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. |
|---|---|---|---|---|---|---|---|---|
| LLKLIMOP_23 | 159694 | 160740 | 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. |
|---|---|---|---|---|---|---|---|
| LLKLIMOP_23 | 159694 | 160737 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| LLKLIMOP_12 | 186808 | 188184 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 87.15 | 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. |
|---|---|---|---|---|---|---|---|---|
| LLKLIMOP_23 | 159694 | 160737 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| LLKLIMOP_12 | 186808 | 188178 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| LLKLIMOP_23 | 157425 | 157943 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| LLKLIMOP_13 | 206783 | 209380 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LLKLIMOP_14 | 377325 | 378506 | capB | 0.0 | Capsule | Immune modulation | 81.87 | 99.66 | NP_391471 |
| LLKLIMOP_14 | 378521 | 378970 | capC | 3.25e-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 |
|---|---|---|---|---|---|---|---|---|
| LLKLIMOP_17 | 27563 | 26427 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| LLKLIMOP_20 | 4288 | 5157 | pdxS | 6.34e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| LLKLIMOP_15 | 335655 | 336431 | CodY | 3.61e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LLKLIMOP_27 | 298767 | 299159 | spxA1 | 4.44e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| LLKLIMOP_23 | 143198 | 143395 | CspA | 3.19e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| LLKLIMOP_12 | 611735 | 611541 | CspD | 1.84e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| LLKLIMOP_12 | 611735 | 611538 | CspB | 3.82e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| LLKLIMOP_23 | 143198 | 143392 | CspR | 1.58e-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 |
|---|---|---|---|
| LLKLIMOP_1 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_2 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_3 | 1.0 | 0.0 | 1.0 |
| LLKLIMOP_4 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_5 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_6 | 1.0 | 0.0 | 1.0 |
| LLKLIMOP_8 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_9 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_10 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_12 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_13 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_14 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_15 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_17 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_19 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_20 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_21 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_22 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_23 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_24 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_26 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_27 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_28 | 0.0 | 1.0 | 0.0 |
| LLKLIMOP_29 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LLKLIMOP_1 | 3941 | 15278 | False | Siphoviridae | VOG0650, VOG4552, VOG4600, VOG1309, VOG9093, VOG0189, VOG0044, VOG0536, VOG1336, VOG4658, VOG8569, VOG0397, VOG6581 |
| LLKLIMOP_1 | 17650 | 41385 | False | Siphoviridae | VOG5447, VOG4972, VOG4681, VOG0796, VOG10227, VOG0720, VOG4564, VOG6778, VOG4555, VOG1329, VOG2621, VOG5872, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG4545, VOG4605, VOG4599, VOG3390, VOG5535 |
| LLKLIMOP_12 | 228744 | 234263 | False | Siphoviridae | VOG4603, VOG4600, VOG1309, VOG11060, VOG0189 |
| LLKLIMOP_12 | 238062 | 265981 | False | Myoviridae | VOG10057, VOG0796, VOG10227, VOG4773, VOG4688, VOG6480, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG0979, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| LLKLIMOP_15 | 3873 | 11895 | False | Myoviridae | VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| LLKLIMOP_15 | 403692 | 428018 | False | Siphoviridae | VOG0054, VOG8537, VOG10230, VOG4660, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG1637, VOG0275, VOG7930, VOG8610, VOG5008, VOG3390, VOG7718 |
| LLKLIMOP_21 | 4947 | 15947 | False | Siphoviridae | VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG9667, VOG4602 |
| LLKLIMOP_27 | 6323 | 38234 | False | Siphoviridae | VOG4566, VOG0189, VOG6931, VOG6587, VOG1336, VOG5407, VOG4658, VOG4658, VOG8569, VOG0397, VOG6581, VOG6517, VOG6242, VOG0198, VOG0275, VOG7884, VOG0531, VOG0519, VOG4544, VOG4556, VOG4556, VOG4573, VOG4553, VOG3435, VOG0204, VOG4589, VOG0704, VOG0539, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641 |
Phigaro v2.4.0 (Database: Jan. 2024 release)