Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| PLIAIPEN_10 | 630582 | 630920 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PLIAIPEN_10 | 630265 | 630582 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PLIAIPEN_13 | 523421 | 524623 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| PLIAIPEN_13 | 505108 | 505962 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| PLIAIPEN_12 | 276994 | 279564 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PLIAIPEN_11 | 207388 | 208557 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PLIAIPEN_14 | 183609 | 185252 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
| PLIAIPEN_16 | 162319 | 162912 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| PLIAIPEN_16 | 111841 | 113280 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| PLIAIPEN_16 | 99027 | 99947 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| PLIAIPEN_2 | 36213 | 37589 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.84 | 100.00 | X08034 |
| PLIAIPEN_13 | 505108 | 505960 | aadK | Streptomycin | 98.71 | 99.77 | M26879 |
| PLIAIPEN_16 | 99027 | 99947 | 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. |
|---|---|---|---|---|---|---|---|---|
| PLIAIPEN_2 | 36213 | 37586 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_003242953.1 |
| PLIAIPEN_14 | 183612 | 185252 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| PLIAIPEN_13 | 505108 | 505959 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| PLIAIPEN_16 | 99027 | 99944 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| PLIAIPEN_2 | 39542 | 40060 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| PLIAIPEN_11 | 503552 | 506149 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PLIAIPEN_11 | 409362 | 410003 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| PLIAIPEN_1 | 726468 | 727406 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| PLIAIPEN_1 | 281602 | 282783 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| PLIAIPEN_1 | 724821 | 726440 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.26 | 100.00 | NP_391078 |
| PLIAIPEN_1 | 722785 | 723570 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| PLIAIPEN_1 | 283266 | 284408 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| PLIAIPEN_1 | 723596 | 724792 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| PLIAIPEN_11 | 551317 | 553080 | dep/capD | 0.0 | Capsule | Immune modulation | 98.87 | 100.00 | NP_389723 |
| PLIAIPEN_1 | 727426 | 734562 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.82 | 100.00 | NP_391076 |
| PLIAIPEN_1 | 282798 | 283247 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| PLIAIPEN_9 | 31770 | 32906 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PLIAIPEN_7 | 4254 | 5123 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PLIAIPEN_10 | 320721 | 319945 | CodY | 2.09e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PLIAIPEN_1 | 424200 | 423631 | ClpP | 5.03e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PLIAIPEN_10 | 782238 | 781846 | spxA1 | 6.75e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PLIAIPEN_10 | 782238 | 781846 | spx | 4.02e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PLIAIPEN_5 | 20509 | 20751 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PLIAIPEN_14 | 136878 | 137075 | CspA | 9.27e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PLIAIPEN_11 | 397400 | 397206 | CspD | 4.21e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| PLIAIPEN_1 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_2 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_5 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_6 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_7 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_8 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_9 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_10 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_11 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_12 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_13 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_14 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_15 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_16 | 0.0 | 1.0 | 0.0 |
| PLIAIPEN_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 |
|---|---|---|---|---|---|
| PLIAIPEN_1 | 623630 | 657637 | False | Siphoviridae | VOG4602, VOG9667, VOG5353, VOG0181, VOG4556, VOG0787, VOG1638, VOG4552, VOG4566, VOG9600, VOG0025, VOG1884, VOG9091, VOG4841, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5008, VOG0641, VOG4574 |
| PLIAIPEN_10 | 42186 | 47741 | False | Unknown | VOG4551, VOG0025, VOG7476, VOG0322, VOG6211 |
| PLIAIPEN_10 | 95796 | 123612 | False | Siphoviridae | VOG7134, VOG9867, VOG6036, VOG5495, VOG9219, VOG9713, VOG6940, VOG5534, VOG7718, VOG3390, VOG4705, VOG5008, VOG8610, VOG7930, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG4660 |
| PLIAIPEN_10 | 660404 | 687725 | False | Myoviridae | VOG0753, VOG4705, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| PLIAIPEN_11 | 6132 | 30380 | False | Myoviridae | VOG7060, VOG0796, VOG9315, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| PLIAIPEN_12 | 7930 | 30970 | False | Siphoviridae | VOG0796, VOG10227, VOG0720, VOG4564, VOG4555, VOG1329, VOG1329, VOG3480, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG2621, VOG0725, VOG4545, VOG4605, VOG4599, VOG5535, VOG4728, VOG0753, VOG0136, VOG4574 |
| PLIAIPEN_13 | 321613 | 350773 | False | Siphoviridae | VOG0044, VOG6517, VOG0198, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5008, VOG0641, VOG4574 |
| PLIAIPEN_15 | 6708 | 31369 | False | Myoviridae | VOG4705, VOG7718, VOG0906, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG1581, VOG0749, VOG4685, VOG4688, VOG4773 |
| PLIAIPEN_15 | 44536 | 49978 | False | Unknown | VOG11060, VOG1292, VOG1309, VOG0083 |
Phigaro v2.4.0 (Database: Jan. 2024 release)