Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 4 | 15.39 |
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. |
|---|---|---|---|---|---|---|---|---|
| PDAMAKEP_1 | 3681622 | 3681939 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PDAMAKEP_1 | 3681284 | 3681622 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| PDAMAKEP_1 | 3200712 | 3203282 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PDAMAKEP_1 | 2651827 | 2652420 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| PDAMAKEP_1 | 2603912 | 2605345 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.00 | JYFL01000006.1 |
| PDAMAKEP_1 | 687792 | 688646 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| PDAMAKEP_1 | 666240 | 667442 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| PDAMAKEP_1 | 439367 | 440536 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
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. |
|---|---|---|---|---|---|---|---|
| PDAMAKEP_1 | 687794 | 688646 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| PDAMAKEP_1 | 2573426 | 2574345 | mph(K) | Spiramycin, Telithromycin | 97.61 | 99.89 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PDAMAKEP_1 | 687795 | 688646 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| PDAMAKEP_1 | 2898077 | 2899717 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 97.81 | 100.00 | WP_003234144.1 |
| PDAMAKEP_1 | 2236811 | 2237203 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 93.13 | 75.72 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PDAMAKEP_1 | 1743696 | 1744877 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| PDAMAKEP_1 | 1290910 | 1291848 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391077 |
| PDAMAKEP_1 | 1742071 | 1743213 | capA | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391469 |
| PDAMAKEP_1 | 1743232 | 1743681 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PDAMAKEP_1 | 235250 | 235891 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| PDAMAKEP_1 | 105038 | 106801 | dep/capD | 0.0 | Capsule | Immune modulation | 99.38 | 100.00 | NP_389723 |
| PDAMAKEP_1 | 1294735 | 1295520 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| PDAMAKEP_1 | 1283754 | 1290890 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.03 | 100.00 | NP_391076 |
| PDAMAKEP_1 | 1293513 | 1294709 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| PDAMAKEP_1 | 1291876 | 1293495 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.78 | 100.00 | NP_391078 |
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 |
|---|---|---|---|---|---|---|---|---|
| PDAMAKEP_1 | 2396283 | 2397419 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PDAMAKEP_1 | 2280952 | 2281821 | pdxS | 6.85e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| PDAMAKEP_1 | 3994608 | 3995384 | CodY | 3.45e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PDAMAKEP_1 | 1592134 | 1592703 | ClpP | 2.56e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| PDAMAKEP_3 | 5079 | 5242 | Col(SD853) | 164 / 194 | 87.20 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| PDAMAKEP_1 | 0.0 | 1.0 | 0.0 |
| PDAMAKEP_2 | 1.0 | 0.0 | 1.0 |
| PDAMAKEP_3 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PDAMAKEP_1 | 615341 | 639714 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG0796 |
| PDAMAKEP_1 | 823587 | 855745 | False | Siphoviridae | VOG3490, VOG4574, VOG0136, VOG5221, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841, VOG2021, VOG0198, VOG0425, VOG0044, VOG7372, VOG2752 |
| PDAMAKEP_1 | 1369396 | 1399519 | False | Siphoviridae | VOG4707, VOG0641, VOG4705, VOG6243, VOG4612, VOG4660, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG9583, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG4556, VOG5221, VOG0275, VOG0198, VOG5447, VOG6581, VOG0397, VOG3444, VOG4567 |
| PDAMAKEP_1 | 2423475 | 2455764 | False | Siphoviridae | VOG4606, VOG7060, VOG2752, VOG10041, VOG7372, VOG0044, VOG0425, VOG0198, VOG0713, VOG4841, VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG6243, VOG4705, VOG0641, VOG4574, VOG6116 |
| PDAMAKEP_1 | 3625397 | 3651798 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| PDAMAKEP_1 | 4213524 | 4236583 | False | Siphoviridae | VOG4841, VOG4581, VOG1886, VOG2935, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641 |
Phigaro v2.4.0 (Database: Jan. 2024 release)