Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 8 | 16.88 |
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. |
|---|---|---|---|---|---|---|---|---|
| BEPBFAHN_1 | 496861 | 497199 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| BEPBFAHN_1 | 496544 | 496861 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| BEPBFAHN_3 | 428105 | 429748 | vmlR | ARO:3004476 | vmlR | 99.09 | 100.00 | NC_000964.3 |
| BEPBFAHN_4 | 329970 | 331139 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| BEPBFAHN_3 | 151160 | 151753 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| BEPBFAHN_4 | 140727 | 141929 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| BEPBFAHN_4 | 122478 | 123332 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| BEPBFAHN_3 | 100662 | 102101 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| BEPBFAHN_3 | 87848 | 88768 | mphK | ARO:3004541 | mphK | 97.06 | 100.00 | CP010314.1 |
| BEPBFAHN_8 | 27416 | 29986 | 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. |
|---|---|---|---|---|---|---|---|
| BEPBFAHN_4 | 122478 | 123332 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| BEPBFAHN_3 | 87848 | 88768 | mph(K) | Spiramycin, Telithromycin | 96.42 | 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. |
|---|---|---|---|---|---|---|---|---|
| BEPBFAHN_3 | 428108 | 429748 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.09 | 100.00 | WP_003234144.1 |
| BEPBFAHN_4 | 122478 | 123329 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| BEPBFAHN_3 | 87848 | 88765 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.06 | 100.00 | WP_003246254.1 |
| BEPBFAHN_6 | 155968 | 158565 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.30 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| BEPBFAHN_2 | 168969 | 170150 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| BEPBFAHN_6 | 61604 | 62245 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| BEPBFAHN_2 | 170633 | 171775 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| BEPBFAHN_2 | 170165 | 170614 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| BEPBFAHN_2 | 561313 | 562509 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| BEPBFAHN_2 | 560502 | 561287 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391080 |
| BEPBFAHN_6 | 202501 | 204264 | dep/capD | 0.0 | Capsule | Immune modulation | 98.87 | 100.00 | NP_389723 |
| BEPBFAHN_2 | 564185 | 565123 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.72 | 100.00 | NP_391077 |
| BEPBFAHN_2 | 565143 | 572279 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.50 | 100.00 | NP_391076 |
| BEPBFAHN_2 | 562538 | 564157 | 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 |
|---|---|---|---|---|---|---|---|---|
| BEPBFAHN_11 | 13639 | 12503 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| BEPBFAHN_13 | 11216 | 10347 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| BEPBFAHN_1 | 185287 | 184511 | CodY | 7.44e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| BEPBFAHN_2 | 312145 | 311576 | ClpP | 4.31e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| BEPBFAHN_1 | 640654 | 640262 | spxA1 | 5.84e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| BEPBFAHN_1 | 640654 | 640262 | spx | 3.49e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| BEPBFAHN_10 | 34728 | 34486 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| BEPBFAHN_3 | 378274 | 378471 | CspA | 1.98e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| BEPBFAHN_6 | 50374 | 50180 | CspD | 9.22e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| BEPBFAHN_6 | 50374 | 50177 | CspB | 1.91e-27 | cold shock protein | 80.30 | 100.00 | 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 |
|---|---|---|---|
| BEPBFAHN_1 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_2 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_3 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_4 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_5 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_6 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_7 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_8 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_9 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_10 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_11 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_12 | 1.0 | 0.0 | 1.0 |
| BEPBFAHN_13 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_14 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_15 | 0.0 | 1.0 | 0.0 |
| BEPBFAHN_17 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| BEPBFAHN_1 | 527048 | 553098 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| BEPBFAHN_2 | 673278 | 698428 | False | Myoviridae | VOG3626, VOG0796, VOG0720, VOG4555, VOG4553, VOG0815, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG5008, VOG0641, VOG4574, VOG1993 |
Phigaro v2.4.0 (Database: Jan. 2024 release)