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. |
|---|---|---|---|---|---|---|---|---|
| PJDNGGHJ_4 | 48063 | 49109 | 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. |
|---|---|---|---|---|---|---|---|
| PJDNGGHJ_4 | 48066 | 49109 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| PJDNGGHJ_1 | 361761 | 363137 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 87.36 | 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. |
|---|---|---|---|---|---|---|---|---|
| PJDNGGHJ_4 | 48066 | 49109 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| PJDNGGHJ_1 | 361761 | 363131 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 87.09 | 99.78 | WP_003242953.1 |
| PJDNGGHJ_4 | 50860 | 51378 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| PJDNGGHJ_5 | 488126 | 490723 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PJDNGGHJ_2 | 484303 | 485484 | capB | 0.0 | Capsule | Immune modulation | 82.04 | 99.66 | NP_391471 |
| PJDNGGHJ_2 | 485499 | 485948 | capC | 3.93e-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 |
|---|---|---|---|---|---|---|---|---|
| PJDNGGHJ_12 | 27754 | 26618 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| PJDNGGHJ_13 | 4615 | 5484 | pdxS | 6.50e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| PJDNGGHJ_5 | 287014 | 287790 | CodY | 6.92e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PJDNGGHJ_3 | 204996 | 204604 | spxA1 | 5.11e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| PJDNGGHJ_4 | 65596 | 65399 | CspA | 3.29e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| PJDNGGHJ_6 | 39852 | 39658 | CspB | 1.52e-27 | cold shock protein | 84.61 | 98.48 | CAD00094 |
| PJDNGGHJ_4 | 65596 | 65402 | CspR | 1.63e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
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 |
|---|---|---|---|
| PJDNGGHJ_1 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_2 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_3 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_4 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_5 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_6 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_7 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_8 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_9 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_10 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_11 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_12 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_13 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_15 | 0.0 | 1.0 | 0.0 |
| PJDNGGHJ_17 | 1.0 | 0.0 | 1.0 |
| PJDNGGHJ_18 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PJDNGGHJ_2 | 874321 | 895129 | False | Siphoviridae | VOG0275, VOG5023, VOG3699, VOG2613, VOG0692, VOG9317, VOG4319, VOG0724, VOG11074, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705 |
| PJDNGGHJ_2 | 1013903 | 1036609 | 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 |
| PJDNGGHJ_3 | 38003 | 63390 | False | Myoviridae | VOG7895, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189 |
| PJDNGGHJ_3 | 127352 | 151395 | False | Myoviridae | VOG10230, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG1643, VOG4572, VOG4555, VOG0720, VOG0796 |
| PJDNGGHJ_3 | 159750 | 163041 | False | Unknown | VOG0189, VOG4566, VOG0186 |
| PJDNGGHJ_3 | 163329 | 167268 | False | Unknown | VOG8241, VOG9667, VOG9667, VOG9576 |
| PJDNGGHJ_7 | 18653 | 35506 | False | Unknown | VOG5042, VOG3389, VOG4910, VOG9312, VOG2090, VOG2091, VOG0275, VOG7930, VOG8610 |
| PJDNGGHJ_7 | 98832 | 109769 | False | Unknown | VOG0048, VOG0156, VOG6464, VOG0322, VOG7627, VOG0025, VOG4551 |
Phigaro v2.4.0 (Database: Jan. 2024 release)