Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 1 | 7 | 7.35 |
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. |
|---|---|---|---|---|---|---|---|---|
| PKDOJPKJ_71 | 52129 | 53178 | 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. |
|---|---|---|---|---|---|---|---|
| PKDOJPKJ_71 | 52143 | 53178 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.32 | 98.67 | KR610408 |
| PKDOJPKJ_69 | 173611 | 174987 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 87.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| PKDOJPKJ_71 | 52135 | 53178 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 97.99 | 99.71 | WP_012116915.1 |
| PKDOJPKJ_69 | 173611 | 174981 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PKDOJPKJ_42 | 457679 | 458860 | capB | 0.0 | Capsule | Immune modulation | 82.46 | 99.66 | NP_391471 |
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 |
|---|---|---|---|---|---|---|---|---|
| PKDOJPKJ_37 | 31667 | 32803 | tufA | 0.0 | elongation factor Tu | 86.81 | 95.69 | AHM69299 |
| PKDOJPKJ_52 | 4451 | 3582 | pdxS | 6.80e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| PKDOJPKJ_62 | 291154 | 291930 | CodY | 4.80e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PKDOJPKJ_20 | 284408 | 284016 | spxA1 | 9.43e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| PKDOJPKJ_71 | 67697 | 67500 | CspA | 1.22e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PKDOJPKJ_21 | 100280 | 100086 | CspD | 4.98e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| PKDOJPKJ_21 | 100280 | 100083 | CspB | 1.03e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| PKDOJPKJ_71 | 67697 | 67503 | CspR | 1.60e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| PKDOJPKJ_42 | 97375 | 96503 | lipA (SAUSA300_0829) | 1.33e-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 |
|---|---|---|---|
| PKDOJPKJ_1 | 1.0 | 0.0 | 1.0 |
| PKDOJPKJ_2 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_3 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_4 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_6 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_7 | 1.0 | 0.0 | 1.0 |
| PKDOJPKJ_20 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_21 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_22 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_23 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_24 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_25 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_26 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_27 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_28 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_29 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_30 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_31 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_32 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_33 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_34 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_35 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_36 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_37 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_38 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_39 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_40 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_41 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_42 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_43 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_44 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_45 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_46 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_47 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_48 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_49 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_50 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_51 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_52 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_53 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_54 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_56 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_57 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_59 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_60 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_62 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_63 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_67 | 1.0 | 0.0 | 1.0 |
| PKDOJPKJ_68 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_69 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_70 | 0.0 | 1.0 | 0.0 |
| PKDOJPKJ_71 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PKDOJPKJ_20 | 93313 | 96668 | False | Myoviridae | VOG4885, VOG5447, VOG4861 |
| PKDOJPKJ_69 | 112568 | 139585 | False | Siphoviridae | VOG1137, VOG6242, VOG0198, VOG0275, VOG7884, VOG4556, VOG0531, VOG0713, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG7896, VOG0641, VOG4707 |
Phigaro v2.4.0 (Database: Jan. 2024 release)