Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 7 | 16.43 |
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. |
|---|---|---|---|---|---|---|---|---|
| LGKKCICM_1 | 634965 | 635819 | aadK | ARO:3002627 | aadK | 99.30 | 100.00 | AL009126.1 |
| LGKKCICM_1 | 605675 | 606877 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| LGKKCICM_3 | 427704 | 428021 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| LGKKCICM_3 | 427366 | 427704 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| LGKKCICM_4 | 409608 | 411245 | vmlR | ARO:3004476 | vmlR | 98.72 | 99.63 | NC_000964.3 |
| LGKKCICM_1 | 376604 | 377773 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| LGKKCICM_5 | 257561 | 260131 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| LGKKCICM_4 | 152233 | 152826 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| LGKKCICM_4 | 101708 | 103147 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.42 | JYFL01000006.1 |
| LGKKCICM_4 | 88896 | 89816 | mphK | ARO:3004541 | mphK | 97.06 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| LGKKCICM_1 | 634965 | 635819 | aadK | Streptomycin | 99.18 | 100.00 | M26879 |
| LGKKCICM_4 | 88896 | 89816 | mph(K) | Spiramycin, Telithromycin | 96.96 | 100.00 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| LGKKCICM_1 | 634968 | 635819 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 99.30 | 100.00 | WP_003229862.1 |
| LGKKCICM_4 | 409605 | 411245 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 98.54 | 99.82 | WP_003234144.1 |
| LGKKCICM_4 | 88896 | 89813 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.06 | 100.00 | WP_003246254.1 |
| LGKKCICM_1 | 70814 | 73411 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LGKKCICM_2 | 527641 | 528822 | capB | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_391471 |
| LGKKCICM_2 | 937261 | 938046 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| LGKKCICM_1 | 177200 | 177841 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| LGKKCICM_2 | 528837 | 529286 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| LGKKCICM_2 | 529305 | 530447 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| LGKKCICM_2 | 938072 | 939268 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| LGKKCICM_1 | 25031 | 26794 | dep/capD | 0.0 | Capsule | Immune modulation | 98.70 | 100.00 | NP_389723 |
| LGKKCICM_2 | 941902 | 949038 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.67 | 100.00 | NP_391076 |
| LGKKCICM_2 | 939297 | 940916 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.46 | 100.00 | NP_391078 |
| LGKKCICM_2 | 940944 | 941882 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.30 | 100.00 | NP_391077 |
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 |
|---|---|---|---|---|---|---|---|---|
| LGKKCICM_6 | 31718 | 32854 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| LGKKCICM_8 | 4306 | 5175 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LGKKCICM_3 | 739598 | 740374 | CodY | 8.33e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LGKKCICM_2 | 685514 | 684945 | ClpP | 6.32e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LGKKCICM_3 | 275347 | 275739 | spxA1 | 6.55e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LGKKCICM_3 | 275347 | 275739 | spx | 3.91e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LGKKCICM_7 | 20590 | 20832 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LGKKCICM_4 | 355774 | 355971 | CspA | 1.90e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| LGKKCICM_1 | 0.0 | 1.0 | 0.0 |
| LGKKCICM_2 | 0.0 | 1.0 | 0.0 |
| LGKKCICM_3 | 0.0 | 1.0 | 0.0 |
| LGKKCICM_4 | 0.0 | 1.0 | 0.0 |
| LGKKCICM_5 | 0.0 | 1.0 | 0.0 |
| LGKKCICM_6 | 0.0 | 1.0 | 0.0 |
| LGKKCICM_7 | 0.0 | 1.0 | 0.0 |
| LGKKCICM_8 | 0.0 | 1.0 | 0.0 |
| LGKKCICM_9 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LGKKCICM_1 | 556851 | 574293 | False | Myoviridae | VOG4862, VOG4691, VOG10989, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
| LGKKCICM_3 | 370008 | 397497 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)