Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| LEFFLKOP_7 | 521665 | 522867 | blt | ARO:3003006 | blt | 98.75 | 100.00 | L32599.1 |
| LEFFLKOP_7 | 502832 | 503686 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| LEFFLKOP_5 | 427209 | 427526 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LEFFLKOP_5 | 426871 | 427209 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LEFFLKOP_8 | 412905 | 414545 | vmlR | ARO:3004476 | vmlR | 98.35 | 99.82 | NC_000964.3 |
| LEFFLKOP_8 | 162710 | 163303 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| LEFFLKOP_6 | 156525 | 157694 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| LEFFLKOP_8 | 112153 | 113586 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| LEFFLKOP_8 | 99338 | 100258 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| LEFFLKOP_9 | 27346 | 29916 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
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. |
|---|---|---|---|---|---|---|---|
| LEFFLKOP_4 | 1002603 | 1003979 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.93 | 100.00 | X08034 |
| LEFFLKOP_8 | 99338 | 100258 | mph(K) | Spiramycin, Telithromycin | 99.13 | 100.00 | NC_000964 |
| LEFFLKOP_7 | 502832 | 503684 | aadK | Streptomycin | 98.12 | 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. |
|---|---|---|---|---|---|---|---|---|
| LEFFLKOP_4 | 1002606 | 1003979 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| LEFFLKOP_8 | 99338 | 100255 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| LEFFLKOP_8 | 412908 | 414545 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| LEFFLKOP_7 | 502832 | 503683 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| LEFFLKOP_4 | 1000132 | 1000650 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| LEFFLKOP_6 | 452819 | 455416 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.71 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LEFFLKOP_4 | 526690 | 527871 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LEFFLKOP_6 | 356174 | 356815 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| LEFFLKOP_4 | 101878 | 109014 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.47 | 100.00 | NP_391076 |
| LEFFLKOP_4 | 112870 | 113655 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LEFFLKOP_4 | 109034 | 109972 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| LEFFLKOP_4 | 111648 | 112844 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| LEFFLKOP_6 | 500619 | 502382 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| LEFFLKOP_4 | 110000 | 111619 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.07 | 100.00 | NP_391078 |
| LEFFLKOP_4 | 525065 | 526207 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| LEFFLKOP_4 | 526226 | 526675 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | 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 |
|---|---|---|---|---|---|---|---|---|
| LEFFLKOP_10 | 27977 | 26841 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LEFFLKOP_1 | 11169 | 10300 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LEFFLKOP_5 | 737021 | 737797 | CodY | 7.64e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LEFFLKOP_4 | 365864 | 366433 | ClpP | 6.24e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LEFFLKOP_5 | 275059 | 275451 | spxA1 | 6.00e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LEFFLKOP_5 | 275059 | 275451 | spx | 3.58e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LEFFLKOP_11 | 20553 | 20795 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LEFFLKOP_8 | 363349 | 363546 | CspA | 1.92e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LEFFLKOP_6 | 344249 | 344055 | CspD | 3.87e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| LEFFLKOP_1 | 0.0 | 1.0 | 0.0 |
| LEFFLKOP_4 | 0.0 | 1.0 | 0.0 |
| LEFFLKOP_5 | 0.0 | 1.0 | 0.0 |
| LEFFLKOP_6 | 0.0 | 1.0 | 0.0 |
| LEFFLKOP_7 | 0.0 | 1.0 | 0.0 |
| LEFFLKOP_8 | 0.0 | 1.0 | 0.0 |
| LEFFLKOP_9 | 0.0 | 1.0 | 0.0 |
| LEFFLKOP_10 | 0.0 | 1.0 | 0.0 |
| LEFFLKOP_11 | 0.0 | 1.0 | 0.0 |
| LEFFLKOP_12 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LEFFLKOP_5 | 369888 | 397387 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| LEFFLKOP_7 | 285845 | 309734 | False | Myoviridae | VOG0720, VOG4555, VOG4553, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG4574, VOG10500, VOG9203, VOG6116 |
| LEFFLKOP_12 | 9542 | 39391 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG0796, VOG4673, VOG4693, VOG0189, VOG11060, VOG1309 |
Phigaro v2.4.0 (Database: Jan. 2024 release)