Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 3 | 2 | 6 | 7.00 |
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. |
|---|---|---|---|---|---|---|---|---|
| KDOOIGDA_3 | 52544 | 53593 | clbA | ARO:3002814 | clbA | 97.71 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| KDOOIGDA_3 | 52558 | 53593 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.22 | 98.67 | KR610408 |
| KDOOIGDA_1 | 381358 | 382734 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 87.29 | 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. |
|---|---|---|---|---|---|---|---|---|
| KDOOIGDA_3 | 52550 | 53593 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 97.99 | 99.71 | WP_012116915.1 |
| KDOOIGDA_1 | 381358 | 382728 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.65 | 99.78 | WP_003242953.1 |
| KDOOIGDA_1 | 1119131 | 1121725 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.46 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| KDOOIGDA_2 | 573602 | 574783 | capB | 0.0 | Capsule | Immune modulation | 82.29 | 99.66 | NP_391471 |
| KDOOIGDA_2 | 573138 | 573587 | capC | 1.88e-112 | Capsule | Immune modulation | 83.37 | 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 |
|---|---|---|---|---|---|---|---|---|
| KDOOIGDA_6 | 28260 | 27124 | tufA | 0.0 | elongation factor Tu | 86.81 | 95.69 | AHM69299 |
| KDOOIGDA_8 | 12499 | 11630 | pdxS | 1.36e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| KDOOIGDA_1 | 1459484 | 1458708 | CodY | 2.64e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| KDOOIGDA_1 | 1963000 | 1962608 | spxA1 | 4.82e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| KDOOIGDA_3 | 81982 | 81785 | CspA | 2.61e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| KDOOIGDA_3 | 81982 | 81788 | CspR | 3.42e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| KDOOIGDA_2 | 182648 | 181776 | lipA (SAUSA300_0829) | 3.50e-162 | lipoic acid synthetase | 80.82 | 95.41 | ABD22039 |
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 |
|---|---|---|---|
| KDOOIGDA_1 | 0.0 | 1.0 | 0.0 |
| KDOOIGDA_2 | 0.0 | 1.0 | 0.0 |
| KDOOIGDA_3 | 0.0 | 1.0 | 0.0 |
| KDOOIGDA_4 | 0.0 | 1.0 | 0.0 |
| KDOOIGDA_5 | 1.0 | 0.0 | 1.0 |
| KDOOIGDA_6 | 0.0 | 1.0 | 0.0 |
| KDOOIGDA_7 | 0.0 | 1.0 | 0.0 |
| KDOOIGDA_8 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| KDOOIGDA_1 | 1226524 | 1257488 | False | Myoviridae / Siphoviridae | VOG4570, VOG5722, VOG5779, VOG5721, VOG6031, VOG6524, VOG6246, VOG6941, VOG6036, VOG6472, VOG9219, VOG9713, VOG6940, VOG5534, VOG7718, VOG3390, VOG5008, VOG8610, VOG7930, VOG0275, VOG9312, VOG4910, VOG3389 |
| KDOOIGDA_1 | 1840561 | 1866756 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189 |
| KDOOIGDA_2 | 10428 | 27191 | True | Siphoviridae | VOG4910, VOG4713, VOG4572, VOG4555, VOG0720, VOG7734, VOG0221, VOG3699, VOG6282, VOG8610, VOG4705, VOG3390 |
Phigaro v2.4.0 (Database: Jan. 2024 release)