Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 7 | 17.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| LMFDPJNC_8 | 610984 | 611838 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| LMFDPJNC_8 | 591811 | 593013 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| LMFDPJNC_9 | 429022 | 429339 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LMFDPJNC_9 | 428684 | 429022 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LMFDPJNC_8 | 362733 | 363902 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LMFDPJNC_11 | 197977 | 199620 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| LMFDPJNC_12 | 113659 | 115098 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| LMFDPJNC_12 | 100843 | 101763 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| LMFDPJNC_10 | 28905 | 31475 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
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. |
|---|---|---|---|---|---|---|---|
| LMFDPJNC_6 | 36108 | 37484 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| LMFDPJNC_8 | 610986 | 611838 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| LMFDPJNC_12 | 100843 | 101763 | 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. |
|---|---|---|---|---|---|---|---|---|
| LMFDPJNC_6 | 36108 | 37481 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| LMFDPJNC_11 | 197980 | 199620 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| LMFDPJNC_12 | 100843 | 101760 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| LMFDPJNC_8 | 610987 | 611838 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| LMFDPJNC_6 | 39483 | 40001 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| LMFDPJNC_8 | 58977 | 61574 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LMFDPJNC_8 | 163545 | 164186 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| LMFDPJNC_6 | 529652 | 530833 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| LMFDPJNC_8 | 8952 | 10715 | dep/capD | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_389723 |
| LMFDPJNC_7 | 282249 | 283034 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| LMFDPJNC_7 | 285932 | 286870 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| LMFDPJNC_7 | 283060 | 284256 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| LMFDPJNC_7 | 286890 | 294024 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.06 | 99.97 | NP_391076 |
| LMFDPJNC_6 | 531316 | 532458 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| LMFDPJNC_6 | 530848 | 531297 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| LMFDPJNC_7 | 284285 | 285904 | 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 |
|---|---|---|---|---|---|---|---|---|
| LMFDPJNC_14 | 29571 | 28435 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LMFDPJNC_1 | 7039 | 7908 | pdxS | 1.43e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LMFDPJNC_9 | 738920 | 739696 | CodY | 8.52e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LMFDPJNC_7 | 29869 | 29300 | ClpP | 2.38e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LMFDPJNC_9 | 276407 | 276799 | spxA1 | 6.69e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LMFDPJNC_9 | 276407 | 276799 | spx | 3.99e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LMFDPJNC_15 | 36228 | 35986 | SpoVG | 8.08e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LMFDPJNC_11 | 147165 | 147362 | CspA | 9.88e-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 |
|---|---|---|---|
| LMFDPJNC_1 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_2 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_3 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_6 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_7 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_8 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_9 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_10 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_11 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_12 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_13 | 1.0 | 0.0 | 1.0 |
| LMFDPJNC_14 | 0.0 | 1.0 | 0.0 |
| LMFDPJNC_15 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LMFDPJNC_8 | 540456 | 558769 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
| LMFDPJNC_9 | 371211 | 399196 | 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 |
| LMFDPJNC_13 | 31086 | 54841 | False | Siphoviridae | VOG0221, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5852, VOG6163, VOG4605, VOG4599, VOG9244, VOG10944, VOG1024 |
Phigaro v2.4.0 (Database: Jan. 2024 release)