Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 3 | 1 | 7 | 7.68 |
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. |
|---|---|---|---|---|---|---|---|---|
| IPENCJMP_14 | 167480 | 168529 | clbA | ARO:3002814 | clbA | 97.42 | 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. |
|---|---|---|---|---|---|---|---|
| IPENCJMP_14 | 167480 | 168515 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 87.74 | 98.67 | KR610408 |
| IPENCJMP_1 | 194356 | 195732 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 86.64 | 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. |
|---|---|---|---|---|---|---|---|---|
| IPENCJMP_14 | 167480 | 168523 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 97.70 | 99.71 | WP_012116915.1 |
| IPENCJMP_1 | 194362 | 195732 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| IPENCJMP_1 | 195945 | 196463 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| IPENCJMP_10 | 493847 | 495028 | capB | 0.0 | Capsule | Immune modulation | 82.29 | 99.66 | NP_391471 |
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 |
|---|---|---|---|---|---|---|---|---|
| IPENCJMP_7 | 31684 | 32820 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| IPENCJMP_11 | 4475 | 5344 | pdxS | 8.95e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| IPENCJMP_13 | 749227 | 750003 | CodY | 1.29e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| IPENCJMP_13 | 250190 | 250582 | spxA1 | 2.35e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| IPENCJMP_14 | 149108 | 149305 | CspA | 1.27e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| IPENCJMP_3 | 325990 | 325796 | CspD | 1.21e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| IPENCJMP_3 | 325990 | 325793 | CspB | 2.51e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| IPENCJMP_14 | 149108 | 149302 | CspR | 1.66e-26 | cold shock protein | 80.00 | 98.48 | AAO82613 |
| IPENCJMP_10 | 137839 | 136967 | lipA (SAUSA300_0829) | 3.16e-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 |
|---|---|---|---|
| IPENCJMP_1 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_2 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_3 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_4 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_5 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_7 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_9 | 1.0 | 0.0 | 1.0 |
| IPENCJMP_10 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_11 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_12 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_13 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_14 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_15 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_16 | 0.0 | 1.0 | 0.0 |
| IPENCJMP_17 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| IPENCJMP_3 | 189174 | 211329 | False | Siphoviridae | VOG10230, VOG4660, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG0275, VOG7930, VOG8610, VOG3390, VOG7718 |
| IPENCJMP_12 | 249328 | 274058 | False | Siphoviridae | VOG3490, VOG10230, VOG0641, VOG5535, VOG4599, VOG4605, VOG4545, VOG0725, VOG2621, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG0815, VOG1125, VOG4553, VOG4555, VOG4564, VOG0720, VOG10439, VOG0796 |
| IPENCJMP_12 | 282979 | 292358 | False | Siphoviridae | VOG8233, VOG4552, VOG0650, VOG4322, VOG0806, VOG4603, VOG9667, VOG3304, VOG4602, VOG0275 |
| IPENCJMP_13 | 351295 | 376664 | False | Myoviridae | VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)