Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 10 | 4 | 10.95 |
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. |
|---|---|---|---|---|---|---|---|---|
| JPPEMCHJ_1 | 2824896 | 2825480 | tmrB | ARO:3003059 | tmrB | 96.77 | 98.48 | 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. |
|---|---|---|---|---|---|---|---|
| JPPEMCHJ_1 | 2884320 | 2885240 | mph(K) | Spiramycin, Telithromycin | 96.42 | 99.78 | 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. |
|---|---|---|---|---|---|---|---|---|
| JPPEMCHJ_1 | 2548595 | 2549695 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 84.31 | 66.91 | WP_003234144.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| JPPEMCHJ_1 | 894693 | 895335 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| JPPEMCHJ_1 | 3746991 | 3748172 | capB | 0.0 | Capsule | Immune modulation | 99.24 | 100.00 | NP_391471 |
| JPPEMCHJ_1 | 1119194 | 1120959 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.06 | NP_389723 |
| JPPEMCHJ_1 | 4275471 | 4276258 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.86 | 100.13 | NP_391080 |
| JPPEMCHJ_1 | 4279161 | 4280100 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.62 | 99.89 | NP_391077 |
| JPPEMCHJ_1 | 3748657 | 3749799 | capA | 0.0 | Capsule | Immune modulation | 98.51 | 100.00 | NP_391469 |
| JPPEMCHJ_1 | 4277513 | 4279133 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.21 | 99.94 | NP_391078 |
| JPPEMCHJ_1 | 4280120 | 4287280 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.75 | 100.10 | NP_391076 |
| JPPEMCHJ_1 | 4276284 | 4277484 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.75 | 99.92 | NP_391079 |
| JPPEMCHJ_1 | 3748187 | 3748638 | capC | 0.0 | Capsule | Immune modulation | 97.57 | 100.22 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| JPPEMCHJ_1 | 3078778 | 3077642 | tufA | 0.0 | elongation factor Tu | 84.70 | 95.69 | AHM69299 |
| JPPEMCHJ_1 | 3919965 | 3919396 | ClpP | 7.59e-98 | part of proteolytic complex | 80.53 | 97.44 | BAB94595 |
| JPPEMCHJ_1 | 1424226 | 1423612 | CodY | 3.10e-95 | nutrient-responsive regulator | 81.95 | 79.15 | ACJ80679 |
| JPPEMCHJ_1 | 1929495 | 1929103 | spxA1 | 2.80e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| JPPEMCHJ_1 | 1929495 | 1929103 | spx | 1.67e-67 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| JPPEMCHJ_1 | 3192620 | 3192069 | pdxS | 2.06e-117 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 80.98 | 62.37 | ACE61268 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| JPPEMCHJ_3 | 11440 | 11607 | Col(SD853) | 168 / 194 | 86.90 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| JPPEMCHJ_1 | 0.0 | 1.0 | 0.0 |
| JPPEMCHJ_2 | 1.0 | 0.0 | 1.0 |
| JPPEMCHJ_3 | 1.0 | 0.0 | 1.0 |
| JPPEMCHJ_4 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JPPEMCHJ_1 | 451097 | 478171 | False | Myoviridae | VOG0189, VOG0189, VOG4693, VOG0143, VOG4673, VOG0796, VOG10227, VOG4773, VOG4564, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4865, VOG4885, VOG4885, VOG3894, VOG4691 |
| JPPEMCHJ_1 | 1219759 | 1230333 | False | Siphoviridae | VOG5532, VOG0944, VOG1198, VOG0918, VOG4551, VOG0025, VOG7476, VOG0944, VOG5532, VOG0322, VOG0322 |
| JPPEMCHJ_1 | 1285516 | 1298751 | False | Myoviridae / Siphoviridae | VOG4894, VOG3390, VOG7895, VOG8610, VOG7930, VOG0275, VOG4779, VOG4910, VOG3389, VOG5042 |
| JPPEMCHJ_1 | 1778634 | 1792395 | False | Myoviridae | VOG7718, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4885, VOG4865, VOG4865, VOG6163, VOG3892, VOG3891, VOG3891, VOG3890, VOG3890, VOG3890, VOG3890 |
| JPPEMCHJ_1 | 1793454 | 1809184 | True | Siphoviridae | VOG0749, VOG4685, VOG4773, VOG4773, VOG10227, VOG0796, VOG5447, VOG5447, VOG0189, VOG3490, VOG9667, VOG4602, VOG0101, VOG0733, VOG0944, VOG5532, VOG0944, VOG8387, VOG4666 |
| JPPEMCHJ_1 | 3000734 | 3009491 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4691, VOG3894, VOG4885, VOG4885, VOG4865, VOG4865, VOG6163, VOG2806 |
| JPPEMCHJ_1 | 3018788 | 3027822 | False | Siphoviridae | VOG4685, VOG4750, VOG6965, VOG4688, VOG4564, VOG4773, VOG4773, VOG4773, VOG10227, VOG9315, VOG4544, VOG1328, VOG4571, VOG4618 |
| JPPEMCHJ_1 | 3036348 | 3042105 | False | Unknown | VOG1292, VOG1309, VOG0083, VOG0083, VOG1878, VOG3549 |
| JPPEMCHJ_1 | 4046478 | 4050788 | False | Siphoviridae | VOG0275, VOG1563, VOG1563, VOG9667, VOG6495 |
| JPPEMCHJ_1 | 4062096 | 4081207 | False | Siphoviridae | VOG4581, VOG1886, VOG3607, VOG4556, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG1266, VOG9583, VOG0704, VOG4586, VOG0541, VOG5910, VOG0083, VOG0801, VOG0801, VOG4772, VOG4772, VOG4619, VOG4619, VOG4626, VOG4626, VOG4612, VOG6243, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)