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. |
|---|---|---|---|---|---|---|---|---|
| CCOFNNOD_1 | 2773797 | 2774651 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| CCOFNNOD_1 | 2756718 | 2757920 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| CCOFNNOD_1 | 2529950 | 2531119 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| CCOFNNOD_1 | 1622779 | 1623096 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| CCOFNNOD_1 | 1622441 | 1622779 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CCOFNNOD_1 | 1142615 | 1145185 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| CCOFNNOD_1 | 837565 | 839211 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| CCOFNNOD_1 | 585261 | 585854 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| CCOFNNOD_1 | 534703 | 536136 | lmrB | ARO:3002813 | lmrB | 100.00 | 100.00 | JYFL01000006.1 |
| CCOFNNOD_1 | 521889 | 522809 | 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. |
|---|---|---|---|---|---|---|---|
| CCOFNNOD_1 | 2773797 | 2774651 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| CCOFNNOD_1 | 521889 | 522809 | 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. |
|---|---|---|---|---|---|---|---|---|
| CCOFNNOD_1 | 837568 | 839211 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| CCOFNNOD_1 | 521889 | 522797 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| CCOFNNOD_1 | 2773800 | 2774651 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| CCOFNNOD_1 | 191284 | 191802 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| CCOFNNOD_1 | 2215409 | 2217997 | rphC | rifamycin-inactivating phosphotransferase RphC | INTERNAL_STOP | 80.25 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CCOFNNOD_1 | 2329213 | 2329854 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| CCOFNNOD_1 | 3404046 | 3404831 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| CCOFNNOD_1 | 3811068 | 3811517 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| CCOFNNOD_1 | 3811532 | 3812713 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| CCOFNNOD_1 | 2162269 | 2164032 | dep/capD | 0.0 | Capsule | Immune modulation | 99.32 | 100.00 | NP_389723 |
| CCOFNNOD_1 | 3809907 | 3811049 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| CCOFNNOD_1 | 3400210 | 3401148 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| CCOFNNOD_1 | 3402824 | 3404020 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| CCOFNNOD_1 | 3393054 | 3400190 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.99 | 100.00 | NP_391076 |
| CCOFNNOD_1 | 3401176 | 3402795 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.10 | 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 |
|---|---|---|---|---|---|---|---|---|
| CCOFNNOD_1 | 350848 | 351984 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CCOFNNOD_1 | 236954 | 237823 | pdxS | 3.05e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CCOFNNOD_1 | 1940907 | 1941683 | CodY | 3.33e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CCOFNNOD_1 | 3656569 | 3657138 | 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 |
|---|---|---|---|
| CCOFNNOD_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 |
|---|---|---|---|---|---|
| CCOFNNOD_1 | 377777 | 405159 | False | Siphoviridae | VOG1936, VOG4606, VOG2752, VOG7372, VOG0044, VOG0198, VOG8909, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG6243, VOG4705, VOG0641 |
| CCOFNNOD_1 | 1566272 | 1592951 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| CCOFNNOD_1 | 2701733 | 2731631 | 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 |
| CCOFNNOD_1 | 2832202 | 2859163 | False | Siphoviridae | VOG0136, VOG5221, VOG4705, VOG6243, VOG4612, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841, VOG2874, VOG0275, VOG0198, VOG4376, VOG6581, VOG0397, VOG4694 |
| CCOFNNOD_1 | 2861383 | 2864416 | False | Unknown | VOG0189, VOG4566, VOG0650, VOG9667 |
| CCOFNNOD_1 | 2938399 | 2971465 | False | Siphoviridae | VOG4972, VOG4574, VOG0641, VOG4705, VOG6243, VOG4612, VOG4626, VOG4619, VOG0801, VOG4545, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3644, VOG1886, VOG4581, VOG4556, VOG4841, VOG0198, VOG4548, VOG0327, VOG4609, VOG0026, VOG1565, VOG0021, VOG1047, VOG7438 |
Phigaro v2.4.0 (Database: Jan. 2024 release)