Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 9 | 18.03 |
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. |
|---|---|---|---|---|---|---|---|---|
| PBAEAKPD_3 | 346381 | 347550 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| PBAEAKPD_6 | 248401 | 249321 | mphK | ARO:3004541 | mphK | 96.08 | 100.00 | CP010314.1 |
| PBAEAKPD_6 | 235101 | 236534 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.00 | JYFL01000006.1 |
| PBAEAKPD_6 | 185387 | 185980 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| PBAEAKPD_2 | 118198 | 119052 | aadK | ARO:3002627 | aadK | 97.18 | 100.00 | AL009126.1 |
| PBAEAKPD_2 | 101557 | 102759 | blt | ARO:3003006 | blt | 98.50 | 100.00 | L32599.1 |
| PBAEAKPD_14 | 41505 | 41822 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PBAEAKPD_14 | 41167 | 41505 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| PBAEAKPD_7 | 27269 | 29839 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| PBAEAKPD_15 | 12287 | 13915 | vmlR | ARO:3004476 | vmlR | 95.38 | 99.09 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| PBAEAKPD_2 | 118198 | 119052 | aadK | Streptomycin | 98.13 | 100.00 | M26879 |
| PBAEAKPD_6 | 248401 | 249321 | mph(K) | Spiramycin, Telithromycin | 96.31 | 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. |
|---|---|---|---|---|---|---|---|---|
| PBAEAKPD_2 | 118201 | 119052 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.18 | 100.00 | WP_003229862.1 |
| PBAEAKPD_6 | 248404 | 249321 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 96.08 | 100.00 | WP_003246254.1 |
| PBAEAKPD_15 | 12293 | 13915 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 95.38 | 98.90 | WP_003234144.1 |
| PBAEAKPD_18 | 27376 | 27894 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| PBAEAKPD_3 | 53581 | 56178 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PBAEAKPD_1 | 533760 | 534209 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PBAEAKPD_1 | 534224 | 535405 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| PBAEAKPD_1 | 532599 | 533741 | capA | 0.0 | Capsule | Immune modulation | 99.12 | 100.00 | NP_391469 |
| PBAEAKPD_1 | 109197 | 110135 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.04 | 100.00 | NP_391077 |
| PBAEAKPD_1 | 113033 | 113818 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391080 |
| PBAEAKPD_3 | 146972 | 147613 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| PBAEAKPD_1 | 102041 | 109177 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.43 | 100.00 | NP_391076 |
| PBAEAKPD_1 | 111811 | 113007 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.41 | 100.00 | NP_391079 |
| PBAEAKPD_3 | 8400 | 10163 | dep/capD | 0.0 | Capsule | Immune modulation | 98.19 | 100.00 | NP_389723 |
| PBAEAKPD_1 | 110163 | 111782 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.84 | 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 |
|---|---|---|---|---|---|---|---|---|
| PBAEAKPD_11 | 27998 | 26862 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PBAEAKPD_28 | 3312 | 2443 | pdxS | 4.67e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PBAEAKPD_4 | 278097 | 277321 | CodY | 3.47e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PBAEAKPD_1 | 376671 | 377240 | ClpP | 4.21e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PBAEAKPD_5 | 272905 | 273297 | spxA1 | 2.43e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PBAEAKPD_5 | 272905 | 273297 | spx | 1.45e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PBAEAKPD_16 | 14391 | 14149 | SpoVG | 4.74e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PBAEAKPD_13 | 45690 | 45493 | CspA | 2.29e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PBAEAKPD_3 | 159576 | 159770 | CspD | 2.64e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PBAEAKPD_5 | 30463 | 30269 | CspB | 3.50e-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 |
|---|---|---|---|
| PBAEAKPD_1 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_2 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_3 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_4 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_5 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_6 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_7 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_8 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_9 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_10 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_11 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_12 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_13 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_14 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_15 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_16 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_17 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_18 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_19 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_20 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_21 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_22 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_23 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_24 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_25 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_26 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_27 | 0.0 | 1.0 | 0.0 |
| PBAEAKPD_28 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PBAEAKPD_5 | 365631 | 375959 | False | Siphoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749 |
| PBAEAKPD_14 | 3536 | 11649 | False | Myoviridae | VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG3390, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)