Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| OMGCKCJF_1 | 1668399 | 1668737 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| OMGCKCJF_1 | 1668082 | 1668399 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| OMGCKCJF_1 | 653206 | 654375 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| OMGCKCJF_1 | 445311 | 446513 | blt | ARO:3003006 | blt | 98.75 | 100.00 | L32599.1 |
| OMGCKCJF_1 | 428498 | 429352 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| OMGCKCJF_3 | 409978 | 411624 | vmlR | ARO:3004476 | vmlR | 99.09 | 100.18 | NC_000964.3 |
| OMGCKCJF_3 | 158938 | 159531 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| OMGCKCJF_3 | 108377 | 109810 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| OMGCKCJF_3 | 95565 | 96485 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
| OMGCKCJF_6 | 27444 | 30017 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.12 | AL009126.3 |
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. |
|---|---|---|---|---|---|---|---|
| OMGCKCJF_3 | 95565 | 96485 | mph(K) | Spiramycin, Telithromycin | 99.35 | 100.00 | NC_000964 |
| OMGCKCJF_1 | 428498 | 429352 | aadK | Streptomycin | 98.95 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| OMGCKCJF_3 | 409981 | 411624 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.09 | 100.00 | WP_003234144.1 |
| OMGCKCJF_3 | 95565 | 96482 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| OMGCKCJF_1 | 428498 | 429349 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| OMGCKCJF_5 | 38220 | 38738 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| OMGCKCJF_1 | 942233 | 944830 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| OMGCKCJF_1 | 851035 | 851676 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| OMGCKCJF_2 | 166424 | 167605 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| OMGCKCJF_2 | 594534 | 595730 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.42 | 100.00 | NP_391079 |
| OMGCKCJF_2 | 593723 | 594508 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| OMGCKCJF_2 | 597406 | 598344 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| OMGCKCJF_1 | 997246 | 999009 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| OMGCKCJF_2 | 168088 | 169230 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| OMGCKCJF_2 | 167620 | 168069 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| OMGCKCJF_2 | 598364 | 605500 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.82 | 100.00 | NP_391076 |
| OMGCKCJF_2 | 595759 | 597378 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.04 | 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 |
|---|---|---|---|---|---|---|---|---|
| OMGCKCJF_7 | 31767 | 32903 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| OMGCKCJF_9 | 4391 | 5260 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| OMGCKCJF_1 | 1356929 | 1356153 | CodY | 1.39e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| OMGCKCJF_2 | 328434 | 327865 | ClpP | 4.25e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| OMGCKCJF_4 | 141806 | 141414 | spxA1 | 2.67e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| OMGCKCJF_4 | 141806 | 141414 | spx | 1.59e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| OMGCKCJF_8 | 20624 | 20866 | SpoVG | 7.53e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| OMGCKCJF_3 | 361266 | 361463 | CspA | 1.90e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| OMGCKCJF_4 | 387302 | 387496 | CspB | 3.84e-27 | cold shock protein | 83.08 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| OMGCKCJF_1 | 0.0 | 1.0 | 0.0 |
| OMGCKCJF_2 | 0.0 | 1.0 | 0.0 |
| OMGCKCJF_3 | 0.0 | 1.0 | 0.0 |
| OMGCKCJF_4 | 0.0 | 1.0 | 0.0 |
| OMGCKCJF_5 | 0.0 | 1.0 | 0.0 |
| OMGCKCJF_6 | 0.0 | 1.0 | 0.0 |
| OMGCKCJF_7 | 0.0 | 1.0 | 0.0 |
| OMGCKCJF_8 | 0.0 | 1.0 | 0.0 |
| OMGCKCJF_9 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| OMGCKCJF_1 | 1129670 | 1152784 | False | Siphoviridae | VOG0136, VOG5221, VOG7896, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581, VOG4841 |
| OMGCKCJF_1 | 1699461 | 1706006 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894 |
| OMGCKCJF_4 | 5771 | 15694 | False | Siphoviridae | VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)