Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| DEKBNHPK_28 | 442930 | 443268 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| DEKBNHPK_28 | 442613 | 442930 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| DEKBNHPK_21 | 421167 | 422021 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| DEKBNHPK_21 | 404007 | 405209 | blt | ARO:3003006 | blt | 98.00 | 100.00 | L32599.1 |
| DEKBNHPK_21 | 213191 | 214360 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| DEKBNHPK_27 | 148521 | 149114 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| DEKBNHPK_27 | 97970 | 99409 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| DEKBNHPK_27 | 85157 | 86077 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
| DEKBNHPK_26 | 29135 | 30781 | vmlR | ARO:3004476 | vmlR | 99.45 | 100.18 | NC_000964.3 |
| DEKBNHPK_22 | 27459 | 30029 | 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. |
|---|---|---|---|---|---|---|---|
| DEKBNHPK_21 | 421167 | 422021 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| DEKBNHPK_27 | 85157 | 86077 | 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. |
|---|---|---|---|---|---|---|---|---|
| DEKBNHPK_26 | 29135 | 30778 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.45 | 100.00 | WP_003234144.1 |
| DEKBNHPK_21 | 421170 | 422021 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| DEKBNHPK_27 | 85157 | 86074 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| DEKBNHPK_25 | 39811 | 40329 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| DEKBNHPK_24 | 174300 | 176897 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| DEKBNHPK_21 | 15934 | 16575 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| DEKBNHPK_11 | 27273 | 28454 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| DEKBNHPK_11 | 449418 | 450614 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.42 | 100.00 | NP_391079 |
| DEKBNHPK_11 | 448607 | 449392 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| DEKBNHPK_24 | 128588 | 130351 | dep/capD | 0.0 | Capsule | Immune modulation | 99.26 | 100.00 | NP_389723 |
| DEKBNHPK_11 | 452290 | 453228 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| DEKBNHPK_11 | 28469 | 28918 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| DEKBNHPK_11 | 28937 | 30079 | capA | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_391469 |
| DEKBNHPK_11 | 453248 | 460384 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.43 | 100.00 | NP_391076 |
| DEKBNHPK_11 | 450643 | 452262 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.04 | 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 |
|---|---|---|---|---|---|---|---|---|
| DEKBNHPK_5 | 31765 | 32901 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| DEKBNHPK_7 | 4392 | 5261 | pdxS | 2.53e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.14 | 98.31 | ACE61268 |
| DEKBNHPK_28 | 131539 | 130763 | CodY | 7.05e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| DEKBNHPK_11 | 184418 | 183849 | ClpP | 3.63e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| DEKBNHPK_28 | 592816 | 592424 | spxA1 | 5.54e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| DEKBNHPK_28 | 592816 | 592424 | spx | 3.30e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| DEKBNHPK_6 | 20673 | 20915 | SpoVG | 7.53e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| DEKBNHPK_26 | 78895 | 78698 | CspA | 9.66e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| DEKBNHPK_21 | 27806 | 28000 | CspD | 1.41e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| DEKBNHPK_21 | 27806 | 28003 | CspB | 2.92e-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. |
|---|---|---|---|---|---|---|
| DEKBNHPK_12 | 4376 | 4543 | Col(SD853) | 168 / 194 | 86.90 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| DEKBNHPK_1 | 1.0 | 0.0 | 1.0 |
| DEKBNHPK_2 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_3 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_4 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_5 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_6 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_7 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_8 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_9 | 1.0 | 0.0 | 1.0 |
| DEKBNHPK_10 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_11 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_12 | 1.0 | 0.0 | 1.0 |
| DEKBNHPK_16 | 1.0 | 0.0 | 1.0 |
| DEKBNHPK_21 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_22 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_23 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_24 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_25 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_26 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_27 | 0.0 | 1.0 | 0.0 |
| DEKBNHPK_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 |
|---|---|---|---|---|---|
| DEKBNHPK_3 | 14068 | 19895 | False | Unknown | VOG5070, VOG9712, VOG5042 |
| DEKBNHPK_11 | 548479 | 556378 | False | Siphoviridae | VOG3304, VOG4566, VOG9667, VOG9667, VOG2703, VOG4552, VOG4600, VOG1309, VOG4566 |
| DEKBNHPK_11 | 563353 | 584362 | False | Siphoviridae | VOG0796, VOG10227, VOG0720, VOG4564, VOG6778, VOG4555, VOG4553, VOG1125, VOG0815, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG4545, VOG4605, VOG4599, VOG5535, VOG0753 |
| DEKBNHPK_28 | 473109 | 500393 | False | Myoviridae | 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)