Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| LHCGIODF_1 | 265105 | 266025 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| LHCGIODF_2 | 255842 | 256696 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| LHCGIODF_1 | 251773 | 253212 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| LHCGIODF_2 | 238795 | 239997 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| LHCGIODF_1 | 202145 | 202738 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| LHCGIODF_5 | 71642 | 71980 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LHCGIODF_5 | 71325 | 71642 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LHCGIODF_21 | 49574 | 51217 | vmlR | ARO:3004476 | vmlR | 99.09 | 100.00 | NC_000964.3 |
| LHCGIODF_26 | 27413 | 29983 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| LHCGIODF_2 | 12451 | 13620 | bmr | ARO:3003007 | bmr | 99.49 | 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. |
|---|---|---|---|---|---|---|---|
| LHCGIODF_2 | 255842 | 256696 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| LHCGIODF_1 | 265105 | 266025 | 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. |
|---|---|---|---|---|---|---|---|---|
| LHCGIODF_21 | 49577 | 51217 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.09 | 100.00 | WP_003234144.1 |
| LHCGIODF_2 | 255845 | 256696 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| LHCGIODF_1 | 265108 | 266025 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| LHCGIODF_14 | 58138 | 58656 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 94.80 | 100.00 | WP_003242546.1 |
| LHCGIODF_25 | 52317 | 54914 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.29 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LHCGIODF_24 | 61585 | 62226 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| LHCGIODF_18 | 41530 | 42711 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LHCGIODF_15 | 72479 | 73264 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LHCGIODF_15 | 73290 | 74486 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| LHCGIODF_25 | 6548 | 8311 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| LHCGIODF_18 | 43194 | 44336 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| LHCGIODF_18 | 42726 | 43175 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| LHCGIODF_15 | 76162 | 77100 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| LHCGIODF_15 | 77120 | 84256 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.36 | 100.00 | NP_391076 |
| LHCGIODF_15 | 74515 | 76134 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| LHCGIODF_30 | 32019 | 33155 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LHCGIODF_41 | 11262 | 10393 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LHCGIODF_34 | 879 | 103 | CodY | 3.11e-126 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LHCGIODF_6 | 172625 | 173194 | ClpP | 1.13e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LHCGIODF_3 | 207460 | 207852 | spxA1 | 1.60e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LHCGIODF_3 | 207460 | 207852 | spx | 9.53e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LHCGIODF_31 | 10546 | 10788 | SpoVG | 6.14e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LHCGIODF_21 | 5781 | 5978 | CspA | 3.47e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LHCGIODF_24 | 50353 | 50159 | CspD | 1.63e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| LHCGIODF_24 | 50353 | 50156 | CspB | 3.37e-28 | cold shock protein | 80.30 | 100.00 | 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 |
|---|---|---|---|
| LHCGIODF_1 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_2 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_3 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_4 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_5 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_6 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_7 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_8 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_9 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_10 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_11 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_12 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_13 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_14 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_15 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_16 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_17 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_18 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_19 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_20 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_21 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_22 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_23 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_24 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_25 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_26 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_27 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_28 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_29 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_30 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_31 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_32 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_33 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_34 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_35 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_36 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_37 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_38 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_39 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_40 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_41 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_42 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_43 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_44 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_45 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_46 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_47 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_48 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_49 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_50 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_52 | 1.0 | 0.0 | 1.0 |
| LHCGIODF_53 | 1.0 | 0.0 | 1.0 |
| LHCGIODF_54 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_55 | 1.0 | 0.0 | 1.0 |
| LHCGIODF_56 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_57 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_58 | 1.0 | 0.0 | 1.0 |
| LHCGIODF_59 | 1.0 | 0.0 | 1.0 |
| LHCGIODF_60 | 0.0 | 1.0 | 0.0 |
| LHCGIODF_61 | 1.0 | 0.0 | 1.0 |
| LHCGIODF_63 | 1.0 | 0.0 | 1.0 |
| LHCGIODF_64 | 1.0 | 0.0 | 1.0 |
| LHCGIODF_65 | 1.0 | 0.0 | 1.0 |
| LHCGIODF_66 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LHCGIODF_2 | 185123 | 202891 | False | Myoviridae | VOG4705, VOG7718, VOG0906, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
| LHCGIODF_5 | 101796 | 128996 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| LHCGIODF_37 | 594 | 17127 | False | Siphoviridae | VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581 |
Phigaro v2.4.0 (Database: Jan. 2024 release)