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. |
|---|---|---|---|---|---|---|---|---|
| ILNADEDF_20 | 355147 | 356193 | 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. |
|---|---|---|---|---|---|---|---|
| ILNADEDF_20 | 355147 | 356190 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| ILNADEDF_19 | 169506 | 170883 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 87.08 | 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. |
|---|---|---|---|---|---|---|---|---|
| ILNADEDF_20 | 355147 | 356190 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| ILNADEDF_19 | 169555 | 170877 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.85 | 96.29 | WP_003242953.1 |
| ILNADEDF_20 | 352884 | 353396 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 81.50 | 100.00 | WP_003242546.1 |
| ILNADEDF_2 | 5191 | 7788 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| ILNADEDF_12 | 352420 | 353601 | capB | 0.0 | Capsule | Immune modulation | 81.87 | 99.66 | NP_391471 |
| ILNADEDF_12 | 351956 | 352405 | capC | 2.67e-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 |
|---|---|---|---|---|---|---|---|---|
| ILNADEDF_3 | 27510 | 26374 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| ILNADEDF_6 | 4234 | 5103 | pdxS | 8.66e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.48 | 98.31 | ACE61268 |
| ILNADEDF_1 | 195249 | 194473 | CodY | 7.76e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| ILNADEDF_1 | 653728 | 653336 | spxA1 | 3.88e-69 | redox-responsive transcription factor | 82.44 | 100.00 | AAF21893 |
| ILNADEDF_20 | 338649 | 338846 | CspA | 5.79e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| ILNADEDF_19 | 542982 | 542788 | CspD | 1.65e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| ILNADEDF_19 | 542982 | 542785 | CspB | 3.43e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| ILNADEDF_20 | 338649 | 338843 | CspR | 2.87e-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. |
|---|---|---|---|---|---|---|
| ILNADEDF_9 | 1719 | 1905 | Col(SD853) | 187 / 194 | 86.63 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| ILNADEDF_1 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_2 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_3 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_4 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_5 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_6 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_7 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_8 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_9 | 1.0 | 0.0 | 1.0 |
| ILNADEDF_10 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_12 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_13 | 1.0 | 0.0 | 1.0 |
| ILNADEDF_14 | 1.0 | 0.0 | 1.0 |
| ILNADEDF_16 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_17 | 1.0 | 0.0 | 1.0 |
| ILNADEDF_18 | 1.0 | 0.0 | 1.0 |
| ILNADEDF_19 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_20 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_21 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_22 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_23 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_24 | 0.0 | 1.0 | 0.0 |
| ILNADEDF_25 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| ILNADEDF_1 | 519943 | 545319 | False | Myoviridae | VOG7895, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189 |
| ILNADEDF_1 | 914912 | 935558 | False | Siphoviridae | VOG0136, VOG5221, VOG4705, VOG0804, VOG4856, VOG4619, VOG3462, VOG0801, VOG6163, VOG5852, VOG4586, VOG0207, VOG4589, VOG0204, VOG4553, VOG4573, VOG4556, VOG4544, VOG4581, VOG4841 |
| ILNADEDF_5 | 4620 | 9119 | False | Siphoviridae | VOG0650, VOG4322, VOG0806, VOG9667, VOG9667, VOG4662, VOG4602 |
| ILNADEDF_19 | 1169 | 24819 | False | Myoviridae | VOG0796, VOG10227, VOG0720, VOG4555, VOG4572, VOG1643, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG7895, VOG0753, VOG0136, VOG10230 |
| ILNADEDF_21 | 926 | 22250 | False | Siphoviridae | VOG0796, VOG10227, VOG0720, VOG4564, VOG1300, VOG4555, VOG1329, VOG2621, VOG5872, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG1323, VOG4545, VOG4605, VOG4599, VOG3390, VOG5535, VOG0753, VOG0136, VOG4574 |
Phigaro v2.4.0 (Database: Jan. 2024 release)