Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 3 | 0 | 1 | 3.16 |
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. |
|---|---|---|---|---|---|---|---|---|
| CPHKOMIA_3 | 20606 | 21982 | tet(L) | ARO:3000179 | tet(L) | 98.03 | 100.00 | M11036.1 |
| CPHKOMIA_3 | 18493 | 20412 | tet(M) | ARO:3000186 | tet(M) | 96.87 | 100.00 | AB039845.1 |
| CPHKOMIA_3 | 1047 | 1781 | ErmC | ARO:3000250 | ErmC | 93.85 | 100.00 | M12730.1 |
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. |
|---|---|---|---|---|---|---|---|
| CPHKOMIA_3 | 1047 | 1781 | erm(C) | Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 99.59 | 100.00 | Y09003 |
| CPHKOMIA_3 | 20607 | 21982 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.42 | 99.93 | AY081910 |
| CPHKOMIA_3 | 18493 | 20412 | tet(M) | Doxycycline, Tetracycline, Minocycline | 97.24 | 100.00 | AM990992 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| CPHKOMIA_3 | 1047 | 1778 | erm(C) | 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C) | BLASTX | 99.59 | 100.00 | WP_032492416.1 |
| CPHKOMIA_3 | 20606 | 21979 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.47 | 100.00 | WP_002294500.1 |
| CPHKOMIA_3 | 18493 | 20409 | tet(M) | tetracycline resistance ribosomal protection protein Tet(M) | BLASTX | 97.81 | 100.00 | WP_024052575.1 |
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 |
|---|---|---|---|---|---|---|---|---|
| CPHKOMIA_1 | 47039 | 47746 | WalR | 5.94e-115 | transcriptional regulatory protein | 85.59 | 100.43 | 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 |
|---|---|---|---|
| CPHKOMIA_1 | 0.0 | 1.0 | 0.0 |
| CPHKOMIA_2 | 1.0 | 0.0 | 1.0 |
| CPHKOMIA_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 |
|---|---|---|---|---|---|
| CPHKOMIA_1 | 714940 | 746179 | False | Siphoviridae | VOG4552, VOG6282, VOG11003, VOG3947, VOG0321, VOG4548, VOG0322, VOG6545, VOG4632, VOG4609, VOG0327, VOG0198, VOG1637, VOG0796, VOG10227, VOG0720, VOG4564, VOG10914, VOG4572, VOG4713, VOG0723, VOG5660, VOG0724, VOG0799, VOG0725, VOG0800, VOG4545, VOG4633, VOG5904, VOG5008, VOG0641, VOG8294 |
Phigaro v2.4.0 (Database: Jan. 2024 release)