Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 9 | 17.38 |
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. |
|---|---|---|---|---|---|---|---|---|
| PLMPKKEI_46 | 172676 | 173530 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| PLMPKKEI_4 | 115717 | 118287 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| PLMPKKEI_13 | 109536 | 109853 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PLMPKKEI_13 | 109198 | 109536 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PLMPKKEI_49 | 93179 | 93772 | tmrB | ARO:3003059 | tmrB | 96.95 | 100.00 | AL009126.3 |
| PLMPKKEI_5 | 71394 | 73040 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| PLMPKKEI_49 | 42856 | 44295 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| PLMPKKEI_49 | 30044 | 30964 | mphK | ARO:3004541 | mphK | 97.39 | 100.00 | CP010314.1 |
| PLMPKKEI_1 | 26935 | 28104 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
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. |
|---|---|---|---|---|---|---|---|
| PLMPKKEI_46 | 172676 | 173530 | aadK | Streptomycin | 98.95 | 100.00 | M26879 |
| PLMPKKEI_49 | 30044 | 30964 | mph(K) | Spiramycin, Telithromycin | 98.26 | 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. |
|---|---|---|---|---|---|---|---|---|
| PLMPKKEI_46 | 172676 | 173527 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| PLMPKKEI_5 | 71397 | 73040 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| PLMPKKEI_49 | 30044 | 30961 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.39 | 100.00 | WP_003246254.1 |
| PLMPKKEI_47 | 34404 | 34922 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 92.49 | 100.00 | WP_003242546.1 |
| PLMPKKEI_1 | 325834 | 328431 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.17 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PLMPKKEI_3 | 3436 | 4617 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PLMPKKEI_2 | 62136 | 63074 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391077 |
| PLMPKKEI_1 | 227065 | 227705 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 99.84 | NP_390062 |
| PLMPKKEI_2 | 54980 | 62116 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.50 | 100.00 | NP_391076 |
| PLMPKKEI_2 | 65972 | 66757 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PLMPKKEI_3 | 2972 | 3421 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| PLMPKKEI_1 | 373892 | 375655 | dep/capD | 0.0 | Capsule | Immune modulation | 99.26 | 100.00 | NP_389723 |
| PLMPKKEI_3 | 1811 | 2953 | capA | 0.0 | Capsule | Immune modulation | 99.12 | 100.00 | NP_391469 |
| PLMPKKEI_2 | 64750 | 65946 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391079 |
| PLMPKKEI_2 | 63102 | 64721 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.33 | 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 |
|---|---|---|---|---|---|---|---|---|
| PLMPKKEI_12 | 31851 | 32987 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PLMPKKEI_28 | 4419 | 5288 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PLMPKKEI_24 | 115147 | 114371 | CodY | 2.15e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PLMPKKEI_2 | 331523 | 332092 | ClpP | 2.57e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PLMPKKEI_7 | 37697 | 37305 | spxA1 | 5.78e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PLMPKKEI_7 | 37697 | 37305 | spx | 3.45e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PLMPKKEI_14 | 20684 | 20926 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PLMPKKEI_5 | 28761 | 28958 | CspA | 4.41e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PLMPKKEI_1 | 215102 | 214908 | CspD | 3.03e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PLMPKKEI_9 | 43896 | 44090 | CspB | 6.99e-28 | 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 |
|---|---|---|---|
| PLMPKKEI_1 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_2 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_3 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_4 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_5 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_6 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_7 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_8 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_9 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_10 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_11 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_12 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_13 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_14 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_15 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_16 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_17 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_18 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_19 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_20 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_21 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_22 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_23 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_24 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_25 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_26 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_27 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_28 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_29 | 1.0 | 0.0 | 1.0 |
| PLMPKKEI_30 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_31 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_32 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_33 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_34 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_35 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_36 | 1.0 | 0.0 | 1.0 |
| PLMPKKEI_37 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_38 | 1.0 | 0.0 | 1.0 |
| PLMPKKEI_39 | 1.0 | 0.0 | 1.0 |
| PLMPKKEI_40 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_41 | 1.0 | 0.0 | 1.0 |
| PLMPKKEI_42 | 1.0 | 0.0 | 1.0 |
| PLMPKKEI_43 | 1.0 | 0.0 | 1.0 |
| PLMPKKEI_44 | 1.0 | 0.0 | 1.0 |
| PLMPKKEI_45 | 1.0 | 0.0 | 1.0 |
| PLMPKKEI_46 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_47 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_48 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_49 | 0.0 | 1.0 | 0.0 |
| PLMPKKEI_50 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PLMPKKEI_13 | 55072 | 79941 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705, VOG0753 |
| PLMPKKEI_48 | 123783 | 144917 | False | Siphoviridae | VOG0058, VOG4548, VOG3866, VOG3801, VOG0536, VOG0044, VOG0189, VOG4566, VOG1309, VOG4600, VOG4603, VOG4552, VOG0650, VOG11075, VOG9667, VOG9607, VOG4602 |
Phigaro v2.4.0 (Database: Jan. 2024 release)