Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 7 | 16.43 |
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. |
|---|---|---|---|---|---|---|---|---|
| CBMIKOBA_3 | 696305 | 697474 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| CBMIKOBA_4 | 600121 | 600459 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| CBMIKOBA_4 | 599804 | 600121 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| CBMIKOBA_3 | 467462 | 468664 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| CBMIKOBA_3 | 438520 | 439374 | aadK | ARO:3002627 | aadK | 99.30 | 100.00 | AL009126.1 |
| CBMIKOBA_1 | 350312 | 351232 | mphK | ARO:3004541 | mphK | 97.06 | 100.00 | CP010314.1 |
| CBMIKOBA_1 | 336981 | 338420 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.42 | JYFL01000006.1 |
| CBMIKOBA_1 | 287288 | 287881 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| CBMIKOBA_5 | 257637 | 260207 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| CBMIKOBA_1 | 29025 | 30662 | vmlR | ARO:3004476 | vmlR | 98.72 | 99.63 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| CBMIKOBA_3 | 438520 | 439374 | aadK | Streptomycin | 99.18 | 100.00 | M26879 |
| CBMIKOBA_1 | 350312 | 351232 | 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. |
|---|---|---|---|---|---|---|---|---|
| CBMIKOBA_3 | 438520 | 439371 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 99.30 | 100.00 | WP_003229862.1 |
| CBMIKOBA_1 | 29025 | 30665 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 98.54 | 99.82 | WP_003234144.1 |
| CBMIKOBA_1 | 350315 | 351232 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.06 | 100.00 | WP_003246254.1 |
| CBMIKOBA_3 | 1000666 | 1003263 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CBMIKOBA_2 | 522301 | 523482 | capB | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_391471 |
| CBMIKOBA_2 | 113060 | 113845 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| CBMIKOBA_3 | 896236 | 896877 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| CBMIKOBA_2 | 521837 | 522286 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| CBMIKOBA_2 | 520676 | 521818 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| CBMIKOBA_2 | 111838 | 113034 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| CBMIKOBA_3 | 1047285 | 1049048 | dep/capD | 0.0 | Capsule | Immune modulation | 98.70 | 100.00 | NP_389723 |
| CBMIKOBA_2 | 102068 | 109204 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.67 | 100.00 | NP_391076 |
| CBMIKOBA_2 | 110190 | 111809 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391078 |
| CBMIKOBA_2 | 109224 | 110162 | 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 |
|---|---|---|---|---|---|---|---|---|
| CBMIKOBA_7 | 31661 | 32797 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| CBMIKOBA_9 | 4325 | 5194 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CBMIKOBA_4 | 288260 | 287484 | CodY | 8.35e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CBMIKOBA_2 | 365592 | 366161 | ClpP | 5.59e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CBMIKOBA_4 | 752547 | 752155 | spxA1 | 6.56e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CBMIKOBA_4 | 752547 | 752155 | spx | 3.91e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CBMIKOBA_8 | 34702 | 34460 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CBMIKOBA_1 | 84499 | 84302 | CspA | 1.90e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| CBMIKOBA_1 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_2 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_3 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_4 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_5 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_6 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_7 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_8 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_9 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_13 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_14 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_16 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_18 | 0.0 | 1.0 | 0.0 |
| CBMIKOBA_19 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CBMIKOBA_3 | 500042 | 517037 | False | Myoviridae | VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG10989, VOG4691, VOG4862 |
| CBMIKOBA_4 | 630005 | 657897 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)