Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 4 | 2 | 6 | 7.48 |
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. |
|---|---|---|---|---|---|---|---|---|
| LOPLIDCK_13 | 48071 | 49117 | 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. |
|---|---|---|---|---|---|---|---|
| LOPLIDCK_13 | 48074 | 49117 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| LOPLIDCK_11 | 176526 | 177902 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 87.07 | 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. |
|---|---|---|---|---|---|---|---|---|
| LOPLIDCK_13 | 48074 | 49117 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| LOPLIDCK_11 | 176526 | 177896 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| LOPLIDCK_13 | 50868 | 51386 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| LOPLIDCK_8 | 276624 | 279221 | rphC | rifamycin-inactivating phosphotransferase RphC | INTERNAL_STOP | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LOPLIDCK_4 | 377360 | 378541 | capB | 0.0 | Capsule | Immune modulation | 81.79 | 99.66 | NP_391471 |
| LOPLIDCK_4 | 378556 | 379005 | capC | 1.75e-114 | Capsule | Immune modulation | 83.59 | 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 |
|---|---|---|---|---|---|---|---|---|
| LOPLIDCK_5 | 27633 | 26497 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| LOPLIDCK_22 | 4254 | 5123 | pdxS | 6.31e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| LOPLIDCK_8 | 72504 | 73280 | CodY | 8.18e-125 | nutrient-responsive regulator | 80.69 | 100.00 | ACJ80679 |
| LOPLIDCK_1 | 327089 | 327481 | spxA1 | 9.08e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| LOPLIDCK_13 | 65603 | 65406 | CspA | 3.14e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| LOPLIDCK_11 | 550116 | 549922 | CspD | 1.68e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| LOPLIDCK_11 | 550116 | 549919 | CspB | 3.49e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| LOPLIDCK_13 | 65603 | 65409 | CspR | 1.56e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
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 |
|---|---|---|---|
| LOPLIDCK_1 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_2 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_3 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_4 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_5 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_7 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_8 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_9 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_10 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_11 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_12 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_13 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_14 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_17 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_18 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_19 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_20 | 1.0 | 0.0 | 1.0 |
| LOPLIDCK_21 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_22 | 0.0 | 1.0 | 0.0 |
| LOPLIDCK_23 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LOPLIDCK_1 | 15467 | 18725 | False | Unknown | VOG6546, VOG10937 |
| LOPLIDCK_1 | 38699 | 66751 | False | Siphoviridae | VOG7541, VOG7742, VOG6495, VOG5327, VOG1183, VOG0275, VOG5023, VOG3699, VOG2613, VOG0692, VOG4555, VOG3676, VOG5361, VOG0724, VOG2565, VOG11074, VOG0083, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5221, VOG4824, VOG0602 |
| LOPLIDCK_1 | 417907 | 444711 | False | Myoviridae | VOG9667, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| LOPLIDCK_2 | 13041 | 26987 | False | Siphoviridae | VOG4602, VOG8483, VOG9667, VOG11075, VOG0650, VOG4552, VOG4600, VOG4600, VOG1309, VOG9093, VOG0189, VOG0044, VOG0536, VOG1336, VOG4658, VOG8569, VOG0397, VOG6581 |
| LOPLIDCK_2 | 29359 | 58426 | False | Siphoviridae | VOG5447, VOG4972, VOG4681, VOG0796, VOG10227, VOG0720, VOG4564, VOG6778, VOG4555, VOG1329, VOG2621, VOG5872, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG4545, VOG4605, VOG4599, VOG3390, VOG5535, VOG0753, VOG0136, VOG4574 |
| LOPLIDCK_2 | 309474 | 339523 | False | Siphoviridae | VOG5353, VOG0181, VOG4552, VOG3547, VOG4566, VOG9600, VOG0025, VOG1884, VOG5969, VOG0425, VOG5447, VOG0376, VOG2545, VOG4841, VOG4581, VOG4544, VOG4556, VOG4573, VOG4553, VOG0204, VOG4589, VOG0207, VOG4586, VOG5852, VOG6163, VOG0801, VOG3462, VOG4619, VOG4856, VOG0804, VOG4705 |
| LOPLIDCK_3 | 237513 | 271412 | False | Siphoviridae | VOG0181, VOG7438, VOG1047, VOG0021, VOG1565, VOG0026, VOG10500, VOG4609, VOG0327, VOG4548, VOG0198, VOG4581, VOG4544, VOG5051, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG7896, VOG0641, VOG4707 |
| LOPLIDCK_10 | 21967 | 44673 | 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 |
Phigaro v2.4.0 (Database: Jan. 2024 release)