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. |
|---|---|---|---|---|---|---|---|---|
| LMEFGPDI_61 | 138904 | 139497 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| LMEFGPDI_61 | 88346 | 89785 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.42 | JYFL01000006.1 |
| LMEFGPDI_61 | 68758 | 69678 | mphK | ARO:3004541 | mphK | 98.04 | 100.00 | CP010314.1 |
| LMEFGPDI_31 | 30719 | 33289 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| LMEFGPDI_26 | 29017 | 29871 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| LMEFGPDI_39 | 16898 | 18067 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| LMEFGPDI_26 | 11949 | 13151 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| LMEFGPDI_16 | 6454 | 6792 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| LMEFGPDI_16 | 6137 | 6454 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| LMEFGPDI_20 | 27568 | 28944 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| LMEFGPDI_26 | 29019 | 29871 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| LMEFGPDI_61 | 68758 | 69678 | mph(K) | Spiramycin, Telithromycin | 97.83 | 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. |
|---|---|---|---|---|---|---|---|---|
| LMEFGPDI_20 | 27571 | 28944 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| LMEFGPDI_61 | 68758 | 69675 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.04 | 100.00 | WP_003246254.1 |
| LMEFGPDI_29 | 34091 | 35731 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 97.62 | 100.00 | WP_003234144.1 |
| LMEFGPDI_26 | 29020 | 29871 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| LMEFGPDI_20 | 25097 | 25615 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| LMEFGPDI_43 | 2736 | 5333 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.83 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LMEFGPDI_34 | 32940 | 34121 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LMEFGPDI_8 | 11719 | 12504 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LMEFGPDI_8 | 15402 | 16340 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| LMEFGPDI_8 | 12530 | 13726 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| LMEFGPDI_8 | 16360 | 23496 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.08 | 100.00 | NP_391076 |
| LMEFGPDI_50 | 36395 | 37036 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| LMEFGPDI_34 | 34604 | 35746 | capA | 0.0 | Capsule | Immune modulation | 98.86 | 100.00 | NP_391469 |
| LMEFGPDI_13 | 53468 | 55231 | dep/capD | 0.0 | Capsule | Immune modulation | 98.81 | 100.00 | NP_389723 |
| LMEFGPDI_34 | 34136 | 34585 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| LMEFGPDI_8 | 13755 | 15374 | 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 |
|---|---|---|---|---|---|---|---|---|
| LMEFGPDI_21 | 27911 | 26775 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| LMEFGPDI_52 | 11114 | 10245 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LMEFGPDI_28 | 110958 | 110182 | CodY | 1.93e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LMEFGPDI_1 | 185422 | 185991 | ClpP | 2.04e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LMEFGPDI_10 | 46301 | 45909 | spxA1 | 6.24e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LMEFGPDI_10 | 46301 | 45909 | spx | 3.72e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LMEFGPDI_22 | 20482 | 20724 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LMEFGPDI_50 | 48266 | 48460 | CspD | 9.57e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| LMEFGPDI_19 | 17327 | 17133 | CspB | 5.95e-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. |
|---|---|---|---|---|---|---|
| LMEFGPDI_65 | 1 | 191 | Col(SD853) | 191 / 194 | 97.91 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LMEFGPDI_1 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_2 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_8 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_9 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_10 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_11 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_12 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_13 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_14 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_15 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_16 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_17 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_18 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_19 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_20 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_21 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_22 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_23 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_24 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_25 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_26 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_27 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_28 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_29 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_30 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_31 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_32 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_33 | 1.0 | 0.0 | 1.0 |
| LMEFGPDI_34 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_35 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_36 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_37 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_38 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_39 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_40 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_41 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_42 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_43 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_44 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_45 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_46 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_47 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_48 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_49 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_50 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_51 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_52 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_53 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_54 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_55 | 1.0 | 0.0 | 1.0 |
| LMEFGPDI_56 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_57 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_58 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_59 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_60 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_61 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_62 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_63 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_64 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_65 | 1.0 | 0.0 | 1.0 |
| LMEFGPDI_66 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_67 | 1.0 | 0.0 | 1.0 |
| LMEFGPDI_68 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_69 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_70 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_72 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_73 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_74 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_75 | 1.0 | 0.0 | 1.0 |
| LMEFGPDI_76 | 1.0 | 0.0 | 1.0 |
| LMEFGPDI_77 | 1.0 | 0.0 | 1.0 |
| LMEFGPDI_78 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_79 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_83 | 0.0 | 1.0 | 0.0 |
| LMEFGPDI_94 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LMEFGPDI_16 | 36595 | 62195 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490 |
| LMEFGPDI_17 | 61872 | 84701 | False | Myoviridae | VOG0720, VOG4555, VOG4553, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0641, VOG4574, VOG1993, VOG2703 |
| LMEFGPDI_33 | 4573 | 30564 | False | Myoviridae / Siphoviridae | VOG4551, VOG5222, VOG0025, VOG0189, VOG4566, VOG0125, VOG0054, VOG8236, VOG7235, VOG5242, VOG1024, VOG0647, VOG5173, VOG4605, VOG4545, VOG5716, VOG7238, VOG11074, VOG0115, VOG4319, VOG0275, VOG0692 |
Phigaro v2.4.0 (Database: Jan. 2024 release)