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. |
|---|---|---|---|---|---|---|---|---|
| LDHOFGLE_8 | 554002 | 555204 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| LDHOFGLE_8 | 535177 | 536031 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| LDHOFGLE_7 | 429514 | 429831 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LDHOFGLE_7 | 429176 | 429514 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LDHOFGLE_9 | 388557 | 389726 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LDHOFGLE_11 | 109000 | 109920 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| LDHOFGLE_11 | 95665 | 97104 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| LDHOFGLE_10 | 29151 | 30794 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| LDHOFGLE_12 | 27476 | 30046 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| LDHOFGLE_6 | 2450 | 3310 | TEM-181 | ARO:3001044 | TEM-181 | 100.00 | 100.00 | AM743197.2 |
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. |
|---|---|---|---|---|---|---|---|
| LDHOFGLE_6 | 2450 | 3310 | blaTEM-181 | Unknown Beta-lactam | 100.00 | 100.00 | KM977568 |
| LDHOFGLE_1 | 1020960 | 1022336 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| LDHOFGLE_8 | 535177 | 536029 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| LDHOFGLE_11 | 109000 | 109920 | mph(K) | Spiramycin, Telithromycin | 97.50 | 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. |
|---|---|---|---|---|---|---|---|---|
| LDHOFGLE_6 | 2450 | 3307 | blaTEM-181 | class A beta-lactamase TEM-181 | ALLELEX | 100.00 | 100.00 | WP_000027060.1 |
| LDHOFGLE_1 | 1020963 | 1022336 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| LDHOFGLE_10 | 29151 | 30791 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| LDHOFGLE_11 | 109003 | 109920 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| LDHOFGLE_8 | 535177 | 536028 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| LDHOFGLE_1 | 1018443 | 1018961 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| LDHOFGLE_9 | 84802 | 87399 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LDHOFGLE_9 | 189370 | 190011 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| LDHOFGLE_1 | 527611 | 528792 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LDHOFGLE_9 | 34777 | 36540 | dep/capD | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_389723 |
| LDHOFGLE_1 | 113092 | 113877 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LDHOFGLE_1 | 109256 | 110194 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| LDHOFGLE_1 | 111870 | 113066 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| LDHOFGLE_1 | 102102 | 109236 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.06 | 99.97 | NP_391076 |
| LDHOFGLE_1 | 525986 | 527128 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| LDHOFGLE_1 | 527147 | 527596 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| LDHOFGLE_1 | 110222 | 111841 | 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 |
|---|---|---|---|---|---|---|---|---|
| LDHOFGLE_3 | 34216 | 35352 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LDHOFGLE_4 | 4512 | 5381 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LDHOFGLE_7 | 739409 | 740185 | CodY | 7.67e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LDHOFGLE_1 | 366256 | 366825 | ClpP | 6.36e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LDHOFGLE_7 | 277061 | 277453 | spxA1 | 6.03e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LDHOFGLE_7 | 277061 | 277453 | spx | 3.60e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LDHOFGLE_10 | 81606 | 81409 | CspA | 9.83e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LDHOFGLE_9 | 201973 | 202167 | CspD | 3.00e-28 | cold shock protein | 81.54 | 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. |
|---|---|---|---|---|---|---|
| LDHOFGLE_6 | 4162 | 4292 | ColRNAI | 131 / 130 | 87.02 | DQ298019 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LDHOFGLE_1 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_2 | 1.0 | 0.0 | 1.0 |
| LDHOFGLE_3 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_4 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_5 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_6 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_7 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_8 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_9 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_10 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_11 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_12 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_13 | 0.0 | 1.0 | 0.0 |
| LDHOFGLE_14 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LDHOFGLE_2 | 9647 | 33296 | False | Siphoviridae | VOG3616, VOG1024, VOG10944, VOG9244, VOG4599, VOG4605, VOG6163, VOG5852, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG4544, VOG4581, VOG0221 |
| LDHOFGLE_2 | 60276 | 72889 | False | Unknown | VOG5292, VOG4549, VOG2725, VOG3531, VOG3851, VOG2352, VOG4714, VOG4561, VOG1198, VOG0397, VOG2352 |
| LDHOFGLE_7 | 371865 | 399366 | 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 |
| LDHOFGLE_8 | 279527 | 283139 | False | Unknown | VOG0186, VOG0189, VOG0044 |
| LDHOFGLE_8 | 290065 | 313277 | False | Myoviridae | VOG0720, VOG4555, VOG4553, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG4574 |
| LDHOFGLE_8 | 371036 | 394442 | False | Siphoviridae | VOG4841, VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG4705, VOG5221, VOG0136 |
Phigaro v2.4.0 (Database: Jan. 2024 release)