Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 6 | 10 | 3 | 12.04 |
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. |
|---|---|---|---|---|---|---|---|---|
| JPHCJIFO_1 | 3227319 | 3227657 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| JPHCJIFO_1 | 3227002 | 3227319 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| JPHCJIFO_1 | 302642 | 303563 | mph(K) | Spiramycin, Telithromycin | 98.26 | 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. |
|---|---|---|---|---|---|---|---|---|
| JPHCJIFO_1 | 681758 | 682129 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 91.13 | 71.68 | WP_003242546.1 |
| JPHCJIFO_1 | 33541 | 34761 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 81.55 | 74.41 | WP_003234144.1 |
| JPHCJIFO_1 | 2660931 | 2663525 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.18 | 100.00 | WP_087347987.1 |
| JPHCJIFO_1 | 302973 | 303563 | mphK | macrolide 2'-phosphotransferase MphK | PARTIALX | 98.48 | 64.38 | WP_003246254.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| JPHCJIFO_1 | 1604508 | 1605293 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| JPHCJIFO_1 | 1151022 | 1152201 | capB | 0.0 | Capsule | Immune modulation | 99.32 | 99.92 | NP_391471 |
| JPHCJIFO_1 | 2555880 | 2556522 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| JPHCJIFO_1 | 1152687 | 1153829 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| JPHCJIFO_1 | 1608186 | 1609127 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.05 | 100.00 | NP_391077 |
| JPHCJIFO_1 | 2712853 | 2714617 | dep/capD | 0.0 | Capsule | Immune modulation | 98.70 | 100.00 | NP_389723 |
| JPHCJIFO_1 | 1609147 | 1616287 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.67 | 99.99 | NP_391076 |
| JPHCJIFO_1 | 1605319 | 1606516 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.66 | 100.00 | NP_391079 |
| JPHCJIFO_1 | 1606534 | 1608158 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.12 | NP_391078 |
| JPHCJIFO_1 | 1152216 | 1152668 | capC | 0.0 | Capsule | Immune modulation | 98.23 | 100.44 | 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 |
|---|---|---|---|---|---|---|---|---|
| JPHCJIFO_1 | 630234 | 629365 | pdxS | 2.93e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| JPHCJIFO_1 | 2915003 | 2914227 | CodY | 3.20e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| JPHCJIFO_1 | 1309973 | 1309404 | ClpP | 2.37e-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. |
|---|---|---|---|---|---|---|
| JPHCJIFO_3 | 3725 | 3885 | Col(SD853) | 161 / 194 | 83.85 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| JPHCJIFO_1 | 0.0 | 1.0 | 0.0 |
| JPHCJIFO_2 | 1.0 | 0.0 | 1.0 |
| JPHCJIFO_3 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JPHCJIFO_1 | 434378 | 463864 | False | Myoviridae | VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4691, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG3890, VOG10055, VOG4870, VOG1581, VOG0749, VOG4685, VOG4688, VOG4688, VOG4773, VOG4773, VOG10227, VOG9315, VOG3699, VOG2185, VOG1328, VOG10181 |
| JPHCJIFO_1 | 474740 | 479360 | False | Unknown | VOG1309, VOG0083, VOG1878 |
| JPHCJIFO_1 | 1507858 | 1538823 | False | Siphoviridae | VOG4602, VOG9667, VOG0181, VOG4556, VOG0787, VOG1638, VOG4552, VOG4566, VOG9600, VOG0025, VOG1884, VOG0198, VOG4841, VOG4581, VOG4544, VOG3644, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG4611, VOG10611, VOG6163, VOG6163, VOG0801, VOG4619, VOG4619, VOG3462, VOG4660, VOG4660, VOG4660, VOG4612, VOG3390 |
| JPHCJIFO_1 | 3260844 | 3275932 | False | Myoviridae | VOG3892, VOG3891, VOG3891, VOG3890, VOG3890, VOG3890, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG9315, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667, VOG4602 |
Phigaro v2.4.0 (Database: Jan. 2024 release)