Probiotic potential risk score
| ARGs (CARD) | VFs (VFDB) | PGs (PHI-base) | PPRS |
|---|---|---|---|
| 6 | 10 | 8 | 14.14 |
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:3003324 | Bacillus subtilis mprF | 97.90 | 100.00 | Bsub_mprF | AL009126.3 |
| ARO:3003064 | ykkD | 97.14 | 100.00 | ykkD | AL009126.1 |
| ARO:3002813 | lmrB | 97.06 | 100.00 | lmrB | JYFL01000006.1 |
| ARO:3004476 | vmlR | 92.87 | 100.00 | vmlR | NC_000964.3 |
| ARO:3002627 | aadK | 89.44 | 100.00 | aadK | AL009126.1 |
| ARO:3004541 | mphK | 89.11 | 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. |
|---|---|---|---|---|
| mph(K) | 92.39 | 98.05 | Warning: gene is missing from Notes file. Please inform curator. | NC_000964 |
| aadK | 91.35 | 100.00 | Aminoglycoside resistance | M26879 |
ResFinder v4.0 (Database: resfinder_db, May 2022 release)
AMRFinderPlus
| Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|
| vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 92.87 | 100.00 | WP_003234144.1 |
| aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 89.44 | 100.00 | WP_003229862.1 |
| mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 89.11 | 99.02 | WP_003246254.1 |
| rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.68 | 100.00 | WP_087347987.1 |
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 | 96.53 | 100.00 | 0.0 | Capsule | Immune modulation | NP_391471 |
| VFG016295 | capC | 96.44 | 100.00 | 0.0 | Capsule | Immune modulation | NP_391470 |
| VFG016291 | capA | 94.66 | 100.00 | 0.0 | Capsule | Immune modulation | NP_391469 |
| VFG016303 | dep/capD | 92.74 | 100.00 | 0.0 | Capsule | Immune modulation | NP_389723 |
| VFG050032 | dhbB | 92.33 | 99.79 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391077 |
| VFG016234 | hlyIII | 92.06 | 100.00 | 0.0 | Hemolysin III | Exotoxin | NP_390062 |
| VFG049999 | dhbA | 91.60 | 100.00 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391080 |
| VFG050021 | dhbE | 91.11 | 100.00 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391078 |
| VFG050043 | dhbF | 91.07 | 99.99 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391076 |
| VFG050010 | dhbC | 88.81 | 99.92 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391079 |
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 | 86.04 | 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 | 5.98e-148 | Nutrient-responsive regulator | ACJ80679 |
| Q9RGX0 | spxA1 | 83.21 | 99.24 | 2.25e-82 | Redox-responsive transcription factor | AAF21893 |
| Q724L7 | SpoVG | 82.72 | 78.64 | 2.49e-47 | RNA-Binding Protein | AAT02994 |
| P0A355 | CspA | 92.42 | 98.51 | 2.02e-40 | Cold shock protein | CAA62903 |
| Q92AD0 | CspD | 81.54 | 97.01 | 2.14e-36 | Cold shock protein | CAC99957 |
| P0A357 | CspB | 83.08 | 97.01 | 3.14e-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. |
|---|---|---|---|
| No hit found | |||
PlasmidFinder 2.0.1 (Database: plasmidfinder_db, Jan. 2023 release)
Prophage
Phigaro
| Scaffold | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NQYD01000001.1 | 2537487 | 2561894 | False | Myoviridae | VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862, VOG7718 |
| NQYD01000001.1 | 3279154 | 3304217 | False | Siphoviridae | VOG0641, VOG4705, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG9583, VOG1266, VOG0204, VOG10223, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG0275 |
| NQYD01000001.1 | 3975816 | 4003099 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.3.0 (Database: Aug. 2017 release)