Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 5 | 10 | 5 | 12.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| PDDBOLEE_1 | 1362370 | 1362687 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PDDBOLEE_1 | 1362032 | 1362370 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| PDDBOLEE_1 | 337316 | 338236 | mph(K) | Spiramycin, Telithromycin | 98.26 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| PDDBOLEE_1 | 337316 | 338233 | mphK | macrolide 2'-phosphotransferase MphK | INTERNAL_STOP | 98.37 | 100.00 | WP_003246254.1 |
| PDDBOLEE_1 | 3904547 | 3904918 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 91.13 | 71.68 | WP_003242546.1 |
| PDDBOLEE_1 | 605661 | 607283 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 83.73 | 98.90 | WP_003234144.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PDDBOLEE_1 | 2032975 | 2033616 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| PDDBOLEE_1 | 2981701 | 2982487 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| PDDBOLEE_1 | 3433034 | 3434176 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| PDDBOLEE_1 | 2977871 | 2978812 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.94 | 100.11 | NP_391077 |
| PDDBOLEE_1 | 3434661 | 3435837 | capB | 0.0 | Capsule | Immune modulation | 98.90 | 99.58 | NP_391471 |
| PDDBOLEE_1 | 2980476 | 2981675 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.67 | 100.08 | NP_391079 |
| PDDBOLEE_1 | 2970716 | 2977851 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.54 | 99.93 | NP_391076 |
| PDDBOLEE_1 | 2978840 | 2980458 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.46 | 99.94 | NP_391078 |
| PDDBOLEE_1 | 3434195 | 3434646 | capC | 0.0 | Capsule | Immune modulation | 98.45 | 100.22 | NP_391470 |
| PDDBOLEE_1 | 1874912 | 1876676 | dep/capD | 0.0 | Capsule | Immune modulation | 98.41 | 99.94 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| PDDBOLEE_1 | 123505 | 124641 | tufA | 0.0 | elongation factor Tu | 84.17 | 95.69 | AHM69299 |
| PDDBOLEE_1 | 9394 | 10263 | pdxS | 2.93e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PDDBOLEE_1 | 1674589 | 1675365 | CodY | 3.20e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PDDBOLEE_1 | 3276933 | 3277502 | ClpP | 2.37e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PDDBOLEE_1 | 1203661 | 1204053 | spxA1 | 2.52e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PDDBOLEE_1 | 2592607 | 2591810 | ClpX | 6.94e-153 | part of proteolytic complex | 80.15 | 63.33 | BAF67840 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| PDDBOLEE_2 | 3169 | 3329 | Col(SD853) | 161 / 194 | 83.85 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| PDDBOLEE_1 | 0.0 | 1.0 | 0.0 |
| PDDBOLEE_2 | 1.0 | 0.0 | 1.0 |
| PDDBOLEE_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 |
|---|---|---|---|---|---|
| PDDBOLEE_1 | 161232 | 165582 | False | Unknown | VOG0083, VOG1309, VOG1292 |
| PDDBOLEE_1 | 177559 | 192356 | False | Myoviridae | VOG2185, VOG9315, VOG4773, VOG4564, VOG4688, VOG6965, VOG4685, VOG0749, VOG1581, VOG4589, VOG4870, VOG10055, VOG3890, VOG3890, VOG3891 |
| PDDBOLEE_1 | 199399 | 201972 | False | Myoviridae | VOG3894, VOG4691, VOG4691, VOG4862 |
| PDDBOLEE_1 | 1313768 | 1328320 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG9315, VOG4773, VOG4685, VOG0749, VOG10055, VOG3890, VOG3890, VOG3890, VOG3890 |
| PDDBOLEE_1 | 3047445 | 3078404 | False | Siphoviridae | VOG0641, VOG4705, VOG3390, VOG4612, VOG4660, VOG4660, VOG4619, VOG4619, VOG4619, VOG0801, VOG6163, VOG4545, VOG4611, VOG5910, VOG0541, VOG4586, VOG0704, VOG0704, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3644, VOG4544, VOG4581, VOG4841, VOG0198, VOG1884, VOG0025, VOG9600, VOG4566, VOG4552, VOG1638, VOG0787, VOG4556, VOG0181 |
Phigaro v2.4.0 (Database: Jan. 2024 release)