Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 16 | 10 | 8 | 20.49 |
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. |
|---|---|---|---|---|---|---|---|---|
| PLLECCHL_2 | 608270 | 609124 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| PLLECCHL_2 | 589533 | 590735 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| PLLECCHL_1 | 432125 | 432442 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PLLECCHL_1 | 431787 | 432125 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PLLECCHL_4 | 396810 | 398453 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| PLLECCHL_2 | 364549 | 365718 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PLLECCHL_5 | 262927 | 265497 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| PLLECCHL_4 | 165601 | 166194 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| PLLECCHL_4 | 115080 | 116519 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| PLLECCHL_4 | 102267 | 103187 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| PLLECCHL_7 | 49250 | 50062 | NDM-1 | ARO:3000589 | NDM-1 | 100.00 | 100.00 | FN396876.1 |
| PLLECCHL_13 | 74 | 934 | SHV-12 | ARO:3001071 | SHV-12 | 100.00 | 100.00 | KF976405.1 |
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. |
|---|---|---|---|---|---|---|---|
| PLLECCHL_7 | 49250 | 50062 | blaNDM-1 | Amoxicillin, Amoxicillin+Clavulanic acid, Ampicillin, Ampicillin+Clavulanic acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ceftazidime+Avibactam, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam, Temocillin | 100.00 | 100.00 | FN396876 |
| PLLECCHL_13 | 74 | 934 | blaSHV-12 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin | 100.00 | 100.00 | KF976405 |
| PLLECCHL_4 | 102267 | 103187 | mph(K) | Spiramycin, Telithromycin | 99.89 | 100.00 | NC_000964 |
| PLLECCHL_3 | 1007274 | 1008650 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.06 | 100.00 | D12567 |
| PLLECCHL_2 | 608272 | 609124 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PLLECCHL_7 | 49250 | 50059 | blaNDM-1 | subclass B1 metallo-beta-lactamase NDM-1 | ALLELEX | 100.00 | 100.00 | WP_004201164.1 |
| PLLECCHL_13 | 74 | 931 | blaSHV-12 | extended-spectrum class A beta-lactamase SHV-12 | ALLELEX | 100.00 | 100.00 | WP_002904004.1 |
| PLLECCHL_7 | 50066 | 50428 | ble | bleomycin binding protein Ble-MBL | EXACTX | 100.00 | 100.00 | WP_004201167.1 |
| PLLECCHL_4 | 102267 | 103184 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| PLLECCHL_3 | 1007277 | 1008650 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| PLLECCHL_4 | 396813 | 398453 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| PLLECCHL_2 | 608273 | 609124 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| PLLECCHL_3 | 1004722 | 1005240 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| PLLECCHL_2 | 55644 | 58238 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PLLECCHL_3 | 113897 | 114835 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| PLLECCHL_3 | 526807 | 527988 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| PLLECCHL_3 | 117733 | 118518 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PLLECCHL_3 | 525182 | 526324 | capA | 0.0 | Capsule | Immune modulation | 99.47 | 100.00 | NP_391469 |
| PLLECCHL_2 | 165182 | 165823 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| PLLECCHL_3 | 526343 | 526792 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| PLLECCHL_2 | 10220 | 11983 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| PLLECCHL_3 | 116511 | 117707 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| PLLECCHL_3 | 106741 | 113877 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391076 |
| PLLECCHL_3 | 114863 | 116482 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.89 | 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 |
|---|---|---|---|---|---|---|---|---|
| PLLECCHL_6 | 31797 | 32933 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PLLECCHL_7 | 49250 | 50059 | NDM-1 | 2.91e-159 | carbapenemase | 100.00 | 100.00 | AJD76950 |
| PLLECCHL_9 | 4390 | 5259 | pdxS | 1.24e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PLLECCHL_1 | 745468 | 746244 | CodY | 9.38e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PLLECCHL_3 | 373585 | 374154 | ClpP | 6.33e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PLLECCHL_1 | 280990 | 281382 | spxA1 | 7.37e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PLLECCHL_1 | 280990 | 281382 | spx | 4.40e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PLLECCHL_8 | 20810 | 21052 | SpoVG | 7.75e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PLLECCHL_4 | 350066 | 350263 | CspA | 1.85e-31 | 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. |
|---|---|---|---|---|---|---|
| PLLECCHL_7 | 7390 | 7763 | IncX3 | 374 / 374 | 100.00 | JN247852 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| PLLECCHL_1 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_2 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_3 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_4 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_5 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_6 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_7 | 1.0 | 0.0 | 1.0 |
| PLLECCHL_8 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_9 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_10 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_11 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_12 | 0.0 | 1.0 | 0.0 |
| PLLECCHL_13 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PLLECCHL_1 | 375840 | 401948 | 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 |
| PLLECCHL_1 | 949261 | 969196 | False | Unknown | VOG4660, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG0275, VOG7930, VOG8610, VOG5008, VOG4705 |
| PLLECCHL_2 | 537253 | 562228 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG0796, VOG4673 |
| PLLECCHL_2 | 788470 | 812911 | False | Myoviridae | VOG4574, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720, VOG0796 |
Phigaro v2.4.0 (Database: Jan. 2024 release)