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. |
|---|---|---|---|---|---|---|---|---|
| OPOHKMFD_1 | 1265505 | 1265843 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| OPOHKMFD_1 | 1265188 | 1265505 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| OPOHKMFD_3 | 411754 | 413397 | vmlR | ARO:3004476 | vmlR | 99.09 | 100.00 | NC_000964.3 |
| OPOHKMFD_1 | 371948 | 373117 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| OPOHKMFD_1 | 193063 | 194265 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| OPOHKMFD_1 | 176318 | 177172 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| OPOHKMFD_3 | 158518 | 159111 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| OPOHKMFD_3 | 108042 | 109481 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| OPOHKMFD_3 | 95228 | 96148 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| OPOHKMFD_4 | 27465 | 30035 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 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. |
|---|---|---|---|---|---|---|---|
| OPOHKMFD_1 | 176318 | 177172 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| OPOHKMFD_3 | 95228 | 96148 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| OPOHKMFD_3 | 411757 | 413397 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.09 | 100.00 | WP_003234144.1 |
| OPOHKMFD_1 | 176318 | 177169 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| OPOHKMFD_3 | 95228 | 96145 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| OPOHKMFD_2 | 1033678 | 1034196 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 94.80 | 100.00 | WP_003242546.1 |
| OPOHKMFD_1 | 697621 | 700218 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.41 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| OPOHKMFD_1 | 585711 | 586352 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| OPOHKMFD_2 | 536317 | 537498 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| OPOHKMFD_2 | 112890 | 113675 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| OPOHKMFD_2 | 111668 | 112864 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| OPOHKMFD_1 | 743579 | 745342 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| OPOHKMFD_2 | 534692 | 535834 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| OPOHKMFD_2 | 535853 | 536302 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| OPOHKMFD_2 | 109054 | 109992 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.62 | 100.00 | NP_391077 |
| OPOHKMFD_2 | 101898 | 109034 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.53 | 100.00 | NP_391076 |
| OPOHKMFD_2 | 110020 | 111639 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.53 | 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 |
|---|---|---|---|---|---|---|---|---|
| OPOHKMFD_7 | 31921 | 33057 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| OPOHKMFD_10 | 11330 | 10461 | pdxS | 1.14e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| OPOHKMFD_1 | 956743 | 955967 | CodY | 1.40e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| OPOHKMFD_2 | 377700 | 378269 | ClpP | 6.46e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| OPOHKMFD_1 | 1443107 | 1442715 | spxA1 | 1.10e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| OPOHKMFD_1 | 1443107 | 1442715 | spx | 6.54e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| OPOHKMFD_8 | 20607 | 20849 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| OPOHKMFD_3 | 368019 | 368216 | CspA | 1.91e-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 |
|---|---|---|---|
| OPOHKMFD_1 | 0.0 | 1.0 | 0.0 |
| OPOHKMFD_2 | 0.0 | 1.0 | 0.0 |
| OPOHKMFD_3 | 0.0 | 1.0 | 0.0 |
| OPOHKMFD_4 | 0.0 | 1.0 | 0.0 |
| OPOHKMFD_5 | 0.0 | 1.0 | 0.0 |
| OPOHKMFD_6 | 0.0 | 1.0 | 0.0 |
| OPOHKMFD_7 | 0.0 | 1.0 | 0.0 |
| OPOHKMFD_8 | 0.0 | 1.0 | 0.0 |
| OPOHKMFD_9 | 0.0 | 1.0 | 0.0 |
| OPOHKMFD_10 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| OPOHKMFD_1 | 1295659 | 1322940 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| OPOHKMFD_4 | 284324 | 307418 | False | Myoviridae | VOG4574, VOG0136, VOG0753, VOG5008, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720 |
| OPOHKMFD_5 | 3 | 20881 | False | Siphoviridae | VOG4612, VOG4626, VOG4619, VOG0801, VOG4545, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5601, VOG4553, VOG4573, VOG4556, VOG4544, VOG4581, VOG4841, VOG6430 |
| OPOHKMFD_5 | 41825 | 59913 | False | Siphoviridae | VOG1093, VOG5543, VOG0982, VOG0026, VOG6497, VOG5324, VOG10937, VOG6546, VOG0052, VOG1563, VOG11003, VOG2215, VOG4551, VOG0025, VOG0189, VOG6168, VOG0152 |
| OPOHKMFD_6 | 152226 | 170976 | False | Siphoviridae | VOG4841, VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619 |
| OPOHKMFD_9 | 13545 | 36698 | False | Myoviridae | VOG4705, VOG7718, VOG0906, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227 |
| OPOHKMFD_9 | 39109 | 41297 | False | Unknown | VOG4693, VOG0189 |
Phigaro v2.4.0 (Database: Jan. 2024 release)