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. |
|---|---|---|---|---|---|---|---|---|
| LGCOMDED_5 | 93432 | 93749 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| LGCOMDED_5 | 93094 | 93432 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| LGCOMDED_45 | 54822 | 56261 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.42 | JYFL01000006.1 |
| LGCOMDED_37 | 20003 | 20857 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| LGCOMDED_32 | 13548 | 15194 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| LGCOMDED_4 | 9325 | 11895 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| LGCOMDED_89 | 8997 | 10166 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| LGCOMDED_37 | 1239 | 2441 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
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. |
|---|---|---|---|---|---|---|---|
| LGCOMDED_9 | 50683 | 52059 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.77 | 100.00 | D12567 |
| LGCOMDED_37 | 20005 | 20857 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| LGCOMDED_45 | 42018 | 42937 | mph(K) | Spiramycin, Telithromycin | 97.61 | 99.89 | 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. |
|---|---|---|---|---|---|---|---|---|
| LGCOMDED_9 | 50686 | 52059 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| LGCOMDED_32 | 13551 | 15194 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| LGCOMDED_37 | 20006 | 20857 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| LGCOMDED_9 | 48190 | 48708 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| LGCOMDED_23 | 30875 | 31813 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| LGCOMDED_30 | 3247 | 4428 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LGCOMDED_30 | 1622 | 2764 | capA | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391469 |
| LGCOMDED_30 | 2783 | 3232 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| LGCOMDED_23 | 34700 | 35485 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LGCOMDED_8 | 1856 | 3619 | dep/capD | 0.0 | Capsule | Immune modulation | 99.09 | 100.00 | NP_389723 |
| LGCOMDED_23 | 23719 | 30855 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.78 | 100.00 | NP_391076 |
| LGCOMDED_23 | 33478 | 34674 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| LGCOMDED_12 | 21390 | 22031 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 97.82 | 100.00 | NP_390062 |
| LGCOMDED_23 | 31841 | 33460 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.72 | 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 |
|---|---|---|---|---|---|---|---|---|
| LGCOMDED_17 | 31673 | 32809 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| LGCOMDED_53 | 11121 | 10252 | pdxS | 1.92e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| LGCOMDED_1 | 112550 | 111774 | CodY | 2.13e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LGCOMDED_78 | 84824 | 85393 | ClpP | 6.88e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LGCOMDED_41 | 23404 | 23012 | spxA1 | 2.09e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LGCOMDED_41 | 23404 | 23012 | spx | 1.25e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LGCOMDED_24 | 20471 | 20713 | SpoVG | 7.47e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LGCOMDED_38 | 3967 | 4164 | CspA | 1.64e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LGCOMDED_39 | 31156 | 30962 | CspB | 3.22e-28 | cold shock protein | 83.08 | 98.48 | CAD00094 |
| LGCOMDED_12 | 33883 | 34077 | CspD | 5.14e-28 | cold shock protein | 80.00 | 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. |
|---|---|---|---|---|---|---|
| LGCOMDED_63 | 101 | 287 | Col(SD853) | 187 / 194 | 86.63 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LGCOMDED_1 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_2 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_3 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_4 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_5 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_6 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_7 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_8 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_9 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_10 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_11 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_12 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_13 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_14 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_15 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_16 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_17 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_18 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_19 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_20 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_21 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_22 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_23 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_24 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_25 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_26 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_27 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_28 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_29 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_30 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_31 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_32 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_33 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_34 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_35 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_36 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_37 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_38 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_39 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_40 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_41 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_42 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_43 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_44 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_45 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_46 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_47 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_48 | 1.0 | 0.0 | 1.0 |
| LGCOMDED_49 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_50 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_51 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_52 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_53 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_54 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_55 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_56 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_57 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_58 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_59 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_60 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_61 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_62 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_63 | 1.0 | 0.0 | 1.0 |
| LGCOMDED_64 | 1.0 | 0.0 | 1.0 |
| LGCOMDED_65 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_66 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_67 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_68 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_69 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_70 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_71 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_72 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_73 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_75 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_76 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_77 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_78 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_79 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_80 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_81 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_82 | 1.0 | 0.0 | 1.0 |
| LGCOMDED_83 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_85 | 1.0 | 0.0 | 1.0 |
| LGCOMDED_86 | 0.0 | 1.0 | 0.0 |
| LGCOMDED_89 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LGCOMDED_5 | 38018 | 63882 | 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, VOG0753 |
| LGCOMDED_11 | 23999 | 49715 | False | Myoviridae | VOG2703, VOG1993, VOG4574, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG1350, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG0815, VOG4553, VOG4555, VOG0720, VOG0796 |
| LGCOMDED_11 | 59705 | 63575 | False | Siphoviridae | VOG4552, VOG0650, VOG9667, VOG9667, VOG4662 |
| LGCOMDED_25 | 4718 | 9312 | False | Unknown | VOG0083, VOG1309, VOG1292 |
| LGCOMDED_25 | 22728 | 45935 | False | Myoviridae | VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862, VOG0906, VOG7718, VOG3390, VOG4705 |
| LGCOMDED_34 | 13214 | 51044 | False | Siphoviridae | VOG7438, VOG1047, VOG0021, VOG1565, VOG0026, VOG4609, VOG0327, VOG4548, VOG0198, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5221, VOG0136, VOG4574 |
| LGCOMDED_78 | 46486 | 74580 | False | Siphoviridae | VOG10095, VOG7508, VOG0602, VOG4574, VOG0753, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG4545, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5601, VOG4553, VOG4573, VOG4556, VOG4544, VOG4581, VOG4841, VOG10599 |
Phigaro v2.4.0 (Database: Jan. 2024 release)