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. |
|---|---|---|---|---|---|---|---|---|
| COMBCLOF_1 | 2724812 | 2725666 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| COMBCLOF_1 | 2707092 | 2708294 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| COMBCLOF_1 | 2503663 | 2504832 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| COMBCLOF_1 | 1368276 | 1368593 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| COMBCLOF_1 | 1367938 | 1368276 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| COMBCLOF_1 | 906157 | 908727 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| COMBCLOF_1 | 600902 | 602545 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
| COMBCLOF_1 | 352639 | 353232 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| COMBCLOF_1 | 302145 | 303578 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| COMBCLOF_1 | 289331 | 290251 | mphK | ARO:3004541 | mphK | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| COMBCLOF_1 | 289331 | 290251 | mph(K) | Spiramycin, Telithromycin | 99.78 | 100.00 | NC_000964 |
| COMBCLOF_1 | 4191639 | 4193015 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.42 | 100.00 | D12567 |
| COMBCLOF_1 | 2724814 | 2725666 | aadK | Streptomycin | 98.71 | 99.77 | 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. |
|---|---|---|---|---|---|---|---|---|
| COMBCLOF_1 | 289331 | 290248 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| COMBCLOF_1 | 4191642 | 4193015 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.13 | 100.00 | WP_063856081.1 |
| COMBCLOF_1 | 600905 | 602545 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| COMBCLOF_1 | 2724815 | 2725666 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| COMBCLOF_1 | 4189232 | 4189750 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 94.22 | 100.00 | WP_003242546.1 |
| COMBCLOF_1 | 2197941 | 2200538 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.48 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| COMBCLOF_1 | 2300947 | 2301588 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| COMBCLOF_1 | 3700491 | 3701672 | capB | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_391471 |
| COMBCLOF_1 | 3280828 | 3281613 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| COMBCLOF_1 | 3700027 | 3700476 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| COMBCLOF_1 | 2146093 | 2147856 | dep/capD | 0.0 | Capsule | Immune modulation | 99.55 | 100.00 | NP_389723 |
| COMBCLOF_1 | 3276992 | 3277930 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.47 | 100.00 | NP_391077 |
| COMBCLOF_1 | 3698866 | 3700008 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| COMBCLOF_1 | 3279606 | 3280802 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| COMBCLOF_1 | 3269836 | 3276972 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.22 | 100.00 | NP_391076 |
| COMBCLOF_1 | 3277958 | 3279577 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.96 | 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 |
|---|---|---|---|---|---|---|---|---|
| COMBCLOF_1 | 132472 | 133608 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| COMBCLOF_1 | 18661 | 19530 | pdxS | 3.13e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| COMBCLOF_1 | 1678824 | 1679600 | CodY | 3.42e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| COMBCLOF_1 | 3535398 | 3535967 | ClpP | 2.54e-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 |
|---|---|---|---|
| COMBCLOF_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 |
|---|---|---|---|---|---|
| COMBCLOF_1 | 1312396 | 1338129 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)