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. |
|---|---|---|---|---|---|---|---|---|
| LOLAAMAE_16 | 692065 | 693234 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LOLAAMAE_38 | 558579 | 558917 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LOLAAMAE_38 | 558262 | 558579 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LOLAAMAE_16 | 464254 | 465456 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| LOLAAMAE_16 | 445433 | 446287 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| LOLAAMAE_49 | 402513 | 404159 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| LOLAAMAE_82 | 255757 | 258327 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| LOLAAMAE_49 | 161474 | 162067 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| LOLAAMAE_49 | 110913 | 112352 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| LOLAAMAE_49 | 98100 | 99020 | mphK | ARO:3004541 | mphK | 98.37 | 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. |
|---|---|---|---|---|---|---|---|
| LOLAAMAE_71 | 34559 | 35935 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 100.00 | 100.00 | X08034 |
| LOLAAMAE_16 | 445433 | 446285 | aadK | Streptomycin | 98.12 | 99.77 | M26879 |
| LOLAAMAE_49 | 98100 | 99020 | mph(K) | Spiramycin, Telithromycin | 97.94 | 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. |
|---|---|---|---|---|---|---|---|---|
| LOLAAMAE_71 | 34559 | 35932 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| LOLAAMAE_49 | 402516 | 404159 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| LOLAAMAE_49 | 98100 | 99017 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| LOLAAMAE_16 | 445433 | 446284 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| LOLAAMAE_71 | 37888 | 38406 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| LOLAAMAE_16 | 1157601 | 1160198 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LOLAAMAE_16 | 891762 | 892403 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| LOLAAMAE_27 | 161679 | 162860 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| LOLAAMAE_27 | 163343 | 164485 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| LOLAAMAE_27 | 580009 | 580947 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| LOLAAMAE_27 | 162875 | 163324 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| LOLAAMAE_27 | 576326 | 577111 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| LOLAAMAE_27 | 577137 | 578333 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| LOLAAMAE_16 | 1208515 | 1210278 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| LOLAAMAE_27 | 580967 | 588103 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.05 | 100.00 | NP_391076 |
| LOLAAMAE_27 | 578362 | 579981 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 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 |
|---|---|---|---|---|---|---|---|---|
| LOLAAMAE_93 | 31693 | 32829 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LOLAAMAE_6 | 11224 | 10355 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LOLAAMAE_38 | 248430 | 247654 | CodY | 4.87e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LOLAAMAE_27 | 324203 | 323634 | ClpP | 1.40e-98 | part of proteolytic complex | 80.53 | 97.44 | BAB94595 |
| LOLAAMAE_60 | 110246 | 109854 | spxA1 | 9.28e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| LOLAAMAE_104 | 20555 | 20797 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LOLAAMAE_49 | 355759 | 355956 | CspA | 1.87e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LOLAAMAE_60 | 353439 | 353633 | CspB | 3.55e-27 | cold shock protein | 83.08 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| LOLAAMAE_6 | 0.0 | 1.0 | 0.0 |
| LOLAAMAE_16 | 0.0 | 1.0 | 0.0 |
| LOLAAMAE_27 | 0.0 | 1.0 | 0.0 |
| LOLAAMAE_38 | 0.0 | 1.0 | 0.0 |
| LOLAAMAE_49 | 0.0 | 1.0 | 0.0 |
| LOLAAMAE_60 | 0.0 | 1.0 | 0.0 |
| LOLAAMAE_71 | 0.0 | 1.0 | 0.0 |
| LOLAAMAE_82 | 0.0 | 1.0 | 0.0 |
| LOLAAMAE_93 | 0.0 | 1.0 | 0.0 |
| LOLAAMAE_104 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LOLAAMAE_16 | 492672 | 514728 | False | Myoviridae | VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862 |
| LOLAAMAE_16 | 925681 | 944742 | False | Unknown | VOG8537, VOG10230, VOG7900, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312 |
| LOLAAMAE_16 | 1109503 | 1132232 | False | Siphoviridae | VOG9029, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4626, VOG4612, VOG3390, VOG4705, VOG5221, VOG0136 |
| LOLAAMAE_38 | 16957 | 46020 | False | Siphoviridae | VOG3490, VOG6495, VOG4666, VOG0136, VOG5221, VOG4705, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581, VOG4841, VOG0713, VOG11015, VOG0198 |
| LOLAAMAE_38 | 588405 | 596878 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885 |
| LOLAAMAE_60 | 5495 | 15415 | False | Siphoviridae | VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)