Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 3 | 2 | 4 | 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. |
|---|---|---|---|---|---|---|---|---|
| CHECDLDK_1 | 520867 | 521958 | clbA | ARO:3002814 | clbA | 99.71 | 104.01 | 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. |
|---|---|---|---|---|---|---|---|
| CHECDLDK_1 | 520923 | 521958 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.71 | 98.67 | KR610408 |
| CHECDLDK_1 | 2564273 | 2565648 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 86.86 | 99.93 | 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. |
|---|---|---|---|---|---|---|---|---|
| CHECDLDK_1 | 520924 | 521958 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 99.71 | 98.85 | WP_012116915.1 |
| CHECDLDK_1 | 2564273 | 2565298 | tet(L) | tetracycline efflux MFS transporter Tet(L) | PARTIALX | 89.47 | 74.67 | WP_003242953.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| CHECDLDK_1 | 1554405 | 1555586 | capB | 0.0 | Capsule | Immune modulation | 82.06 | 99.58 | NP_391471 |
| CHECDLDK_1 | 1555601 | 1556050 | capC | 6.92e-112 | Capsule | Immune modulation | 83.37 | 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 |
|---|---|---|---|---|---|---|---|---|
| CHECDLDK_1 | 937940 | 936804 | tufA | 0.0 | elongation factor Tu | 86.81 | 95.69 | AHM69299 |
| CHECDLDK_1 | 1052669 | 1051800 | pdxS | 3.36e-150 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| CHECDLDK_1 | 3471055 | 3470294 | CodY | 1.93e-122 | nutrient-responsive regulator | 81.50 | 98.07 | ACJ80679 |
| CHECDLDK_1 | 1917211 | 1918008 | lipA (SAUSA300_0829) | 1.72e-146 | lipoic acid synthetase | 80.08 | 87.21 | 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 |
|---|---|---|---|
| CHECDLDK_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 |
|---|---|---|---|---|---|
| CHECDLDK_1 | 2058544 | 2079182 | False | Siphoviridae | VOG0796, VOG10439, VOG0720, VOG0720, VOG4564, VOG4555, VOG4553, VOG1125, VOG0815, VOG4623, VOG0816, VOG0724, VOG0799, VOG2621, VOG0725, VOG1323, VOG4545, VOG4605, VOG4599 |
| CHECDLDK_1 | 2356168 | 2380633 | False | Myoviridae | VOG8642, VOG0796, VOG0720, VOG1183, VOG0045, VOG4555, VOG4572, VOG1643, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG9745, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG10230 |
| CHECDLDK_1 | 2434437 | 2463149 | False | Siphoviridae | VOG3547, VOG11060, VOG9600, VOG0025, VOG1884, VOG10961, VOG2981, VOG5447, VOG0376, VOG2545, VOG0531, VOG4841, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG7006, VOG0204, VOG1266, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG0801, VOG4772, VOG4619, VOG4660, VOG4660, VOG4612, VOG3390 |
| CHECDLDK_1 | 3847550 | 3875152 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG4894, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG7947, VOG3892, VOG3891, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667, VOG4602 |
Phigaro v2.4.0 (Database: Jan. 2024 release)