Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 10 | 10 | 4 | 14.70 |
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. |
|---|---|---|---|---|---|---|---|---|
| PNGPFILG_1 | 3773793 | 3775226 | lmrB | ARO:3002813 | lmrB | 100.00 | 100.00 | JYFL01000006.1 |
| PNGPFILG_1 | 3725539 | 3726132 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| PNGPFILG_1 | 3486549 | 3488195 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| PNGPFILG_1 | 3178187 | 3180757 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| PNGPFILG_1 | 2698347 | 2698685 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| PNGPFILG_1 | 2698030 | 2698347 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PNGPFILG_1 | 1611398 | 1612600 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| PNGPFILG_1 | 1594777 | 1595631 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| PNGPFILG_1 | 1594777 | 1595631 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| PNGPFILG_1 | 3787120 | 3788039 | mph(K) | Spiramycin, Telithromycin | 97.83 | 99.89 | 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. |
|---|---|---|---|---|---|---|---|---|
| PNGPFILG_1 | 3486549 | 3488192 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| PNGPFILG_1 | 1594777 | 1595628 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| PNGPFILG_1 | 28966 | 29484 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PNGPFILG_1 | 525976 | 527157 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| PNGPFILG_1 | 998965 | 999750 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PNGPFILG_1 | 527640 | 528782 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| PNGPFILG_1 | 1002648 | 1003586 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| PNGPFILG_1 | 999776 | 1000972 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| PNGPFILG_1 | 2145062 | 2146825 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| PNGPFILG_1 | 2007147 | 2007788 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| PNGPFILG_1 | 527172 | 527621 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| PNGPFILG_1 | 1003606 | 1010742 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.72 | 100.00 | NP_391076 |
| PNGPFILG_1 | 1001001 | 1002620 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.73 | 100.00 | NP_391078 |
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 |
|---|---|---|---|---|---|---|---|---|
| PNGPFILG_1 | 3942737 | 3941601 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PNGPFILG_1 | 4056555 | 4055686 | pdxS | 5.30e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| PNGPFILG_1 | 2378903 | 2378127 | CodY | 3.31e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PNGPFILG_1 | 677193 | 676624 | ClpP | 2.45e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| PNGPFILG_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PNGPFILG_1 | 763774 | 802178 | True | Siphoviridae | VOG3490, VOG0275, VOG0275, VOG1563, VOG9667, VOG9667, VOG7581, VOG4566, VOG0189, VOG6587, VOG1336, VOG0245, VOG5836, VOG0397, VOG0102, VOG0044, VOG0198, VOG0275, VOG4841, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG10223, VOG0204, VOG9583, VOG0704, VOG4586, VOG0541, VOG5910, VOG0801, VOG4772, VOG4626, VOG4612, VOG6243, VOG4705 |
| PNGPFILG_1 | 1442949 | 1469949 | False | Siphoviridae | VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG6243, VOG4705, VOG0641, VOG4918 |
| PNGPFILG_1 | 2728166 | 2756485 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667, VOG4602 |
Phigaro v2.4.0 (Database: Jan. 2024 release)