Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 9 | 17.38 |
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. |
|---|---|---|---|---|---|---|---|---|
| HONPPGBL_4 | 618389 | 619243 | aadK | ARO:3002627 | aadK | 99.30 | 100.00 | AL009126.1 |
| HONPPGBL_7 | 600212 | 600550 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| HONPPGBL_7 | 599895 | 600212 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| HONPPGBL_4 | 589099 | 590301 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| HONPPGBL_4 | 360289 | 361458 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| HONPPGBL_9 | 350176 | 351096 | mphK | ARO:3004541 | mphK | 97.06 | 100.00 | CP010314.1 |
| HONPPGBL_9 | 336845 | 338284 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.42 | JYFL01000006.1 |
| HONPPGBL_9 | 287152 | 287745 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| HONPPGBL_9 | 28889 | 30526 | vmlR | ARO:3004476 | vmlR | 98.72 | 99.63 | NC_000964.3 |
| HONPPGBL_1 | 27303 | 29873 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 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. |
|---|---|---|---|---|---|---|---|
| HONPPGBL_4 | 618389 | 619243 | aadK | Streptomycin | 99.18 | 100.00 | M26879 |
| HONPPGBL_9 | 350176 | 351096 | 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. |
|---|---|---|---|---|---|---|---|---|
| HONPPGBL_4 | 618392 | 619243 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 99.30 | 100.00 | WP_003229862.1 |
| HONPPGBL_9 | 28889 | 30529 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 98.54 | 99.82 | WP_003234144.1 |
| HONPPGBL_9 | 350179 | 351096 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.06 | 100.00 | WP_003246254.1 |
| HONPPGBL_4 | 54500 | 57097 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HONPPGBL_2 | 522300 | 523481 | capB | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_391471 |
| HONPPGBL_2 | 113059 | 113844 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| HONPPGBL_4 | 160886 | 161527 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| HONPPGBL_2 | 521836 | 522285 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| HONPPGBL_2 | 520675 | 521817 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| HONPPGBL_2 | 111837 | 113033 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| HONPPGBL_4 | 8715 | 10478 | dep/capD | 0.0 | Capsule | Immune modulation | 98.70 | 100.00 | NP_389723 |
| HONPPGBL_2 | 102067 | 109203 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.67 | 100.00 | NP_391076 |
| HONPPGBL_2 | 110189 | 111808 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391078 |
| HONPPGBL_2 | 109223 | 110161 | 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 |
|---|---|---|---|---|---|---|---|---|
| HONPPGBL_5 | 28067 | 26931 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| HONPPGBL_14 | 4346 | 5215 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HONPPGBL_7 | 288351 | 287575 | CodY | 7.84e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HONPPGBL_2 | 365591 | 366160 | ClpP | 6.50e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HONPPGBL_7 | 752638 | 752246 | spxA1 | 6.16e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HONPPGBL_7 | 752638 | 752246 | spx | 3.67e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HONPPGBL_6 | 34824 | 34582 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HONPPGBL_9 | 84363 | 84166 | CspA | 1.90e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| HONPPGBL_4 | 173486 | 173680 | CspD | 4.82e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| HONPPGBL_11 | 33115 | 32921 | CspB | 5.74e-28 | 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 |
|---|---|---|---|
| HONPPGBL_1 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_2 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_3 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_4 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_5 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_6 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_7 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_8 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_9 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_11 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_12 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_14 | 0.0 | 1.0 | 0.0 |
| HONPPGBL_16 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HONPPGBL_4 | 540726 | 557721 | False | Myoviridae | VOG4862, VOG4691, VOG10989, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
| HONPPGBL_7 | 630096 | 657988 | 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)