Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| PJPCNGDJ_2 | 1618815 | 1619153 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PJPCNGDJ_2 | 1618498 | 1618815 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PJPCNGDJ_2 | 630664 | 631833 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PJPCNGDJ_2 | 456420 | 457622 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| PJPCNGDJ_2 | 437615 | 438469 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| PJPCNGDJ_6 | 413070 | 414713 | vmlR | ARO:3004476 | vmlR | 98.90 | 100.00 | NC_000964.3 |
| PJPCNGDJ_1 | 178309 | 180879 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| PJPCNGDJ_6 | 162040 | 162633 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| PJPCNGDJ_6 | 111479 | 112918 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| PJPCNGDJ_6 | 98663 | 99583 | mphK | ARO:3004541 | mphK | 98.69 | 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. |
|---|---|---|---|---|---|---|---|
| PJPCNGDJ_2 | 437615 | 438469 | aadK | Streptomycin | 99.30 | 100.00 | M26879 |
| PJPCNGDJ_6 | 98663 | 99583 | mph(K) | Spiramycin, Telithromycin | 99.13 | 100.00 | NC_000964 |
| PJPCNGDJ_3 | 34679 | 36055 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.40 | 100.00 | D12567 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PJPCNGDJ_2 | 437615 | 438466 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| PJPCNGDJ_6 | 413073 | 414713 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.90 | 100.00 | WP_003234144.1 |
| PJPCNGDJ_6 | 98663 | 99580 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| PJPCNGDJ_3 | 34679 | 36052 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.25 | 100.00 | WP_063856081.1 |
| PJPCNGDJ_3 | 37914 | 38432 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 94.22 | 100.00 | WP_003242546.1 |
| PJPCNGDJ_2 | 938132 | 940726 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PJPCNGDJ_3 | 531093 | 532274 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PJPCNGDJ_2 | 989349 | 991112 | dep/capD | 0.0 | Capsule | Immune modulation | 99.60 | 100.00 | NP_389723 |
| PJPCNGDJ_3 | 532289 | 532738 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PJPCNGDJ_3 | 939618 | 940403 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PJPCNGDJ_3 | 940429 | 941625 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| PJPCNGDJ_3 | 532757 | 533899 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| PJPCNGDJ_2 | 830551 | 831192 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| PJPCNGDJ_3 | 943301 | 944239 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| PJPCNGDJ_3 | 944259 | 951395 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.05 | 100.00 | NP_391076 |
| PJPCNGDJ_3 | 941654 | 943273 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.67 | 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 |
|---|---|---|---|---|---|---|---|---|
| PJPCNGDJ_7 | 28152 | 27016 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PJPCNGDJ_4 | 11376 | 10507 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PJPCNGDJ_2 | 1305515 | 1304739 | CodY | 1.66e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PJPCNGDJ_3 | 685498 | 684929 | ClpP | 6.34e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PJPCNGDJ_2 | 1767934 | 1767542 | spxA1 | 1.30e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PJPCNGDJ_2 | 1767934 | 1767542 | spx | 7.77e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PJPCNGDJ_9 | 20666 | 20908 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PJPCNGDJ_6 | 360211 | 360408 | CspA | 1.92e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| PJPCNGDJ_1 | 0.0 | 1.0 | 0.0 |
| PJPCNGDJ_2 | 0.0 | 1.0 | 0.0 |
| PJPCNGDJ_3 | 0.0 | 1.0 | 0.0 |
| PJPCNGDJ_4 | 0.0 | 1.0 | 0.0 |
| PJPCNGDJ_5 | 0.0 | 1.0 | 0.0 |
| PJPCNGDJ_6 | 0.0 | 1.0 | 0.0 |
| PJPCNGDJ_7 | 0.0 | 1.0 | 0.0 |
| PJPCNGDJ_9 | 0.0 | 1.0 | 0.0 |
| PJPCNGDJ_12 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PJPCNGDJ_2 | 1648961 | 1675075 | 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)