Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 1 | 2 | 7 | 7.35 |
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. |
|---|---|---|---|---|---|---|---|---|
| CPJEIFNL_3 | 367094 | 368143 | clbA | ARO:3002814 | clbA | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| CPJEIFNL_3 | 367094 | 368129 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 89.00 | 98.67 | KR610408 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| CPJEIFNL_3 | 367094 | 368140 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | EXACTX | 100.00 | 100.00 | WP_012116915.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| CPJEIFNL_1 | 500256 | 501437 | capB | 0.0 | Capsule | Immune modulation | 81.96 | 99.66 | NP_391471 |
| CPJEIFNL_1 | 499792 | 500241 | capC | 1.04e-115 | Capsule | Immune modulation | 83.81 | 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 |
|---|---|---|---|---|---|---|---|---|
| CPJEIFNL_8 | 28199 | 27063 | tufA | 0.0 | elongation factor Tu | 86.81 | 95.69 | AHM69299 |
| CPJEIFNL_11 | 12542 | 11673 | pdxS | 1.36e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| CPJEIFNL_2 | 333550 | 332774 | CodY | 1.25e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CPJEIFNL_2 | 810532 | 810140 | spxA1 | 2.29e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| CPJEIFNL_3 | 344716 | 344913 | CspA | 2.48e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CPJEIFNL_4 | 149559 | 149753 | CspD | 8.80e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| CPJEIFNL_4 | 149559 | 149756 | CspB | 1.82e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| CPJEIFNL_3 | 344716 | 344910 | CspR | 3.25e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| CPJEIFNL_1 | 138265 | 137393 | lipA (SAUSA300_0829) | 4.20e-162 | lipoic acid synthetase | 80.82 | 95.41 | ABD22039 |
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 |
|---|---|---|---|
| CPJEIFNL_1 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_2 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_3 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_4 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_5 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_6 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_7 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_8 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_9 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_10 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_11 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_12 | 0.0 | 1.0 | 0.0 |
| CPJEIFNL_13 | 1.0 | 0.0 | 1.0 |
| CPJEIFNL_17 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CPJEIFNL_2 | 713255 | 718173 | False | Siphoviridae | VOG4705, VOG3390, VOG4612, VOG11003, VOG5447, VOG4861, VOG0189 |
Phigaro v2.4.0 (Database: Jan. 2024 release)