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. |
|---|---|---|---|---|---|---|---|---|
| CNHDDKAJ_11 | 36533 | 37579 | 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. |
|---|---|---|---|---|---|---|---|
| CNHDDKAJ_11 | 36533 | 37576 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| CNHDDKAJ_288 | 477233 | 478609 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 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. |
|---|---|---|---|---|---|---|---|---|
| CNHDDKAJ_11 | 36533 | 37576 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| CNHDDKAJ_288 | 477239 | 478609 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| CNHDDKAJ_11 | 34264 | 34782 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| CNHDDKAJ_279 | 469150 | 471747 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CNHDDKAJ_268 | 377212 | 378393 | capB | 0.0 | Capsule | Immune modulation | 81.79 | 99.66 | NP_391471 |
| CNHDDKAJ_268 | 378408 | 378857 | capC | 3.53e-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 |
|---|---|---|---|---|---|---|---|---|
| CNHDDKAJ_321 | 27634 | 26498 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| CNHDDKAJ_107 | 12476 | 11607 | pdxS | 6.35e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| CNHDDKAJ_279 | 265030 | 265806 | CodY | 1.37e-124 | nutrient-responsive regulator | 80.69 | 100.00 | ACJ80679 |
| CNHDDKAJ_108 | 327195 | 327587 | spxA1 | 5.65e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| CNHDDKAJ_11 | 20047 | 20244 | CspA | 1.31e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| CNHDDKAJ_11 | 20047 | 20241 | CspR | 6.49e-27 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| CNHDDKAJ_108 | 106731 | 106537 | CspB | 8.90e-27 | cold shock protein | 84.61 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| CNHDDKAJ_11 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_22 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_43 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_54 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_65 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_76 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_87 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_107 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_108 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_119 | 1.0 | 0.0 | 1.0 |
| CNHDDKAJ_130 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_219 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_268 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_279 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_288 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_299 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_310 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_321 | 0.0 | 1.0 | 0.0 |
| CNHDDKAJ_332 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CNHDDKAJ_54 | 58675 | 66719 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885 |
| CNHDDKAJ_108 | 15573 | 18831 | False | Unknown | VOG6546, VOG10937 |
| CNHDDKAJ_108 | 38805 | 66857 | 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 |
| CNHDDKAJ_108 | 418013 | 428382 | False | Siphoviridae | VOG9667, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749 |
| CNHDDKAJ_268 | 708988 | 742887 | 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 |
| CNHDDKAJ_268 | 906602 | 929308 | False | Siphoviridae | VOG4841, VOG4556, VOG6052, VOG0531, VOG4581, VOG4544, VOG5051, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641 |
| CNHDDKAJ_310 | 16127 | 46176 | False | Siphoviridae | VOG5221, VOG4705, VOG0804, VOG4856, VOG4619, VOG3462, VOG0801, VOG6163, VOG5852, VOG4586, VOG0207, VOG4589, VOG0204, VOG4553, VOG4573, VOG4556, VOG4544, VOG4581, VOG4841, VOG2545, VOG0376, VOG5447, VOG0425, VOG5969, VOG1884, VOG0025, VOG9600, VOG4566, VOG3547, VOG4552, VOG0181 |
| CNHDDKAJ_332 | 135401 | 164468 | False | Siphoviridae | VOG4666, VOG4574, VOG0136, VOG0753, VOG5535, VOG3390, VOG4599, VOG4605, VOG4545, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG5872, VOG2621, VOG1329, VOG4555, VOG6778, VOG4564, VOG0720, VOG10227, VOG0796, VOG4681, VOG4972, VOG5447 |
| CNHDDKAJ_332 | 166840 | 180786 | False | Siphoviridae | VOG0102, VOG6581, VOG0397, VOG8569, VOG4658, VOG1336, VOG0536, VOG0044, VOG0189, VOG9093, VOG1309, VOG4600, VOG4600, VOG4552, VOG0650, VOG11075, VOG9667, VOG8483 |
Phigaro v2.4.0 (Database: Jan. 2024 release)