Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 3 | 15.17 |
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. |
|---|---|---|---|---|---|---|---|---|
| NPADCIJD_1 | 2534948 | 2535802 | aadK | ARO:3002627 | aadK | 99.30 | 100.00 | AL009126.1 |
| NPADCIJD_1 | 2505658 | 2506860 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| NPADCIJD_1 | 2335911 | 2337080 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| NPADCIJD_1 | 1347790 | 1348107 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| NPADCIJD_1 | 1347452 | 1347790 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| NPADCIJD_1 | 884403 | 886973 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| NPADCIJD_1 | 587557 | 589194 | vmlR | ARO:3004476 | vmlR | 98.53 | 99.63 | NC_000964.3 |
| NPADCIJD_1 | 330341 | 330934 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| NPADCIJD_1 | 279808 | 281241 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.00 | JYFL01000006.1 |
| NPADCIJD_1 | 266996 | 267916 | mphK | ARO:3004541 | mphK | 96.73 | 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. |
|---|---|---|---|---|---|---|---|
| NPADCIJD_1 | 2534948 | 2535802 | aadK | Streptomycin | 99.18 | 100.00 | M26879 |
| NPADCIJD_1 | 266996 | 267916 | mph(K) | Spiramycin, Telithromycin | 96.96 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| NPADCIJD_1 | 2534951 | 2535802 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 99.30 | 100.00 | WP_003229862.1 |
| NPADCIJD_1 | 587554 | 589194 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 98.35 | 99.82 | WP_003234144.1 |
| NPADCIJD_1 | 266996 | 267913 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 96.73 | 100.00 | WP_003246254.1 |
| NPADCIJD_1 | 2030094 | 2032691 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NPADCIJD_1 | 3570397 | 3571578 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| NPADCIJD_1 | 2136494 | 2137135 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| NPADCIJD_1 | 3161135 | 3161920 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| NPADCIJD_1 | 3569933 | 3570382 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| NPADCIJD_1 | 3568772 | 3569914 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| NPADCIJD_1 | 3159913 | 3161109 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| NPADCIJD_1 | 1984300 | 1986063 | dep/capD | 0.0 | Capsule | Immune modulation | 98.70 | 100.00 | NP_389723 |
| NPADCIJD_1 | 3150143 | 3157279 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.61 | 100.00 | NP_391076 |
| NPADCIJD_1 | 3158265 | 3159884 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 100.00 | NP_391078 |
| NPADCIJD_1 | 3157299 | 3158237 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.30 | 100.00 | NP_391077 |
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 |
|---|---|---|---|---|---|---|---|---|
| NPADCIJD_1 | 132339 | 133475 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| NPADCIJD_1 | 18601 | 19470 | pdxS | 3.04e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NPADCIJD_1 | 3413674 | 3414243 | ClpP | 2.46e-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 |
|---|---|---|---|
| NPADCIJD_1 | 0.0 | 1.0 | 0.0 |
| NPADCIJD_2 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NPADCIJD_1 | 1290014 | 1317906 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| NPADCIJD_1 | 2703856 | 2728205 | False | Siphoviridae | VOG6116, VOG8440, VOG0602, VOG4574, VOG0753, VOG4705, VOG4626, VOG4619, VOG0801, VOG4545, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5601, VOG4553, VOG4573, VOG4556, VOG4544, VOG4581, VOG4841 |
| NPADCIJD_1 | 2750567 | 2766674 | False | Siphoviridae | VOG0982, VOG0026, VOG10937, VOG5753, VOG7255, VOG1563, VOG2215, VOG4551, VOG0025, VOG0189, VOG6168, VOG7015, VOG0586 |
| NPADCIJD_2 | 968 | 24997 | False | Siphoviridae | VOG9258, VOG6163, VOG0801, VOG4619, VOG4626, VOG4705, VOG0753, VOG4574, VOG0602, VOG8440, VOG6116, VOG0705, VOG7531, VOG5216, VOG0275, VOG3375, VOG4841, VOG4566, VOG0586, VOG7015, VOG6168, VOG0189, VOG0025 |
Phigaro v2.4.0 (Database: Jan. 2024 release)