 3.25e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| HMPMLPCN_6 | 27493 | 28179 | CovR | 5.34e-121 | serves to repress GAS virulence factor-encoding genes | 82.10 | 100.00 | ACE75886 |
| HMPMLPCN_18 | 1815 | 2519 | walR | 1.13e-120 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| HMPMLPCN_9 | 30317 | 30718 | SpxA1 | 2.54e-70 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| HMPMLPCN_10 | 27606 | 28019 | GrpE | 4.23e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| HMPMLPCN_6 | 50693 | 50980 | spr0479 | 1.69e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| HMPMLPCN_44 | 47310 | 47056 | spr1327 | 4.03e-46 | essential gene | 94.12 | 100.00 | AAL00131 |
| HMPMLPCN_5 | 54252 | 53989 | spr0175 | 3.52e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| HMPMLPCN_5 | 53427 | 53161 | spr0177 | 7.81e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| HMPMLPCN_10 | 42833 | 43324 | RopE (M5005_Spy_1611) | 2.63e-73 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| HMPMLPCN_58 | 96760 | 99060 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.22 | 98.08 | MYN69560 |
| HMPMLPCN_1 | 56592 | 55573 | 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 |
|---|---|---|---|
| HMPMLPCN_1 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_2 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_3 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_4 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_5 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_6 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_7 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_8 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_9 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_10 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_11 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_12 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_13 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_14 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_15 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_16 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_17 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_18 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_19 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_20 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_21 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_22 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_23 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_24 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_25 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_26 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_27 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_28 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_29 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_30 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_31 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_32 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_33 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_34 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_35 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_36 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_37 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_39 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_40 | 1.0 | 0.0 | 1.0 |
| HMPMLPCN_43 | 1.0 | 0.0 | 1.0 |
| HMPMLPCN_44 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_45 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_46 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_47 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_48 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_49 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_50 | 1.0 | 0.0 | 1.0 |
| HMPMLPCN_52 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_53 | 1.0 | 0.0 | 1.0 |
| HMPMLPCN_55 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_56 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_57 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_58 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_59 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_60 | 0.0 | 1.0 | 0.0 |
| HMPMLPCN_61 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HMPMLPCN_4 | 75206 | 87685 | False | Siphoviridae | VOG5353, VOG11077, VOG1564, VOG9469, VOG4555, VOG0651, VOG0651, VOG5996, VOG4566, VOG0189, VOG3430, VOG1309, VOG0685, VOG0226, VOG4693, VOG0655, VOG3468, VOG6414, VOG0656 |
Phigaro v2.4.0 (Database: Jan. 2024 release)