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. |
|---|---|---|---|---|---|---|---|---|
| ONCKDIPA_2 | 159903 | 160949 | 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. |
|---|---|---|---|---|---|---|---|
| ONCKDIPA_2 | 159903 | 160946 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| ONCKDIPA_10 | 59145 | 60521 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 87.36 | 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. |
|---|---|---|---|---|---|---|---|---|
| ONCKDIPA_2 | 159903 | 160946 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| ONCKDIPA_10 | 59145 | 60515 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 87.09 | 99.78 | WP_003242953.1 |
| ONCKDIPA_2 | 157636 | 158154 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| ONCKDIPA_7 | 145953 | 148550 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| ONCKDIPA_4 | 377030 | 378211 | capB | 0.0 | Capsule | Immune modulation | 81.87 | 99.66 | NP_391471 |
| ONCKDIPA_4 | 378226 | 378675 | capC | 3.45e-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 |
|---|---|---|---|---|---|---|---|---|
| ONCKDIPA_8 | 31664 | 32800 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| ONCKDIPA_19 | 12463 | 11594 | pdxS | 8.83e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.48 | 98.31 | ACE61268 |
| ONCKDIPA_1 | 55133 | 54357 | CodY | 6.55e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| ONCKDIPA_1 | 532284 | 531892 | spxA1 | 1.03e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| ONCKDIPA_2 | 143403 | 143600 | CspA | 3.19e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| ONCKDIPA_6 | 164571 | 164377 | CspD | 6.81e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| ONCKDIPA_6 | 164571 | 164374 | CspB | 1.41e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| ONCKDIPA_2 | 143403 | 143597 | CspR | 1.58e-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. |
|---|---|---|---|---|---|---|
| ONCKDIPA_22 | 6216 | 6409 | Col(SD853) | 194 / 194 | 87.63 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| ONCKDIPA_1 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_2 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_3 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_4 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_5 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_6 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_7 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_8 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_9 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_10 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_11 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_14 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_15 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_16 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_17 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_18 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_19 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_20 | 1.0 | 0.0 | 1.0 |
| ONCKDIPA_22 | 1.0 | 0.0 | 1.0 |
| ONCKDIPA_23 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_24 | 0.0 | 1.0 | 0.0 |
| ONCKDIPA_27 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| ONCKDIPA_1 | 379969 | 405355 | False | Myoviridae | VOG7895, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189 |
| ONCKDIPA_1 | 461746 | 483309 | False | Siphoviridae | VOG7508, VOG0602, VOG4574, VOG0753, VOG4705, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG4544, VOG4581, VOG8909 |
| ONCKDIPA_4 | 892333 | 899542 | True | Siphoviridae | VOG6282, VOG3699, VOG0221, VOG7734, VOG0720, VOG4555, VOG4572 |
| ONCKDIPA_9 | 121532 | 146894 | False | Myoviridae | VOG10230, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG5000, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG1643, VOG4572, VOG4555, VOG0720, VOG10227, VOG0796, VOG4681, VOG4972 |
| ONCKDIPA_10 | 1005 | 24281 | False | Siphoviridae | VOG0275, VOG9077, VOG0531, VOG4841, VOG4581, VOG4544, VOG4556, VOG4573, VOG4553, VOG0204, VOG4589, VOG0207, VOG4586, VOG5852, VOG6163, VOG0801, VOG3462, VOG4619, VOG4856, VOG0804, VOG4705, VOG5221, VOG0136 |
| ONCKDIPA_11 | 11745 | 37093 | False | Siphoviridae | VOG0054, VOG8537, VOG4574, VOG4660, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG1637, VOG0275, VOG8610, VOG3390, VOG7718, VOG5534 |
| ONCKDIPA_16 | 227519 | 233907 | False | Unknown | VOG4322, VOG4552, VOG4600, VOG1309, VOG4566 |
Phigaro v2.4.0 (Database: Jan. 2024 release)