Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 1 | 2 | 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. |
|---|---|---|---|---|---|---|---|---|
| PPOOMCEP_47 | 103004 | 104053 | clbA | ARO:3002814 | clbA | 99.71 | 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. |
|---|---|---|---|---|---|---|---|
| PPOOMCEP_47 | 103004 | 104039 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.80 | 98.67 | KR610408 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PPOOMCEP_47 | 103004 | 104050 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 99.71 | 100.00 | WP_012116915.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PPOOMCEP_45 | 255574 | 256755 | capB | 0.0 | Capsule | Immune modulation | 81.87 | 99.66 | NP_391471 |
| PPOOMCEP_45 | 256770 | 257219 | capC | 2.00e-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 |
|---|---|---|---|---|---|---|---|---|
| PPOOMCEP_15 | 27952 | 26816 | tufA | 0.0 | elongation factor Tu | 86.81 | 95.69 | AHM69299 |
| PPOOMCEP_20 | 12392 | 11523 | pdxS | 1.34e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| PPOOMCEP_49 | 199022 | 198246 | CodY | 2.99e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PPOOMCEP_23 | 260780 | 261172 | spxA1 | 9.21e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| PPOOMCEP_47 | 89437 | 89634 | CspA | 8.93e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PPOOMCEP_11 | 103908 | 103714 | CspD | 3.25e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| PPOOMCEP_11 | 103908 | 103711 | CspB | 6.74e-28 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| PPOOMCEP_47 | 89437 | 89631 | CspR | 1.17e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| PPOOMCEP_18 | 1370 | 2242 | lipA (SAUSA300_0829) | 4.49e-163 | 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 |
|---|---|---|---|
| PPOOMCEP_1 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_2 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_3 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_6 | 1.0 | 0.0 | 1.0 |
| PPOOMCEP_7 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_8 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_9 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_10 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_11 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_12 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_14 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_15 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_16 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_17 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_18 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_19 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_20 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_21 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_23 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_24 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_25 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_26 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_29 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_30 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_31 | 1.0 | 0.0 | 1.0 |
| PPOOMCEP_32 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_33 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_34 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_35 | 1.0 | 0.0 | 1.0 |
| PPOOMCEP_36 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_37 | 1.0 | 0.0 | 1.0 |
| PPOOMCEP_42 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_45 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_46 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_47 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_48 | 0.0 | 1.0 | 0.0 |
| PPOOMCEP_49 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PPOOMCEP_11 | 47175 | 52917 | False | Unknown | VOG9667, VOG9667, VOG0650, VOG4552, VOG1878, VOG8233, VOG0186 |
| PPOOMCEP_11 | 56118 | 85531 | False | Siphoviridae | VOG9667, VOG5447, VOG2703, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG7896, VOG0641, VOG10230 |
| PPOOMCEP_23 | 350214 | 376515 | False | Myoviridae | VOG9667, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG3390, VOG4705, VOG0753 |
| PPOOMCEP_34 | 204712 | 220897 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589 |
| PPOOMCEP_46 | 88555 | 93888 | False | Siphoviridae | VOG0025, VOG4551, VOG4692 |
Phigaro v2.4.0 (Database: Jan. 2024 release)