Probiotic potential risk score
| ARGs (CARD) | VFs (VFDB) | PGs (PHI-base) | PPRS |
|---|---|---|---|
| 10 | 10 | 9 | 16.76 |
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:3002813 | lmrB | 99.58 | 100.00 | lmrB | JYFL01000006.1 |
| ARO:3003324 | Bacillus subtilis mprF | 98.48 | 100.00 | Bsub_mprF | AL009126.3 |
| ARO:3003007 | bmr | 98.20 | 100.00 | bmr | M33768.1 |
| ARO:3003064 | ykkD | 98.10 | 100.00 | ykkD | AL009126.1 |
| ARO:3003006 | blt | 96.50 | 100.00 | blt | L32599.1 |
| ARO:3003063 | ykkC | 96.43 | 100.00 | ykkC | AL009126.1 |
| ARO:3004476 | vmlR | 96.15 | 100.00 | vmlR | NC_000964.3 |
| ARO:3002627 | aadK | 94.37 | 100.00 | aadK | AL009126.1 |
| ARO:3003059 | tmrB | 92.39 | 101.02 | tmrB | AL009126.3 |
| ARO:3004541 | mphK | 90.52 | 114.38 | 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 | 94.16 | 99.88 | Aminoglycoside resistance | M26879 |
| mph(K) | 91.54 | 99.89 | 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. |
|---|---|---|---|---|---|
| satA | streptothricin N-acetyltransferase SatA | BLASTX | 99.42 | 100.00 | WP_003242546.1 |
| vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 96.15 | 99.82 | WP_003234144.1 |
| aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 94.37 | 100.00 | WP_003229862.1 |
| mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 90.52 | 100.00 | WP_003246254.1 |
| rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.92 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|
| VFG016295 | capC | 98.44 | 100.00 | 0.0 | Capsule | Immune modulation | NP_391470 |
| VFG016299 | capB | 97.97 | 100.00 | 0.0 | Capsule | Immune modulation | NP_391471 |
| VFG016291 | capA | 96.33 | 100.00 | 0.0 | Capsule | Immune modulation | NP_391469 |
| VFG050032 | dhbB | 95.85 | 99.89 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391077 |
| VFG016303 | dep/capD | 95.75 | 99.94 | 0.0 | Capsule | Immune modulation | NP_389723 |
| VFG050043 | dhbF | 95.06 | 99.99 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391076 |
| VFG049999 | dhbA | 95.04 | 100.00 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391080 |
| VFG050021 | dhbE | 93.52 | 100.00 | 0.0 | Bacillibactin | Nutritional/Metabolic factor | NP_391078 |
| VFG016234 | hlyIII | 92.99 | 100.00 | 0.0 | Hemolysin III | Exotoxin | NP_390062 |
| VFG050010 | dhbC | 92.06 | 100.00 | 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 | 85.53 | 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 | 5.71e-148 | Nutrient-responsive regulator | ACJ80679 |
| P63786 | ClpP | 81.05 | 96.94 | 1.53e-114 | Part of proteolytic complex | BAB94595 |
| Q9RGX0 | spxA1 | 83.21 | 99.24 | 4.15e-82 | Redox-responsive transcription factor | AAF21893 |
| Q724L7 | SpoVG | 82.72 | 78.64 | 2.37e-47 | RNA-Binding Protein | AAT02994 |
| P0A355 | CspA | 90.91 | 98.51 | 7.84e-40 | Cold shock protein | CAA62903 |
| Q92AD0 | CspD | 80.00 | 97.01 | 1.13e-35 | Cold shock protein | CAC99957 |
| P0A357 | CspB | 83.08 | 97.01 | 3.00e-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 |
|---|---|---|---|---|---|
| LYMC01000002.1 | 1307728 | 1334382 | False | Myoviridae | VOG4602, VOG9667, VOG10994, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136 |
| LYMC01000002.1 | 2945278 | 2967971 | False | Siphoviridae | VOG4707, VOG0136, VOG0753, VOG5535, VOG4599, VOG4605, VOG4545, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG0815, VOG1125, VOG4553, VOG4555, VOG4564, VOG0720, VOG10227, VOG0796 |
| LYMC01000002.1 | 2974007 | 2977874 | False | Unknown | VOG0189, VOG4566, VOG1309, VOG4600 |
Phigaro v2.3.0 (Database: Aug. 2017 release)