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. |
|---|---|---|---|---|---|---|---|---|
| PHMJEDCH_1 | 502497 | 503543 | clbA | ARO:3002814 | clbA | 92.77 | 99.71 | 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. |
|---|---|---|---|---|---|---|---|
| PHMJEDCH_1 | 502497 | 503540 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| PHMJEDCH_1 | 2522714 | 2524090 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 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. |
|---|---|---|---|---|---|---|---|---|
| PHMJEDCH_1 | 502497 | 503540 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| PHMJEDCH_1 | 2522720 | 2524090 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 87.31 | 99.78 | WP_003242953.1 |
| PHMJEDCH_1 | 500228 | 500746 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| PHMJEDCH_1 | 1588687 | 1591284 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PHMJEDCH_1 | 3463643 | 3464824 | capB | 0.0 | Capsule | Immune modulation | 82.04 | 99.66 | NP_391471 |
| PHMJEDCH_1 | 3463179 | 3463628 | capC | 6.84e-107 | Capsule | Immune modulation | 82.70 | 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 |
|---|---|---|---|---|---|---|---|---|
| PHMJEDCH_1 | 123173 | 124354 | tufA | 0.0 | elongation factor Tu | 86.29 | 99.49 | AHM69299 |
| PHMJEDCH_1 | 14221 | 15090 | pdxS | 1.55e-150 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| PHMJEDCH_1 | 1792396 | 1791620 | CodY | 3.26e-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 |
|---|---|---|---|
| PHMJEDCH_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 |
|---|---|---|---|---|---|
| PHMJEDCH_1 | 1198383 | 1215683 | False | Unknown | VOG5042, VOG3389, VOG4910, VOG9312, VOG2090, VOG2091, VOG0275, VOG7930, VOG8610, VOG5008 |
| PHMJEDCH_1 | 1278562 | 1289499 | False | Unknown | VOG0048, VOG0156, VOG6464, VOG0322, VOG7627, VOG0025, VOG4551 |
| PHMJEDCH_1 | 2117208 | 2143324 | False | Myoviridae | VOG7895, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189 |
| PHMJEDCH_1 | 2207288 | 2231331 | False | Myoviridae | VOG10230, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG1643, VOG4572, VOG4555, VOG0720, VOG0796 |
| PHMJEDCH_1 | 2239686 | 2242977 | False | Unknown | VOG0189, VOG4566, VOG0186 |
| PHMJEDCH_1 | 2243265 | 2247204 | False | Unknown | VOG8241, VOG9667, VOG9667, VOG9576 |
| PHMJEDCH_1 | 2912555 | 2935261 | False | Siphoviridae | VOG4972, VOG0641, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG5051, VOG4544, VOG4581, VOG0531, VOG6052, VOG4556 |
| PHMJEDCH_1 | 3054033 | 3074841 | False | Siphoviridae | VOG5221, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG11074, VOG0724, VOG4319, VOG9317, VOG0692, VOG2613, VOG3699, VOG5023 |
Phigaro v2.4.0 (Database: Jan. 2024 release)