Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 3 | 2 | 8 | 8.77 |
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. |
|---|---|---|---|---|---|---|---|---|
| PAILFIKI_24 | 52376 | 53425 | clbA | ARO:3002814 | clbA | 99.43 | 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. |
|---|---|---|---|---|---|---|---|
| PAILFIKI_24 | 52390 | 53425 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.61 | 98.67 | KR610408 |
| PAILFIKI_33 | 206479 | 207855 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 86.87 | 99.93 | 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. |
|---|---|---|---|---|---|---|---|---|
| PAILFIKI_24 | 52379 | 53425 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 99.43 | 100.00 | WP_012116915.1 |
| PAILFIKI_33 | 206485 | 207855 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 87.31 | 99.78 | WP_003242953.1 |
| PAILFIKI_33 | 208068 | 208586 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 80.35 | 100.00 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PAILFIKI_15 | 515026 | 516207 | capB | 0.0 | Capsule | Immune modulation | 82.21 | 99.66 | NP_391471 |
| PAILFIKI_15 | 514562 | 515011 | capC | 3.75e-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 |
|---|---|---|---|---|---|---|---|---|
| PAILFIKI_12 | 27951 | 26815 | tufA | 0.0 | elongation factor Tu | 86.81 | 95.69 | AHM69299 |
| PAILFIKI_13 | 4316 | 5185 | pdxS | 1.36e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| PAILFIKI_32 | 338592 | 337816 | CodY | 7.36e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PAILFIKI_31 | 168090 | 167698 | spxA1 | 9.07e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| PAILFIKI_24 | 73226 | 73029 | CspA | 1.30e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PAILFIKI_25 | 191230 | 191036 | CspD | 1.29e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PAILFIKI_31 | 383497 | 383691 | CspB | 8.64e-27 | cold shock protein | 84.61 | 98.48 | CAD00094 |
| PAILFIKI_24 | 73226 | 73032 | CspR | 1.71e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| PAILFIKI_15 | 138006 | 137134 | lipA (SAUSA300_0829) | 3.25e-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 |
|---|---|---|---|
| PAILFIKI_4 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_5 | 1.0 | 0.0 | 1.0 |
| PAILFIKI_6 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_7 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_8 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_9 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_10 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_11 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_12 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_13 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_15 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_16 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_17 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_20 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_24 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_25 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_26 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_27 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_28 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_29 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_31 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_32 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_33 | 0.0 | 1.0 | 0.0 |
| PAILFIKI_34 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PAILFIKI_31 | 41830 | 67925 | False | Myoviridae | VOG7895, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189 |
Phigaro v2.4.0 (Database: Jan. 2024 release)