Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| PDMDIDEI_2 | 1557243 | 1558100 | aadK | ARO:3002627 | aadK | 97.18 | 100.35 | AL009126.1 |
| PDMDIDEI_2 | 1540148 | 1541350 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| PDMDIDEI_2 | 1343939 | 1345108 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PDMDIDEI_2 | 363907 | 364224 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PDMDIDEI_2 | 363569 | 363907 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PDMDIDEI_12 | 124861 | 127431 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PDMDIDEI_8 | 109248 | 110168 | mphK | ARO:3004541 | mphK | 99.01 | 100.00 | CP010314.1 |
| PDMDIDEI_8 | 95914 | 97353 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| PDMDIDEI_8 | 46264 | 46857 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| PDMDIDEI_3 | 29082 | 30728 | vmlR | ARO:3004476 | vmlR | 98.18 | 100.18 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| PDMDIDEI_8 | 109248 | 110168 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| PDMDIDEI_1 | 748615 | 749991 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.47 | 100.00 | D12567 |
| PDMDIDEI_2 | 1557249 | 1558100 | aadK | Streptomycin | 98.24 | 99.65 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PDMDIDEI_8 | 109260 | 110168 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.01 | 99.02 | WP_003246254.1 |
| PDMDIDEI_1 | 748618 | 749991 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.25 | 100.00 | WP_063856081.1 |
| PDMDIDEI_3 | 29082 | 30725 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.18 | 100.00 | WP_003234144.1 |
| PDMDIDEI_2 | 1557249 | 1558100 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.18 | 100.00 | WP_003229862.1 |
| PDMDIDEI_1 | 746123 | 746641 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| PDMDIDEI_2 | 1049898 | 1052492 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | WP_087347987.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PDMDIDEI_2 | 1146439 | 1147080 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| PDMDIDEI_1 | 249994 | 251175 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PDMDIDEI_5 | 159493 | 160278 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| PDMDIDEI_5 | 160304 | 161500 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| PDMDIDEI_5 | 163176 | 164114 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| PDMDIDEI_1 | 249530 | 249979 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| PDMDIDEI_2 | 1000406 | 1002169 | dep/capD | 0.0 | Capsule | Immune modulation | 98.81 | 100.00 | NP_389723 |
| PDMDIDEI_1 | 248369 | 249511 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| PDMDIDEI_5 | 161529 | 163148 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391078 |
| PDMDIDEI_5 | 164134 | 171270 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391076 |
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 |
|---|---|---|---|---|---|---|---|---|
| PDMDIDEI_7 | 27941 | 26805 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PDMDIDEI_14 | 4286 | 5155 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PDMDIDEI_2 | 674566 | 675342 | CodY | 1.63e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PDMDIDEI_1 | 94062 | 94631 | ClpP | 4.73e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PDMDIDEI_2 | 213750 | 214142 | spx | 7.63e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PDMDIDEI_11 | 20630 | 20872 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PDMDIDEI_3 | 84600 | 84403 | CspA | 1.04e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PDMDIDEI_10 | 29389 | 29583 | CspB | 5.73e-28 | cold shock protein | 83.08 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| PDMDIDEI_1 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_2 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_3 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_4 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_5 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_6 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_7 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_8 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_10 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_11 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_12 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_13 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_14 | 0.0 | 1.0 | 0.0 |
| PDMDIDEI_17 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PDMDIDEI_2 | 307658 | 334019 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4843, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
| PDMDIDEI_6 | 62104 | 67129 | False | Unknown | VOG8241, VOG4552, VOG1878, VOG8233, VOG0186 |
| PDMDIDEI_6 | 72308 | 93359 | False | Siphoviridae | VOG0044, VOG7007, VOG0198, VOG7983, VOG0796, VOG10227, VOG0691, VOG0692, VOG9317, VOG4572, VOG2621, VOG0695, VOG0696, VOG0697, VOG0698, VOG10044, VOG0701, VOG9745, VOG4605, VOG4599, VOG5535 |
Phigaro v2.4.0 (Database: Jan. 2024 release)