Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 4 | 16.88 |
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. |
|---|---|---|---|---|---|---|---|---|
| LKPMIMII_1 | 2564248 | 2565102 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| LKPMIMII_1 | 2545511 | 2546713 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| LKPMIMII_1 | 2323222 | 2324391 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LKPMIMII_1 | 1341041 | 1341358 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LKPMIMII_1 | 1340703 | 1341041 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LKPMIMII_1 | 878999 | 881569 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| LKPMIMII_1 | 580711 | 582354 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| LKPMIMII_1 | 338741 | 339334 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| LKPMIMII_1 | 288221 | 289654 | lmrB | ARO:3002813 | lmrB | 100.00 | 100.00 | JYFL01000006.1 |
| LKPMIMII_1 | 275408 | 276328 | mphK | ARO:3004541 | mphK | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| LKPMIMII_1 | 275408 | 276328 | mph(K) | Spiramycin, Telithromycin | 99.89 | 100.00 | NC_000964 |
| LKPMIMII_1 | 4053518 | 4054894 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.06 | 100.00 | D12567 |
| LKPMIMII_1 | 2564250 | 2565102 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| LKPMIMII_1 | 275408 | 276325 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| LKPMIMII_1 | 4053521 | 4054894 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| LKPMIMII_1 | 580714 | 582354 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| LKPMIMII_1 | 2564251 | 2565102 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| LKPMIMII_1 | 4050966 | 4051484 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| LKPMIMII_1 | 2014321 | 2016915 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LKPMIMII_1 | 3167152 | 3168090 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| LKPMIMII_1 | 3573044 | 3574225 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| LKPMIMII_1 | 3170988 | 3171773 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| LKPMIMII_1 | 3571419 | 3572561 | capA | 0.0 | Capsule | Immune modulation | 99.47 | 100.00 | NP_391469 |
| LKPMIMII_1 | 2123859 | 2124500 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| LKPMIMII_1 | 3572580 | 3573029 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| LKPMIMII_1 | 1968897 | 1970660 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| LKPMIMII_1 | 3169766 | 3170962 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| LKPMIMII_1 | 3159996 | 3167132 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391076 |
| LKPMIMII_1 | 3168118 | 3169737 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.89 | 100.00 | NP_391078 |
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 |
|---|---|---|---|---|---|---|---|---|
| LKPMIMII_1 | 132476 | 133612 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LKPMIMII_1 | 18665 | 19534 | pdxS | 3.03e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LKPMIMII_1 | 1654384 | 1655160 | CodY | 3.31e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LKPMIMII_1 | 3426840 | 3427409 | ClpP | 2.46e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| LKPMIMII_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LKPMIMII_1 | 1284756 | 1310864 | 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 |
| LKPMIMII_1 | 2495926 | 2525821 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309, VOG4600 |
| LKPMIMII_1 | 2743960 | 2768049 | False | Myoviridae | VOG6116, VOG6613, VOG4574, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720 |
Phigaro v2.4.0 (Database: Jan. 2024 release)