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. |
|---|---|---|---|---|---|---|---|---|
| JEFNGCLP_1 | 2569959 | 2570813 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| JEFNGCLP_1 | 2551593 | 2552795 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| JEFNGCLP_1 | 2354955 | 2356124 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| JEFNGCLP_1 | 1346242 | 1346559 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| JEFNGCLP_1 | 1345904 | 1346242 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| JEFNGCLP_1 | 875881 | 878451 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| JEFNGCLP_1 | 580899 | 582524 | vmlR | ARO:3004476 | vmlR | 98.15 | 98.90 | NC_000964.3 |
| JEFNGCLP_1 | 329768 | 330361 | tmrB | ARO:3003059 | tmrB | 98.98 | 100.00 | AL009126.3 |
| JEFNGCLP_1 | 279248 | 280681 | lmrB | ARO:3002813 | lmrB | 100.00 | 100.00 | JYFL01000006.1 |
| JEFNGCLP_1 | 266437 | 267357 | mphK | ARO:3004541 | mphK | 99.35 | 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. |
|---|---|---|---|---|---|---|---|
| JEFNGCLP_1 | 266437 | 267357 | mph(K) | Spiramycin, Telithromycin | 99.35 | 100.00 | NC_000964 |
| JEFNGCLP_1 | 2569961 | 2570813 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| JEFNGCLP_1 | 266437 | 267354 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.35 | 100.00 | WP_003246254.1 |
| JEFNGCLP_1 | 580902 | 582524 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.15 | 98.90 | WP_003234144.1 |
| JEFNGCLP_1 | 2569962 | 2570813 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| JEFNGCLP_1 | 4073508 | 4074026 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| JEFNGCLP_1 | 2041318 | 2043915 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| JEFNGCLP_1 | 3569917 | 3571098 | capB | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_391471 |
| JEFNGCLP_1 | 1991304 | 1993067 | dep/capD | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_389723 |
| JEFNGCLP_1 | 3168521 | 3169306 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| JEFNGCLP_1 | 3569453 | 3569902 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| JEFNGCLP_1 | 2151917 | 2152558 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| JEFNGCLP_1 | 3167299 | 3168495 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.50 | 100.00 | NP_391079 |
| JEFNGCLP_1 | 3164685 | 3165623 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.47 | 100.00 | NP_391077 |
| JEFNGCLP_1 | 3568292 | 3569434 | capA | 0.0 | Capsule | Immune modulation | 99.12 | 100.00 | NP_391469 |
| JEFNGCLP_1 | 3157529 | 3164665 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.05 | 100.00 | NP_391076 |
| JEFNGCLP_1 | 3165651 | 3167270 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.89 | 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 |
|---|---|---|---|---|---|---|---|---|
| JEFNGCLP_1 | 132044 | 133180 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| JEFNGCLP_1 | 18339 | 19208 | pdxS | 3.05e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| JEFNGCLP_1 | 1656835 | 1657611 | CodY | 3.33e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| JEFNGCLP_1 | 3423724 | 3424293 | ClpP | 2.47e-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 |
|---|---|---|---|
| JEFNGCLP_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 |
|---|---|---|---|---|---|
| JEFNGCLP_1 | 1290053 | 1316054 | 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 |
| JEFNGCLP_1 | 3031585 | 3053783 | False | Siphoviridae | VOG4574, VOG0136, VOG0753, VOG5535, VOG4599, VOG4605, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG0815, VOG1125, VOG4553, VOG4555, VOG4564, VOG0720, VOG10227, VOG0796 |
| JEFNGCLP_1 | 3061230 | 3063665 | False | Unknown | VOG0189, VOG4566 |
Phigaro v2.4.0 (Database: Jan. 2024 release)