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. |
|---|---|---|---|---|---|---|---|---|
| CPNJBJCF_1 | 1648729 | 1649583 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| CPNJBJCF_1 | 1631462 | 1632664 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| CPNJBJCF_1 | 1409722 | 1410891 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| CPNJBJCF_1 | 427073 | 427390 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| CPNJBJCF_1 | 426735 | 427073 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CPNJBJCF_4 | 412919 | 414547 | vmlR | ARO:3004476 | vmlR | 99.08 | 99.09 | NC_000964.3 |
| CPNJBJCF_4 | 160550 | 161143 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| CPNJBJCF_4 | 110025 | 111464 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| CPNJBJCF_4 | 97210 | 98076 | mphK | ARO:3004541 | mphK | 98.61 | 94.12 | CP010314.1 |
| CPNJBJCF_5 | 27443 | 30013 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 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. |
|---|---|---|---|---|---|---|---|
| CPNJBJCF_1 | 1648731 | 1649583 | aadK | Streptomycin | 98.94 | 99.77 | M26879 |
| CPNJBJCF_3 | 37988 | 39364 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.91 | 100.00 | D12567 |
| CPNJBJCF_4 | 97210 | 98130 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| CPNJBJCF_4 | 412922 | 414547 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.08 | 98.90 | WP_003234144.1 |
| CPNJBJCF_1 | 1648732 | 1649583 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| CPNJBJCF_3 | 37988 | 39361 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| CPNJBJCF_4 | 97210 | 98127 | mphK | macrolide 2'-phosphotransferase MphK | INTERNAL_STOP | 98.04 | 100.00 | WP_003246254.1 |
| CPNJBJCF_3 | 41317 | 41835 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| CPNJBJCF_1 | 1107063 | 1109651 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.37 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CPNJBJCF_3 | 936889 | 937674 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| CPNJBJCF_3 | 941530 | 948666 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.99 | 100.00 | NP_391076 |
| CPNJBJCF_3 | 940572 | 941510 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| CPNJBJCF_3 | 529600 | 530781 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| CPNJBJCF_3 | 938925 | 940544 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391078 |
| CPNJBJCF_3 | 530796 | 531245 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| CPNJBJCF_3 | 937700 | 938896 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.50 | 100.00 | NP_391079 |
| CPNJBJCF_1 | 1210366 | 1211007 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| CPNJBJCF_3 | 531264 | 532406 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| CPNJBJCF_1 | 1052682 | 1054445 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 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 |
|---|---|---|---|---|---|---|---|---|
| CPNJBJCF_6 | 31799 | 32935 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CPNJBJCF_8 | 11297 | 10428 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CPNJBJCF_1 | 737086 | 737862 | CodY | 1.71e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CPNJBJCF_3 | 685921 | 685352 | ClpP | 6.32e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CPNJBJCF_1 | 277899 | 278291 | spxA1 | 1.34e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CPNJBJCF_1 | 277899 | 278291 | spx | 8.00e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CPNJBJCF_7 | 34755 | 34513 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CPNJBJCF_4 | 359997 | 360194 | 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 |
|---|---|---|---|
| CPNJBJCF_1 | 0.0 | 1.0 | 0.0 |
| CPNJBJCF_3 | 0.0 | 1.0 | 0.0 |
| CPNJBJCF_4 | 0.0 | 1.0 | 0.0 |
| CPNJBJCF_5 | 0.0 | 1.0 | 0.0 |
| CPNJBJCF_6 | 0.0 | 1.0 | 0.0 |
| CPNJBJCF_7 | 0.0 | 1.0 | 0.0 |
| CPNJBJCF_8 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CPNJBJCF_1 | 370766 | 397248 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
| CPNJBJCF_1 | 1584507 | 1613642 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060 |
Phigaro v2.4.0 (Database: Jan. 2024 release)