Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 3 | 2 | 7 | 7.87 |
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. |
|---|---|---|---|---|---|---|---|---|
| LPNANANF_14 | 52740 | 53789 | clbA | ARO:3002814 | clbA | 96.85 | 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. |
|---|---|---|---|---|---|---|---|
| LPNANANF_14 | 52754 | 53789 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 87.74 | 98.67 | KR610408 |
| LPNANANF_7 | 195188 | 196558 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 86.38 | 99.35 | 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. |
|---|---|---|---|---|---|---|---|---|
| LPNANANF_14 | 52743 | 53789 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 96.85 | 100.00 | WP_012116915.1 |
| LPNANANF_7 | 196770 | 197288 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LPNANANF_12 | 505609 | 506790 | capB | 0.0 | Capsule | Immune modulation | 82.21 | 99.66 | NP_391471 |
| LPNANANF_12 | 506805 | 507254 | capC | 1.72e-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 |
|---|---|---|---|---|---|---|---|---|
| LPNANANF_15 | 28320 | 27184 | tufA | 0.0 | elongation factor Tu | 86.81 | 95.69 | AHM69299 |
| LPNANANF_6 | 4585 | 5454 | pdxS | 1.39e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| LPNANANF_5 | 740047 | 740823 | CodY | 1.27e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LPNANANF_5 | 253563 | 253955 | spxA1 | 2.32e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| LPNANANF_14 | 71375 | 71178 | CspA | 1.32e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LPNANANF_8 | 145147 | 145341 | CspD | 2.08e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| LPNANANF_14 | 71375 | 71181 | CspR | 1.73e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| LPNANANF_12 | 860105 | 860977 | lipA (SAUSA300_0829) | 3.21e-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 |
|---|---|---|---|
| LPNANANF_2 | 0.0 | 1.0 | 0.0 |
| LPNANANF_3 | 0.0 | 1.0 | 0.0 |
| LPNANANF_4 | 0.0 | 1.0 | 0.0 |
| LPNANANF_5 | 0.0 | 1.0 | 0.0 |
| LPNANANF_6 | 0.0 | 1.0 | 0.0 |
| LPNANANF_7 | 0.0 | 1.0 | 0.0 |
| LPNANANF_8 | 0.0 | 1.0 | 0.0 |
| LPNANANF_10 | 0.0 | 1.0 | 0.0 |
| LPNANANF_11 | 0.0 | 1.0 | 0.0 |
| LPNANANF_12 | 0.0 | 1.0 | 0.0 |
| LPNANANF_13 | 0.0 | 1.0 | 0.0 |
| LPNANANF_14 | 0.0 | 1.0 | 0.0 |
| LPNANANF_15 | 0.0 | 1.0 | 0.0 |
| LPNANANF_16 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LPNANANF_5 | 337092 | 363476 | 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 |
Phigaro v2.4.0 (Database: Jan. 2024 release)