Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 0 | 6 | 6.32 |
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. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
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. |
|---|---|---|---|---|---|---|---|
| PGMMCNJC_1 | 1406614 | 1407828 | mef(A) | Erythromycin, Azithromycin | 94.24 | 99.75 | AF227520 |
| PGMMCNJC_1 | 1407954 | 1409404 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 92.90 | 99.11 | AF274302 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PGMMCNJC_1 | 1406614 | 1407837 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_012102963.1 |
| PGMMCNJC_1 | 1407954 | 1409408 | msr(D) | ABC-F type ribosomal protection protein Msr(D) | BLASTX | 92.99 | 99.59 | WP_000420313.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| No hit found | |||||||||
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 |
|---|---|---|---|---|---|---|---|---|
| PGMMCNJC_1 | 1285239 | 1286417 | tufA | 0.0 | elongation factor Tu | 85.75 | 99.49 | AHM69299 |
| PGMMCNJC_1 | 956994 | 955489 | atpA | 0.0 | ATP synthase subunit alpha | 80.08 | 100.00 | ABD31377 |
| PGMMCNJC_1 | 1228206 | 1229075 | pdxS | 3.47e-150 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PGMMCNJC_1 | 2564458 | 2565234 | CodY | 6.22e-127 | nutrient-responsive regulator | 81.85 | 100.00 | ACJ80679 |
| PGMMCNJC_1 | 2564458 | 2565234 | codY | 3.00e-123 | global regulator and isoleucine sensor | 80.69 | 100.00 | ASW39076 |
| PGMMCNJC_1 | 2136485 | 2135916 | ClpP | 1.55e-102 | part of proteolytic complex | 83.68 | 97.44 | BAB94595 |
| PGMMCNJC_1 | 1115931 | 1115245 | WalR | 4.57e-102 | transcriptional regulatory protein | 80.79 | 97.44 | EPH95667 |
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 |
|---|---|---|---|
| PGMMCNJC_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 |
|---|---|---|---|---|---|
| PGMMCNJC_1 | 11925 | 40472 | False | Siphoviridae | VOG0703, VOG4918, VOG8197, VOG5008, VOG3498, VOG4763, VOG4599, VOG4605, VOG3379, VOG0701, VOG10044, VOG7238, VOG0698, VOG0697, VOG0696, VOG0695, VOG5007, VOG4572, VOG9317, VOG1183, VOG0692, VOG0691, VOG10227, VOG0796, VOG3412, VOG0198, VOG10904, VOG8445 |
| PGMMCNJC_1 | 47823 | 55141 | False | Siphoviridae | VOG0189, VOG4799, VOG1309, VOG4600, VOG1879, VOG1878, VOG3549, VOG8241, VOG4552 |
Phigaro v2.4.0 (Database: Jan. 2024 release)