Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 2 | 6 | 6.63 |
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. |
|---|---|---|---|---|---|---|---|---|
| JOKINOCI_23 | 45744 | 46793 | clbA | ARO:3002814 | clbA | 92.55 | 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. |
|---|---|---|---|---|---|---|---|
| JOKINOCI_23 | 45744 | 46793 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 89.05 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| JOKINOCI_23 | 45747 | 46793 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.55 | 100.00 | WP_012116915.1 |
| JOKINOCI_12 | 679345 | 681942 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 100.00 | WP_087347987.1 |
| JOKINOCI_23 | 49260 | 49589 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 84.55 | 63.58 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| JOKINOCI_1 | 477005 | 478186 | capB | 0.0 | Capsule | Immune modulation | 81.96 | 99.66 | NP_391471 |
| JOKINOCI_1 | 478201 | 478650 | capC | 3.59e-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 |
|---|---|---|---|---|---|---|---|---|
| JOKINOCI_24 | 27657 | 26521 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| JOKINOCI_10 | 4249 | 5118 | pdxS | 2.45e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| JOKINOCI_12 | 334262 | 335038 | CodY | 1.36e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| JOKINOCI_19 | 256935 | 257327 | spxA1 | 3.99e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| JOKINOCI_13 | 10653 | 10850 | CspA | 7.91e-33 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| JOKINOCI_19 | 39057 | 38863 | CspB | 3.79e-28 | cold shock protein | 84.61 | 98.48 | CAD00094 |
| JOKINOCI_13 | 10653 | 10847 | CspR | 1.04e-27 | 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. |
|---|---|---|---|---|---|---|
| JOKINOCI_21 | 4712 | 4879 | Col(SD853) | 168 / 194 | 86.90 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| JOKINOCI_1 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_2 | 1.0 | 0.0 | 1.0 |
| JOKINOCI_3 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_4 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_5 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_7 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_8 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_9 | 1.0 | 0.0 | 1.0 |
| JOKINOCI_10 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_11 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_12 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_13 | 1.0 | 0.0 | 1.0 |
| JOKINOCI_14 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_15 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_19 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_20 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_21 | 1.0 | 0.0 | 1.0 |
| JOKINOCI_22 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_23 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_24 | 0.0 | 1.0 | 0.0 |
| JOKINOCI_26 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JOKINOCI_3 | 4846 | 14365 | False | Siphoviridae | VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189 |
| JOKINOCI_4 | 7901 | 11451 | False | Unknown | VOG0753, VOG0136, VOG10230, VOG9953 |
| JOKINOCI_12 | 3739 | 11792 | False | Myoviridae | VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG3390, VOG4705 |
| JOKINOCI_12 | 542320 | 574015 | False | Siphoviridae | VOG0054, VOG4574, VOG4660, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG7893, VOG0275, VOG7930, VOG8610, VOG3390, VOG7718, VOG5534, VOG6940, VOG9713, VOG9219, VOG6472, VOG6036, VOG6941, VOG6246, VOG6524, VOG6031 |
| JOKINOCI_12 | 628999 | 636890 | False | Unknown | VOG6464, VOG0322, VOG7627, VOG0025, VOG4551 |
| JOKINOCI_19 | 294580 | 297961 | False | Unknown | VOG3304, VOG9667, VOG9667, VOG8241, VOG4552 |
| JOKINOCI_19 | 298734 | 300596 | False | Unknown | VOG8233, VOG0186 |
Phigaro v2.4.0 (Database: Jan. 2024 release)