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. |
|---|---|---|---|---|---|---|---|---|
| PLHLKKDO_1 | 1810267 | 1810605 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PLHLKKDO_1 | 1809950 | 1810267 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PLHLKKDO_1 | 698614 | 699783 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PLHLKKDO_1 | 504178 | 505380 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| PLHLKKDO_1 | 485789 | 486643 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| PLHLKKDO_3 | 162521 | 163114 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| PLHLKKDO_4 | 117820 | 120390 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PLHLKKDO_3 | 112045 | 113484 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| PLHLKKDO_3 | 99231 | 100151 | mphK | ARO:3004541 | mphK | 98.04 | 100.00 | CP010314.1 |
| PLHLKKDO_6 | 28897 | 30543 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| PLHLKKDO_2 | 995119 | 996495 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | D12567 |
| PLHLKKDO_1 | 485789 | 486641 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
| PLHLKKDO_3 | 99231 | 100151 | 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. |
|---|---|---|---|---|---|---|---|---|
| PLHLKKDO_2 | 995122 | 996495 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_063856081.1 |
| PLHLKKDO_6 | 28897 | 30540 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| PLHLKKDO_3 | 99231 | 100148 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.04 | 100.00 | WP_003246254.1 |
| PLHLKKDO_1 | 485789 | 486640 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| PLHLKKDO_2 | 992621 | 993139 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| PLHLKKDO_1 | 994781 | 997378 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PLHLKKDO_2 | 109005 | 109943 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| PLHLKKDO_2 | 504913 | 506094 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| PLHLKKDO_2 | 109971 | 111590 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.26 | 100.00 | NP_391078 |
| PLHLKKDO_2 | 112841 | 113626 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| PLHLKKDO_1 | 900590 | 901231 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| PLHLKKDO_2 | 503288 | 504430 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| PLHLKKDO_2 | 111619 | 112815 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| PLHLKKDO_1 | 1042556 | 1044319 | dep/capD | 0.0 | Capsule | Immune modulation | 98.87 | 100.00 | NP_389723 |
| PLHLKKDO_2 | 101849 | 108985 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.86 | 100.00 | NP_391076 |
| PLHLKKDO_2 | 504449 | 504898 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| PLHLKKDO_7 | 27977 | 26841 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PLHLKKDO_9 | 11176 | 10307 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PLHLKKDO_1 | 1500264 | 1499488 | CodY | 1.81e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PLHLKKDO_2 | 363504 | 364073 | ClpP | 6.20e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PLHLKKDO_1 | 1961087 | 1960695 | spxA1 | 1.43e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PLHLKKDO_1 | 1961087 | 1960695 | spx | 8.50e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PLHLKKDO_8 | 34635 | 34393 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PLHLKKDO_6 | 77302 | 77105 | CspA | 3.63e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| PLHLKKDO_1 | 0.0 | 1.0 | 0.0 |
| PLHLKKDO_2 | 0.0 | 1.0 | 0.0 |
| PLHLKKDO_3 | 0.0 | 1.0 | 0.0 |
| PLHLKKDO_4 | 0.0 | 1.0 | 0.0 |
| PLHLKKDO_5 | 0.0 | 1.0 | 0.0 |
| PLHLKKDO_6 | 0.0 | 1.0 | 0.0 |
| PLHLKKDO_7 | 0.0 | 1.0 | 0.0 |
| PLHLKKDO_8 | 0.0 | 1.0 | 0.0 |
| PLHLKKDO_9 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PLHLKKDO_1 | 272552 | 276370 | False | Unknown | VOG4600, VOG1309, VOG0189 |
| PLHLKKDO_1 | 282950 | 306913 | False | Myoviridae | VOG0796, VOG0720, VOG4555, VOG4553, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG1350, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG4574 |
| PLHLKKDO_1 | 1276547 | 1293884 | False | Siphoviridae | VOG3390, VOG4705, VOG5008, VOG8610, VOG7930, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042 |
| PLHLKKDO_1 | 1840086 | 1866569 | False | Myoviridae | VOG0753, VOG4705, VOG4612, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)