Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 4 | 16.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| LMCBPJPK_1 | 2518768 | 2519622 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| LMCBPJPK_1 | 2499469 | 2500671 | blt | ARO:3003006 | blt | 98.50 | 100.00 | L32599.1 |
| LMCBPJPK_1 | 2315380 | 2316549 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| LMCBPJPK_1 | 1344805 | 1345122 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| LMCBPJPK_1 | 1344467 | 1344805 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| LMCBPJPK_1 | 885912 | 888482 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| LMCBPJPK_1 | 589008 | 590636 | vmlR | ARO:3004476 | vmlR | 95.38 | 99.09 | NC_000964.3 |
| LMCBPJPK_1 | 330247 | 330840 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| LMCBPJPK_1 | 279684 | 281117 | lmrB | ARO:3002813 | lmrB | 100.00 | 100.00 | JYFL01000006.1 |
| LMCBPJPK_1 | 266864 | 267784 | mphK | ARO:3004541 | mphK | 98.04 | 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. |
|---|---|---|---|---|---|---|---|
| LMCBPJPK_1 | 2518768 | 2519622 | aadK | Streptomycin | 98.25 | 100.00 | M26879 |
| LMCBPJPK_1 | 266864 | 267784 | mph(K) | Spiramycin, Telithromycin | 97.39 | 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. |
|---|---|---|---|---|---|---|---|---|
| LMCBPJPK_1 | 266864 | 267781 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.04 | 100.00 | WP_003246254.1 |
| LMCBPJPK_1 | 2518771 | 2519622 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| LMCBPJPK_1 | 589014 | 590636 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 95.38 | 98.90 | WP_003234144.1 |
| LMCBPJPK_1 | 3995965 | 3996483 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| LMCBPJPK_1 | 2023079 | 2025676 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.29 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LMCBPJPK_1 | 3495524 | 3496705 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| LMCBPJPK_1 | 3495060 | 3495509 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| LMCBPJPK_1 | 3493899 | 3495041 | capA | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_391469 |
| LMCBPJPK_1 | 3071389 | 3072174 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391080 |
| LMCBPJPK_1 | 2115769 | 2116410 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.75 | 100.00 | NP_390062 |
| LMCBPJPK_1 | 3067553 | 3068491 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.72 | 100.00 | NP_391077 |
| LMCBPJPK_1 | 3070167 | 3071363 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.50 | 100.00 | NP_391079 |
| LMCBPJPK_1 | 3060403 | 3067533 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.32 | 99.99 | NP_391076 |
| LMCBPJPK_1 | 1978135 | 1979898 | dep/capD | 0.0 | Capsule | Immune modulation | 98.02 | 100.00 | NP_389723 |
| LMCBPJPK_1 | 3068519 | 3070138 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.59 | 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 |
|---|---|---|---|---|---|---|---|---|
| LMCBPJPK_1 | 132388 | 133524 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LMCBPJPK_1 | 18681 | 19550 | pdxS | 2.99e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LMCBPJPK_1 | 1654100 | 1654876 | CodY | 3.27e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LMCBPJPK_1 | 3339024 | 3339593 | ClpP | 2.42e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| LMCBPJPK_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LMCBPJPK_1 | 1288497 | 1314633 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)