Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 4 | 16.88 |
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. |
|---|---|---|---|---|---|---|---|---|
| HOJCAODL_1 | 2617362 | 2618216 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| HOJCAODL_1 | 2600095 | 2601297 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| HOJCAODL_1 | 2381814 | 2382983 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| HOJCAODL_1 | 1394582 | 1394899 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| HOJCAODL_1 | 1394244 | 1394582 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| HOJCAODL_1 | 933015 | 935585 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| HOJCAODL_1 | 581190 | 582818 | vmlR | ARO:3004476 | vmlR | 99.08 | 99.09 | NC_000964.3 |
| HOJCAODL_1 | 328796 | 329389 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| HOJCAODL_1 | 278290 | 279723 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| HOJCAODL_1 | 265475 | 266341 | mphK | ARO:3004541 | mphK | 98.61 | 94.12 | 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. |
|---|---|---|---|---|---|---|---|
| HOJCAODL_1 | 4084614 | 4085990 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.06 | 100.00 | D12567 |
| HOJCAODL_1 | 2617364 | 2618216 | aadK | Streptomycin | 98.94 | 99.77 | M26879 |
| HOJCAODL_1 | 265475 | 266395 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| HOJCAODL_1 | 581193 | 582818 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.08 | 98.90 | WP_003234144.1 |
| HOJCAODL_1 | 2617365 | 2618216 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| HOJCAODL_1 | 4084617 | 4085990 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| HOJCAODL_1 | 265475 | 266392 | mphK | macrolide 2'-phosphotransferase MphK | INTERNAL_STOP | 98.04 | 100.00 | WP_003246254.1 |
| HOJCAODL_1 | 4082151 | 4082669 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| HOJCAODL_1 | 2075721 | 2078318 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HOJCAODL_1 | 3591175 | 3592317 | capA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391469 |
| HOJCAODL_1 | 3592336 | 3592785 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| HOJCAODL_1 | 3189373 | 3190158 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| HOJCAODL_1 | 3178381 | 3185517 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.99 | 100.00 | NP_391076 |
| HOJCAODL_1 | 3592800 | 3593981 | capB | 0.0 | Capsule | Immune modulation | 99.92 | 100.00 | NP_391471 |
| HOJCAODL_1 | 3185537 | 3186475 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| HOJCAODL_1 | 3186503 | 3188122 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391078 |
| HOJCAODL_1 | 3188151 | 3189347 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.50 | 100.00 | NP_391079 |
| HOJCAODL_1 | 2179022 | 2179663 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| HOJCAODL_1 | 2020208 | 2021971 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| HOJCAODL_1 | 131066 | 132202 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| HOJCAODL_1 | 17325 | 18194 | pdxS | 3.05e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HOJCAODL_1 | 1704584 | 1705360 | CodY | 3.34e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HOJCAODL_1 | 3438701 | 3439270 | ClpP | 2.47e-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 |
|---|---|---|---|
| HOJCAODL_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 |
|---|---|---|---|---|---|
| HOJCAODL_1 | 631606 | 634310 | False | Unknown | VOG9667, VOG9667, VOG0650, VOG4552 |
| HOJCAODL_1 | 644988 | 668188 | False | Siphoviridae | VOG0796, VOG10227, VOG0720, VOG4564, VOG6778, VOG4555, VOG4553, VOG1125, VOG0815, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG4545, VOG4605, VOG4599, VOG5535, VOG10940, VOG0753, VOG0136, VOG4707 |
| HOJCAODL_1 | 1338275 | 1364757 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
| HOJCAODL_1 | 2553600 | 2583497 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309, VOG4600 |
Phigaro v2.4.0 (Database: Jan. 2024 release)