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. |
|---|---|---|---|---|---|---|---|---|
| LCFPBBNC_1 | 289535 | 290581 | clbA | ARO:3002814 | clbA | 93.35 | 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. |
|---|---|---|---|---|---|---|---|
| LCFPBBNC_1 | 289535 | 290578 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 89.00 | 99.33 | KR610408 |
| LCFPBBNC_3 | 2135701 | 2137077 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 87.22 | 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. |
|---|---|---|---|---|---|---|---|---|
| LCFPBBNC_1 | 289535 | 290578 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.82 | 99.71 | WP_012116915.1 |
| LCFPBBNC_3 | 2135707 | 2137077 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 87.31 | 99.78 | WP_003242953.1 |
| LCFPBBNC_1 | 287266 | 287784 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 84.39 | 100.00 | WP_003242546.1 |
| LCFPBBNC_3 | 1497890 | 1500484 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.57 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LCFPBBNC_3 | 467470 | 468651 | capB | 0.0 | Capsule | Immune modulation | 82.21 | 99.66 | NP_391471 |
| LCFPBBNC_3 | 468666 | 469115 | capC | 9.62e-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 |
|---|---|---|---|---|---|---|---|---|
| LCFPBBNC_1 | 612318 | 613454 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| LCFPBBNC_3 | 2578663 | 2577794 | pdxS | 1.02e-150 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| LCFPBBNC_3 | 1291319 | 1292095 | CodY | 2.15e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LCFPBBNC_2 | 51212 | 51604 | spxA1 | 6.50e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| LCFPBBNC_1 | 272994 | 273191 | CspA | 1.17e-31 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| LCFPBBNC_2 | 328635 | 328441 | CspB | 1.02e-26 | cold shock protein | 84.61 | 98.48 | CAD00094 |
| LCFPBBNC_1 | 272994 | 273188 | CspR | 5.80e-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. |
|---|---|---|---|---|---|---|
| LCFPBBNC_5 | 564 | 750 | Col(SD853) | 187 / 194 | 85.56 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LCFPBBNC_1 | 0.0 | 1.0 | 0.0 |
| LCFPBBNC_2 | 0.0 | 1.0 | 0.0 |
| LCFPBBNC_3 | 0.0 | 1.0 | 0.0 |
| LCFPBBNC_4 | 0.0 | 1.0 | 0.0 |
| LCFPBBNC_5 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LCFPBBNC_1 | 355439 | 361782 | False | Siphoviridae | VOG0275, VOG4602, VOG8483, VOG9667, VOG9667, VOG0806, VOG4322, VOG0650, VOG4552 |
| LCFPBBNC_1 | 372931 | 402554 | False | Siphoviridae | VOG5447, VOG3631, VOG4972, VOG4681, VOG0796, VOG0720, VOG0720, VOG4564, VOG4564, VOG4555, VOG4553, VOG4553, VOG3649, VOG5660, VOG1886, VOG4556, VOG4573, VOG4553, VOG0204, VOG4589, VOG4586, VOG5852, VOG6163, VOG4754, VOG8263, VOG0801, VOG3462, VOG4619, VOG4856, VOG0804, VOG4705 |
| LCFPBBNC_1 | 648643 | 656568 | False | Unknown | VOG8241, VOG6495, VOG9894, VOG0083, VOG1309, VOG1292, VOG11060, VOG9600 |
| LCFPBBNC_1 | 663392 | 695703 | False | Myoviridae | VOG0198, VOG6242, VOG4618, VOG4567, VOG1328, VOG5249, VOG5532, VOG4544, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG10989, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| LCFPBBNC_2 | 92113 | 99514 | False | Unknown | VOG8598, VOG4551, VOG0025, VOG0189 |
| LCFPBBNC_2 | 175245 | 188044 | False | Myoviridae / Siphoviridae | VOG9091, VOG10230, VOG6413, VOG4608, VOG5986, VOG5164, VOG0052, VOG0535, VOG0094, VOG4724, VOG0020, VOG5090, VOG0052 |
| LCFPBBNC_2 | 210895 | 269420 | False | Siphoviridae | VOG3375, VOG0275, VOG4602, VOG3304, VOG11077, VOG8241, VOG4552, VOG4600, VOG1309, VOG4566, VOG0189, VOG4693, VOG1336, VOG5407, VOG4694, VOG5969, VOG0397, VOG0102, VOG0044, VOG9071, VOG4376, VOG1137, VOG5447, VOG3631, VOG4972, VOG4681, VOG0796, VOG0720, VOG4564, VOG4555, VOG4553, VOG1125, VOG3649, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG1323, VOG4545, VOG0727, VOG4599, VOG4599, VOG4598, VOG1125, VOG1886, VOG4556, VOG4573, VOG4553, VOG0204, VOG4589, VOG4586, VOG5852, VOG6163, VOG0801, VOG3462, VOG4619, VOG4856, VOG0804, VOG4705 |
| LCFPBBNC_3 | 717811 | 746192 | False | Siphoviridae | VOG0102, VOG0044, VOG4376, VOG5447, VOG0198, VOG0275, VOG0531, VOG0713, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG7896, VOG0641, VOG4707, VOG8483 |
| LCFPBBNC_3 | 864574 | 896207 | False | Siphoviridae | VOG4581, VOG1886, VOG4556, VOG4573, VOG4573, VOG4553, VOG4553, VOG0204, VOG4589, VOG0207, VOG4586, VOG5852, VOG5852, VOG9745, VOG6163, VOG0801, VOG4555, VOG4553, VOG0815, VOG0724, VOG0799, VOG0725, VOG1323, VOG9745, VOG4605, VOG4599, VOG5535, VOG0753 |
| LCFPBBNC_3 | 940133 | 966415 | False | Myoviridae | VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG10055, VOG3890, VOG3891, VOG3892, VOG4545, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)