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. |
|---|---|---|---|---|---|---|---|---|
| PLNPAPJP_5 | 90714 | 92153 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| PLNPAPJP_24 | 79929 | 81131 | blt | ARO:3003006 | blt | 98.00 | 100.00 | L32599.1 |
| PLNPAPJP_5 | 78524 | 79444 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| PLNPAPJP_24 | 62094 | 62948 | aadK | ARO:3002627 | aadK | 96.83 | 100.00 | AL009126.1 |
| PLNPAPJP_18 | 59207 | 60376 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PLNPAPJP_31 | 44560 | 46206 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| PLNPAPJP_8 | 21065 | 23635 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| PLNPAPJP_52 | 11186 | 11503 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PLNPAPJP_52 | 10848 | 11186 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| PLNPAPJP_6 | 34411 | 35790 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 97.97 | 100.00 | X08034 |
| PLNPAPJP_24 | 62094 | 62948 | aadK | Streptomycin | 97.78 | 100.00 | M26879 |
| PLNPAPJP_5 | 78524 | 79444 | 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. |
|---|---|---|---|---|---|---|---|---|
| PLNPAPJP_31 | 44563 | 46206 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| PLNPAPJP_6 | 34411 | 35787 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 97.82 | 100.00 | WP_003242953.1 |
| PLNPAPJP_5 | 78524 | 79441 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| PLNPAPJP_24 | 62094 | 62945 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 96.83 | 100.00 | WP_003229862.1 |
| PLNPAPJP_6 | 37829 | 38347 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 95.95 | 100.00 | WP_003242546.1 |
| PLNPAPJP_14 | 55907 | 58504 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.83 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PLNPAPJP_1 | 38138 | 38779 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| PLNPAPJP_9 | 458101 | 459282 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| PLNPAPJP_2 | 72032 | 72817 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| PLNPAPJP_2 | 72843 | 74039 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| PLNPAPJP_9 | 459765 | 460907 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| PLNPAPJP_2 | 76673 | 83809 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.57 | 100.00 | NP_391076 |
| PLNPAPJP_9 | 459297 | 459746 | capC | 0.0 | Capsule | Immune modulation | 98.44 | 100.00 | NP_391470 |
| PLNPAPJP_2 | 75715 | 76653 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.19 | 100.00 | NP_391077 |
| PLNPAPJP_2 | 74068 | 75687 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.90 | 100.00 | NP_391078 |
| PLNPAPJP_14 | 103496 | 105259 | dep/capD | 0.0 | Capsule | Immune modulation | 97.73 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| PLNPAPJP_37 | 1572 | 2708 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PLNPAPJP_44 | 4249 | 5118 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PLNPAPJP_9 | 608282 | 607713 | ClpP | 4.80e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PLNPAPJP_25 | 5667 | 5335 | spxA1 | 2.71e-56 | redox-responsive transcription factor | 81.08 | 84.73 | AAF21893 |
| PLNPAPJP_10 | 34586 | 34344 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PLNPAPJP_19 | 149864 | 150061 | CspA | 6.73e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PLNPAPJP_1 | 50741 | 50935 | CspD | 9.58e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PLNPAPJP_13 | 32162 | 31968 | CspB | 2.47e-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 |
|---|---|---|---|
| PLNPAPJP_1 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_2 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_3 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_4 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_5 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_6 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_7 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_8 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_9 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_10 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_11 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_12 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_13 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_14 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_15 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_16 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_17 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_18 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_19 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_20 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_21 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_22 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_23 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_24 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_25 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_26 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_28 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_30 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_31 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_32 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_33 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_34 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_36 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_37 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_38 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_39 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_40 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_42 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_43 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_44 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_45 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_46 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_48 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_49 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_50 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_51 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_52 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_53 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_54 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_55 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_56 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_57 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_58 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_59 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_60 | 0.0 | 1.0 | 0.0 |
| PLNPAPJP_61 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PLNPAPJP_33 | 18380 | 44508 | 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)