Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 4 | 2 | 3 | 5.39 |
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. |
|---|---|---|---|---|---|---|---|---|
| KNPJIOME_1 | 505757 | 506806 | clbA | ARO:3002814 | clbA | 92.26 | 100.00 | CP006845.1 |
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. |
|---|---|---|---|---|---|---|---|
| KNPJIOME_1 | 505757 | 506806 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.77 | 99.90 | KR610408 |
| KNPJIOME_1 | 2479982 | 2481358 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 87.44 | 100.00 | X08034 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| KNPJIOME_1 | 505757 | 506803 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.26 | 100.00 | WP_012116915.1 |
| KNPJIOME_1 | 2479988 | 2481358 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 87.53 | 99.78 | WP_003242953.1 |
| KNPJIOME_1 | 502783 | 503301 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 85.55 | 100.00 | WP_003242546.1 |
| KNPJIOME_1 | 1790113 | 1792710 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.17 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| KNPJIOME_1 | 3362446 | 3363627 | capB | 0.0 | Capsule | Immune modulation | 81.87 | 99.66 | NP_391471 |
| KNPJIOME_1 | 3361982 | 3362431 | capC | 1.42e-113 | Capsule | Immune modulation | 83.59 | 99.78 | 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 |
|---|---|---|---|---|---|---|---|---|
| KNPJIOME_1 | 133472 | 134608 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| KNPJIOME_1 | 18631 | 19500 | pdxS | 1.51e-150 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| KNPJIOME_1 | 1591974 | 1592750 | CodY | 3.18e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
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 |
|---|---|---|---|
| KNPJIOME_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 |
|---|---|---|---|---|---|
| KNPJIOME_1 | 1186921 | 1213612 | False | Myoviridae | VOG9667, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705, VOG0753 |
| KNPJIOME_1 | 2108874 | 2135746 | False | Siphoviridae | VOG3532, VOG0052, VOG10230, VOG0641, VOG7896, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581 |
Phigaro v2.4.0 (Database: Jan. 2024 release)