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. |
|---|---|---|---|---|---|---|---|---|
| LEIJOGGE_1 | 2423475 | 2424521 | 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. |
|---|---|---|---|---|---|---|---|
| LEIJOGGE_1 | 2423475 | 2424518 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| LEIJOGGE_1 | 540981 | 542357 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 87.15 | 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. |
|---|---|---|---|---|---|---|---|---|
| LEIJOGGE_1 | 2423475 | 2424518 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| LEIJOGGE_1 | 540987 | 542357 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| LEIJOGGE_1 | 2421206 | 2421724 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| LEIJOGGE_1 | 3852428 | 3855025 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LEIJOGGE_1 | 1427135 | 1428316 | capB | 0.0 | Capsule | Immune modulation | 81.87 | 99.66 | NP_391471 |
| LEIJOGGE_1 | 1426671 | 1427120 | capC | 1.43e-113 | 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 |
|---|---|---|---|---|---|---|---|---|
| LEIJOGGE_1 | 2048337 | 2049473 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| LEIJOGGE_1 | 1933559 | 1934428 | pdxS | 1.52e-150 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| LEIJOGGE_1 | 3542478 | 3543254 | CodY | 3.20e-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 |
|---|---|---|---|
| LEIJOGGE_1 | 0.0 | 1.0 | 0.0 |
| LEIJOGGE_2 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LEIJOGGE_1 | 463184 | 491103 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG0979, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG6480, VOG4688, VOG4773, VOG10227, VOG0796, VOG10057 |
| LEIJOGGE_1 | 494902 | 500421 | False | Siphoviridae | VOG4693, VOG0189, VOG11060, VOG1309, VOG4600, VOG4603 |
| LEIJOGGE_1 | 2490186 | 2504143 | False | Siphoviridae | VOG4602, VOG8483, VOG9667, VOG11075, VOG0650, VOG4552, VOG4600, VOG1309, VOG9093, VOG0189, VOG0044, VOG0536, VOG1336, VOG4658, VOG8569, VOG0397, VOG6581 |
| LEIJOGGE_1 | 2506513 | 2531554 | 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 |
| LEIJOGGE_1 | 2805455 | 2838191 | False | Siphoviridae | VOG6495, VOG0181, VOG4566, VOG0189, VOG6931, VOG6587, VOG1336, VOG5407, VOG4658, VOG8569, VOG0397, VOG6581, VOG6517, VOG6242, VOG0198, VOG0275, VOG7884, VOG0531, VOG0519, VOG4544, VOG4556, VOG4556, VOG4573, VOG4553, VOG3435, VOG0204, VOG4589, VOG0704, VOG0539, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641 |
| LEIJOGGE_1 | 3190509 | 3218775 | False | Myoviridae | VOG0101, VOG4602, VOG9667, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| LEIJOGGE_1 | 3610515 | 3636770 | False | Siphoviridae | VOG0054, VOG8537, VOG10230, VOG4660, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG1637, VOG0275, VOG7930, VOG8610, VOG5008, VOG4705, VOG3390, VOG7718, VOG5534, VOG6940, VOG9713 |
Phigaro v2.4.0 (Database: Jan. 2024 release)