Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 4 | 16.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| PNOABPKD_1 | 3504300 | 3505154 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| PNOABPKD_1 | 3486004 | 3487206 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| PNOABPKD_1 | 3250455 | 3251624 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PNOABPKD_1 | 2136072 | 2136389 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PNOABPKD_1 | 2135734 | 2136072 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PNOABPKD_1 | 1674534 | 1677104 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.42 | 100.00 | AL009126.3 |
| PNOABPKD_1 | 1363406 | 1365052 | vmlR | ARO:3004476 | vmlR | 98.72 | 100.18 | NC_000964.3 |
| PNOABPKD_1 | 1084700 | 1085293 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| PNOABPKD_1 | 1034200 | 1035633 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| PNOABPKD_1 | 1021386 | 1022306 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| PNOABPKD_1 | 1021386 | 1022306 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| PNOABPKD_1 | 3504300 | 3505154 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PNOABPKD_1 | 1363409 | 1365052 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.72 | 100.00 | WP_003234144.1 |
| PNOABPKD_1 | 1021386 | 1022294 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| PNOABPKD_1 | 3504303 | 3505154 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| PNOABPKD_1 | 717976 | 718494 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| PNOABPKD_1 | 2821599 | 2824196 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 100.00 | WP_087347987.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PNOABPKD_1 | 3052926 | 3053567 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| PNOABPKD_1 | 242634 | 243815 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| PNOABPKD_1 | 4067037 | 4067822 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PNOABPKD_1 | 4063201 | 4064139 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| PNOABPKD_1 | 2775911 | 2777674 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| PNOABPKD_1 | 241009 | 242151 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| PNOABPKD_1 | 242170 | 242619 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| PNOABPKD_1 | 4056045 | 4063181 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 100.00 | NP_391076 |
| PNOABPKD_1 | 4065815 | 4067011 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.41 | 100.00 | NP_391079 |
| PNOABPKD_1 | 4064167 | 4065786 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.53 | 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 |
|---|---|---|---|---|---|---|---|---|
| PNOABPKD_1 | 886861 | 887997 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PNOABPKD_1 | 773122 | 773991 | pdxS | 2.01e-148 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| PNOABPKD_1 | 2447717 | 2448493 | CodY | 3.43e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PNOABPKD_1 | 84465 | 85034 | ClpP | 2.55e-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 |
|---|---|---|---|
| PNOABPKD_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 |
|---|---|---|---|---|---|
| PNOABPKD_1 | 2079361 | 2106181 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| PNOABPKD_1 | 2995003 | 3003194 | False | Myoviridae | VOG5779, VOG5721, VOG10940, VOG7134, VOG9867, VOG6036 |
| PNOABPKD_1 | 3008427 | 3028212 | False | Siphoviridae | VOG7930, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG4626, VOG3390, VOG4705, VOG8440, VOG10230 |
| PNOABPKD_1 | 3431615 | 3455174 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796 |
Phigaro v2.4.0 (Database: Jan. 2024 release)