Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 7 | 17.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| PDEDJCAP_8 | 675534 | 676703 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PDEDJCAP_9 | 596563 | 596901 | ykkC | ARO:3003063 | ykkC | 97.32 | 100.00 | AL009126.1 |
| PDEDJCAP_9 | 596246 | 596563 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PDEDJCAP_8 | 481187 | 482389 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| PDEDJCAP_8 | 454183 | 455037 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| PDEDJCAP_10 | 353957 | 354877 | mphK | ARO:3004541 | mphK | 97.06 | 100.00 | CP010314.1 |
| PDEDJCAP_10 | 340626 | 342065 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| PDEDJCAP_10 | 290919 | 291512 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| PDEDJCAP_11 | 262028 | 264598 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| PDEDJCAP_10 | 28788 | 30434 | vmlR | ARO:3004476 | vmlR | 99.27 | 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. |
|---|---|---|---|---|---|---|---|
| PDEDJCAP_8 | 454183 | 455037 | aadK | Streptomycin | 98.95 | 100.00 | M26879 |
| PDEDJCAP_7 | 60272 | 61648 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.77 | 100.00 | X08034 |
| PDEDJCAP_10 | 353957 | 354877 | mph(K) | Spiramycin, Telithromycin | 96.96 | 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. |
|---|---|---|---|---|---|---|---|---|
| PDEDJCAP_10 | 28788 | 30431 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.27 | 100.00 | WP_003234144.1 |
| PDEDJCAP_8 | 454183 | 455034 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| PDEDJCAP_7 | 60272 | 61642 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 99.78 | WP_003242953.1 |
| PDEDJCAP_10 | 353960 | 354877 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.06 | 100.00 | WP_003246254.1 |
| PDEDJCAP_7 | 63672 | 64190 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PDEDJCAP_7 | 557381 | 558562 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PDEDJCAP_8 | 875630 | 876270 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 99.84 | NP_390062 |
| PDEDJCAP_7 | 966551 | 967336 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PDEDJCAP_7 | 559045 | 560187 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| PDEDJCAP_7 | 558577 | 559026 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| PDEDJCAP_7 | 967362 | 968558 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| PDEDJCAP_8 | 1013270 | 1015033 | dep/capD | 0.0 | Capsule | Immune modulation | 98.87 | 100.00 | NP_389723 |
| PDEDJCAP_7 | 968587 | 970206 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.64 | 100.00 | NP_391078 |
| PDEDJCAP_7 | 971192 | 978328 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.64 | 100.00 | NP_391076 |
| PDEDJCAP_7 | 970234 | 971172 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.19 | 100.00 | NP_391077 |
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 |
|---|---|---|---|---|---|---|---|---|
| PDEDJCAP_12 | 31745 | 32881 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PDEDJCAP_14 | 11247 | 10378 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PDEDJCAP_9 | 284856 | 284080 | CodY | 8.29e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PDEDJCAP_7 | 714795 | 714226 | ClpP | 6.50e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PDEDJCAP_9 | 747402 | 747010 | spxA1 | 6.52e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PDEDJCAP_9 | 747402 | 747010 | spx | 3.89e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PDEDJCAP_13 | 20555 | 20797 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PDEDJCAP_10 | 84287 | 84090 | CspA | 1.93e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| PDEDJCAP_1 | 0.0 | 1.0 | 0.0 |
| PDEDJCAP_7 | 0.0 | 1.0 | 0.0 |
| PDEDJCAP_8 | 0.0 | 1.0 | 0.0 |
| PDEDJCAP_9 | 0.0 | 1.0 | 0.0 |
| PDEDJCAP_10 | 0.0 | 1.0 | 0.0 |
| PDEDJCAP_11 | 0.0 | 1.0 | 0.0 |
| PDEDJCAP_12 | 0.0 | 1.0 | 0.0 |
| PDEDJCAP_13 | 0.0 | 1.0 | 0.0 |
| PDEDJCAP_14 | 0.0 | 1.0 | 0.0 |
| PDEDJCAP_15 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PDEDJCAP_9 | 626153 | 654579 | False | Myoviridae | VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)