Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 7 | 17.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| OLOPCOLM_6 | 685118 | 686287 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| OLOPCOLM_7 | 475661 | 475978 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| OLOPCOLM_7 | 475323 | 475661 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| OLOPCOLM_6 | 463823 | 465025 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| OLOPCOLM_6 | 445417 | 446271 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| OLOPCOLM_8 | 345144 | 346064 | mphK | ARO:3004541 | mphK | 97.39 | 100.00 | CP010314.1 |
| OLOPCOLM_8 | 331812 | 333251 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| OLOPCOLM_8 | 282137 | 282730 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| OLOPCOLM_8 | 29197 | 30840 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| OLOPCOLM_9 | 27472 | 30042 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| OLOPCOLM_6 | 445417 | 446271 | aadK | Streptomycin | 98.71 | 100.00 | M26879 |
| OLOPCOLM_8 | 345144 | 346064 | mph(K) | Spiramycin, Telithromycin | 97.39 | 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. |
|---|---|---|---|---|---|---|---|---|
| OLOPCOLM_6 | 445417 | 446268 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| OLOPCOLM_8 | 29197 | 30837 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| OLOPCOLM_8 | 345147 | 346064 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.39 | 100.00 | WP_003246254.1 |
| OLOPCOLM_1 | 1025857 | 1026375 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.64 | 100.00 | WP_003242546.1 |
| OLOPCOLM_6 | 979202 | 981799 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.65 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| OLOPCOLM_1 | 535645 | 536826 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| OLOPCOLM_1 | 113002 | 113787 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| OLOPCOLM_6 | 882959 | 883600 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| OLOPCOLM_1 | 111780 | 112976 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| OLOPCOLM_6 | 1034279 | 1036042 | dep/capD | 0.0 | Capsule | Immune modulation | 99.32 | 100.00 | NP_389723 |
| OLOPCOLM_1 | 535181 | 535630 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| OLOPCOLM_1 | 534020 | 535162 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| OLOPCOLM_1 | 102010 | 109146 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.74 | 100.00 | NP_391076 |
| OLOPCOLM_1 | 109166 | 110104 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| OLOPCOLM_1 | 110132 | 111751 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| OLOPCOLM_11 | 31778 | 32914 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| OLOPCOLM_13 | 11332 | 10463 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| OLOPCOLM_7 | 787077 | 787853 | CodY | 6.74e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| OLOPCOLM_1 | 376375 | 376944 | ClpP | 6.40e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| OLOPCOLM_7 | 277636 | 278028 | spxA1 | 5.30e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| OLOPCOLM_7 | 277636 | 278028 | spx | 3.16e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| OLOPCOLM_12 | 20625 | 20867 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| OLOPCOLM_8 | 79254 | 79057 | CspA | 1.89e-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 |
|---|---|---|---|
| OLOPCOLM_1 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_2 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_3 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_6 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_7 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_8 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_9 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_10 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_11 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_12 | 0.0 | 1.0 | 0.0 |
| OLOPCOLM_13 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| OLOPCOLM_6 | 484587 | 514623 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862 |
| OLOPCOLM_7 | 314685 | 320486 | False | Unknown | VOG3304, VOG9576, VOG9667, VOG9667, VOG8241, VOG4552 |
| OLOPCOLM_7 | 331550 | 355069 | False | Myoviridae | VOG0796, VOG10227, VOG0720, VOG4555, VOG4572, VOG1643, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG4574 |
| OLOPCOLM_7 | 418482 | 445833 | False | Myoviridae | VOG4602, 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)