Probiotic potential risk score
| ARGs (CARD) | VFs (VFDB) | PGs (PHI-base) | PPRS |
|---|---|---|---|
| 9 | 10 | 9 | 16.19 |
PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).
Antibiotic resistance genes
Comprehensive Antibiotic Resistance Database (CARD)
| ARO accession | ARO name | Identity | Coverage | CARD name | Accession no. |
|---|---|---|---|---|---|
| ARO:3003063 | ykkC | 100.00 | 100.00 | ykkC | AL009126.1 |
| ARO:3003324 | Bacillus subtilis mprF | 99.77 | 100.00 | Bsub_mprF | AL009126.3 |
| ARO:3003007 | bmr | 99.23 | 100.00 | bmr | M33768.1 |
| ARO:3003064 | ykkD | 99.05 | 100.00 | ykkD | AL009126.1 |
| ARO:3003059 | tmrB | 98.98 | 100.00 | tmrB | AL009126.3 |
| ARO:3002627 | aadK | 98.59 | 100.00 | aadK | AL009126.1 |
| ARO:3004476 | vmlR | 98.54 | 100.18 | vmlR | NC_000964.3 |
| ARO:3002813 | lmrB | 98.53 | 100.42 | lmrB | JYFL01000006.1 |
| ARO:3004541 | mphK | 97.39 | 100.00 | mphK | CP010314.1 |
RGI v6.0.0 (Database: CARD Variants v4.0.0, Jul. 2022 release)
ResFinder
| Resistance gene | Identity | Coverage | Phenotype | Accession no. |
|---|---|---|---|---|
| aadK | 98.71 | 100.00 | Aminoglycoside resistance | M26879 |
| mph(K) | 97.94 | 100.00 | Warning: gene is missing from Notes file. Please inform curator. | NC_000964 |
ResFinder v4.0 (Database: resfinder_db, May 2022 release)
AMRFinderPlus
| Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|
| aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.39 | 100.00 | WP_003246254.1 |
| rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.17 | 100.00 | WP_087347987.1 |
| satA | streptothricin N-acetyltransferase SatA | PARTIALX | 92.79 | 64.16 | WP_003242546.1 |
AMRFinderPlus v3.10.42 (Database: Oct. 2022 release)
Virulence factors
Virulence Factor Database (VFDB)
| Gene ID | Gene name | Identity | Coverage | e-value | VF name | VF category | Accession no. |
|---|---|---|---|---|---|---|---|
| VFG016299 | capB | 99.66 | 100.00 | 0.0 | Capsule | Immune modulation | NP_391471 |
| VFG049999 | dhbA | 99.36 | 100.00 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391080 |
| VFG016295 | capC | 99.33 | 100.00 | 0.0 | Capsule | Immune modulation | NP_391470 |
| VFG050043 | dhbF | 99.27 | 100.00 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391076 |
| VFG016234 | hlyIII | 99.22 | 100.00 | 0.0 | Hemolysin III | Exotoxin | NP_390062 |
| VFG050010 | dhbC | 99.17 | 100.00 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391079 |
| VFG016303 | dep/capD | 98.98 | 100.00 | 0.0 | Capsule | Immune modulation | NP_389723 |
| VFG016291 | capA | 98.86 | 100.00 | 0.0 | Capsule | Immune modulation | NP_391469 |
| VFG050032 | dhbB | 98.83 | 100.00 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391077 |
| VFG050021 | dhbE | 98.39 | 100.00 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391078 |
BLASTN v2.8.1+ (Database: VFDB, Jun. 2022 release)
VirulenceFinder
| Database | Virulence factor | Identity | Coverage | Protein function | Accession no. |
|---|---|---|---|---|---|
| No hit found | |||||
VirulenceFinder v2.0.3 (Database: virulencefinder_db, Dec. 2022 release)
Pathogenic genes
PHI-base
| Protein ID | Gene name | Identity | Coverage | e-value | Function | Gene ID |
|---|---|---|---|---|---|---|
| W8TRT9 | tufA | 85.79 | 99.24 | 0.0 | Elongation factor Tu | AHM69299 |
| B3GXB6 | pdxS | 83.79 | 97.97 | 0.0 | Encodes the putative pyridoxal 5-phosphate synthase subunit PdxS | ACE61268 |
| B7HLG1 | CodY | 81.08 | 99.62 | 6.14e-148 | Nutrient-responsive regulator | ACJ80679 |
| P63786 | ClpP | 81.05 | 96.94 | 1.74e-114 | Part of proteolytic complex | BAB94595 |
| Q9RGX0 | spxA1 | 83.97 | 99.24 | 9.93e-83 | Redox-responsive transcription factor | AAF21893 |
| Q724L7 | SpoVG | 82.72 | 78.64 | 2.55e-47 | RNA-Binding Protein | AAT02994 |
| P0A355 | CspA | 90.91 | 98.51 | 8.43e-40 | Cold shock protein | CAA62903 |
| Q92AD0 | CspD | 81.54 | 97.01 | 2.19e-36 | Cold shock protein | CAC99957 |
| P0A357 | CspB | 83.08 | 97.01 | 3.23e-34 | Cold shock protein | CAD00094 |
BLASTP v2.8.1+ (Database: PHI-base v4.14, Nov. 2022 release)
Plasmid
PlasmidFinder
| Plasmid | Identity | Query / Template | Accession no. |
|---|---|---|---|
| Col440II | 97.52 | 282 / 282 | CP023921 |
| Col(pHAD28) | 92.91 | 127 / 131 | KU674895 |
PlasmidFinder 2.0.1 (Database: plasmidfinder_db, Jan. 2023 release)
Prophage
Phigaro
| Scaffold | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JAGFPW010000001.1 | 450027 | 475925 | False | Myoviridae | VOG0221, VOG6116, VOG6422, VOG4574, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720, VOG10227 |
| JAGFPW010000022.1 | 38210 | 53779 | True | Myoviridae | VOG8484, VOG0275, VOG11077, VOG1563, VOG6362, VOG0705, VOG1026, VOG6282, VOG5219, VOG5220, VOG5243, VOG5356, VOG4910, VOG5208, VOG1013 |
| JAGFPW010000032.1 | 7909 | 19748 | False | Myoviridae / Siphoviridae | VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG1328 |
| JAGFPW010000032.1 | 29704 | 34500 | False | Unknown | VOG1292, VOG1309, VOG0083 |
| JAGFPW010000034.1 | 8688 | 28679 | False | Siphoviridae | VOG1198, VOG4581, VOG1886, VOG4556, VOG4573, VOG4553, VOG0204, VOG4589, VOG0704, VOG4586, VOG0541, VOG0801, VOG4619, VOG4626, VOG4612, VOG3390, VOG4705 |
| JAGFPW010000006.1 | 150479 | 161467 | False | Unknown | VOG5042, VOG3389, VOG4910 |
| JAGFPW010000008.1 | 2816 | 4693 | False | Myoviridae | VOG4691, VOG4862 |
Phigaro v2.3.0 (Database: Aug. 2017 release)