Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| AMOKLEEE_2 | 678155 | 679324 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| AMOKLEEE_2 | 455810 | 457012 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| AMOKLEEE_2 | 437267 | 438121 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| AMOKLEEE_4 | 427818 | 429461 | vmlR | ARO:3004476 | vmlR | 100.00 | 100.00 | NC_000964.3 |
| AMOKLEEE_3 | 427479 | 427796 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| AMOKLEEE_3 | 427141 | 427479 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| AMOKLEEE_4 | 162876 | 163469 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| AMOKLEEE_4 | 112349 | 113788 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| AMOKLEEE_4 | 99534 | 100454 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| AMOKLEEE_5 | 27199 | 29769 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| AMOKLEEE_2 | 437267 | 438121 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| AMOKLEEE_1 | 34479 | 35855 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| AMOKLEEE_4 | 99534 | 100454 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| AMOKLEEE_2 | 437267 | 438118 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| AMOKLEEE_1 | 34479 | 35852 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| AMOKLEEE_4 | 427821 | 429461 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| AMOKLEEE_4 | 99534 | 100451 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| AMOKLEEE_1 | 37796 | 38314 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| AMOKLEEE_2 | 985659 | 988253 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| AMOKLEEE_1 | 522065 | 523246 | capB | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391471 |
| AMOKLEEE_1 | 523261 | 523710 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| AMOKLEEE_2 | 1033147 | 1034910 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| AMOKLEEE_1 | 930419 | 931204 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| AMOKLEEE_2 | 878063 | 878704 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| AMOKLEEE_1 | 523729 | 524871 | capA | 0.0 | Capsule | Immune modulation | 99.91 | 100.00 | NP_391469 |
| AMOKLEEE_1 | 934102 | 935040 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| AMOKLEEE_1 | 931230 | 932426 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.67 | 100.00 | NP_391079 |
| AMOKLEEE_1 | 935060 | 942196 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.58 | 100.00 | NP_391076 |
| AMOKLEEE_1 | 932455 | 934074 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 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 |
|---|---|---|---|---|---|---|---|---|
| AMOKLEEE_6 | 27978 | 26842 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| AMOKLEEE_8 | 4229 | 5098 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| AMOKLEEE_3 | 740777 | 741553 | CodY | 8.35e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| AMOKLEEE_1 | 676482 | 675913 | ClpP | 6.28e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| AMOKLEEE_3 | 276381 | 276773 | spxA1 | 6.56e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| AMOKLEEE_3 | 276381 | 276773 | spx | 3.91e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| AMOKLEEE_7 | 34584 | 34342 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| AMOKLEEE_4 | 381937 | 382134 | CspA | 1.98e-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 |
|---|---|---|---|
| AMOKLEEE_1 | 0.0 | 1.0 | 0.0 |
| AMOKLEEE_2 | 0.0 | 1.0 | 0.0 |
| AMOKLEEE_3 | 0.0 | 1.0 | 0.0 |
| AMOKLEEE_4 | 0.0 | 1.0 | 0.0 |
| AMOKLEEE_5 | 0.0 | 1.0 | 0.0 |
| AMOKLEEE_6 | 0.0 | 1.0 | 0.0 |
| AMOKLEEE_7 | 0.0 | 1.0 | 0.0 |
| AMOKLEEE_8 | 0.0 | 1.0 | 0.0 |
| AMOKLEEE_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 |
|---|---|---|---|---|---|
| AMOKLEEE_2 | 476564 | 506941 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| AMOKLEEE_3 | 371232 | 397340 | 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)