Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 14 | 10 | 4 | 17.66 |
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. |
|---|---|---|---|---|---|---|---|---|
| LDPDIDCE_1 | 2861688 | 2863064 | tet(L) | ARO:3000179 | tet(L) | 99.78 | 100.00 | M11036.1 |
| LDPDIDCE_1 | 2707458 | 2708312 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| LDPDIDCE_1 | 2688749 | 2689951 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| LDPDIDCE_1 | 2466432 | 2467601 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LDPDIDCE_1 | 1348598 | 1348912 | ykkD | ARO:3003064 | ykkD | 99.05 | 99.05 | AL009126.1 |
| LDPDIDCE_1 | 1348260 | 1348598 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LDPDIDCE_1 | 885370 | 887940 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| LDPDIDCE_1 | 574722 | 576368 | vmlR | ARO:3004476 | vmlR | 98.36 | 100.18 | NC_000964.3 |
| LDPDIDCE_1 | 326843 | 327436 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| LDPDIDCE_1 | 279012 | 280445 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.00 | JYFL01000006.1 |
| LDPDIDCE_1 | 266197 | 267117 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| LDPDIDCE_1 | 200291 | 201052 | ANT(4')-Ia | ARO:3002623 | ANT(4')-Ia | 99.60 | 100.00 | K02551.1 |
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. |
|---|---|---|---|---|---|---|---|
| LDPDIDCE_1 | 200291 | 201052 | aadD | Amikacin, Tobramycin | 100.00 | 100.00 | M19465 |
| LDPDIDCE_1 | 2707458 | 2708312 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| LDPDIDCE_1 | 2861688 | 2863064 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 100.00 | 100.00 | M29725 |
| LDPDIDCE_1 | 266197 | 267117 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| LDPDIDCE_1 | 200294 | 201061 | aadD1 | aminoglycoside O-nucleotidyltransferase ANT(4')-Ia | EXACTX | 100.00 | 100.00 | WP_001795128.1 |
| LDPDIDCE_1 | 2707461 | 2708312 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| LDPDIDCE_1 | 2861691 | 2863064 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_001574277.1 |
| LDPDIDCE_1 | 266197 | 267105 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| LDPDIDCE_1 | 574725 | 576368 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.36 | 100.00 | WP_003234144.1 |
| LDPDIDCE_1 | 4185372 | 4185890 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| LDPDIDCE_1 | 2023115 | 2025709 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LDPDIDCE_1 | 1976457 | 1978220 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| LDPDIDCE_1 | 2267080 | 2267721 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| LDPDIDCE_1 | 3694483 | 3695664 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LDPDIDCE_1 | 3264925 | 3265710 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| LDPDIDCE_1 | 3692858 | 3694000 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| LDPDIDCE_1 | 3253933 | 3261069 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.30 | 100.00 | NP_391076 |
| LDPDIDCE_1 | 3261089 | 3262027 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.04 | 100.00 | NP_391077 |
| LDPDIDCE_1 | 3263703 | 3264899 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| LDPDIDCE_1 | 3694019 | 3694468 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| LDPDIDCE_1 | 3262055 | 3263674 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.73 | 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 |
|---|---|---|---|---|---|---|---|---|
| LDPDIDCE_1 | 126618 | 127754 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LDPDIDCE_1 | 18665 | 19534 | pdxS | 3.13e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LDPDIDCE_1 | 1661896 | 1662672 | CodY | 3.42e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LDPDIDCE_1 | 3541288 | 3541857 | ClpP | 2.54e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| LDPDIDCE_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LDPDIDCE_1 | 1292313 | 1318421 | 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 |
| LDPDIDCE_1 | 2638821 | 2669065 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309, VOG4600 |
Phigaro v2.4.0 (Database: Jan. 2024 release)