Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| LNCJCNME_2 | 503345 | 503683 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| LNCJCNME_2 | 503028 | 503345 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| LNCJCNME_4 | 362164 | 363333 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| LNCJCNME_3 | 346390 | 347310 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| LNCJCNME_3 | 333058 | 334497 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| LNCJCNME_3 | 283384 | 283977 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| LNCJCNME_4 | 140869 | 142071 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| LNCJCNME_4 | 122463 | 123317 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| LNCJCNME_3 | 28970 | 30613 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| LNCJCNME_6 | 27423 | 29993 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 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. |
|---|---|---|---|---|---|---|---|
| LNCJCNME_4 | 122463 | 123317 | aadK | Streptomycin | 98.71 | 100.00 | M26879 |
| LNCJCNME_3 | 346390 | 347310 | 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. |
|---|---|---|---|---|---|---|---|---|
| LNCJCNME_4 | 122463 | 123314 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| LNCJCNME_3 | 28970 | 30610 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| LNCJCNME_3 | 346393 | 347310 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| LNCJCNME_1 | 1025948 | 1026466 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.64 | 100.00 | WP_003242546.1 |
| LNCJCNME_7 | 157839 | 160436 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.65 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| LNCJCNME_1 | 535627 | 536808 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| LNCJCNME_1 | 112966 | 113751 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| LNCJCNME_7 | 61596 | 62237 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| LNCJCNME_1 | 111744 | 112940 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| LNCJCNME_7 | 212917 | 214680 | dep/capD | 0.0 | Capsule | Immune modulation | 99.32 | 100.00 | NP_389723 |
| LNCJCNME_1 | 535163 | 535612 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| LNCJCNME_1 | 101974 | 109110 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.74 | 100.00 | NP_391076 |
| LNCJCNME_1 | 534002 | 535144 | capA | 0.0 | Capsule | Immune modulation | 98.69 | 100.00 | NP_391469 |
| LNCJCNME_1 | 109130 | 110068 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| LNCJCNME_1 | 110096 | 111715 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| LNCJCNME_11 | 13636 | 12500 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| LNCJCNME_12 | 11264 | 10395 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| LNCJCNME_2 | 191929 | 191153 | CodY | 7.96e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| LNCJCNME_1 | 376372 | 376941 | ClpP | 6.40e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| LNCJCNME_2 | 703510 | 703118 | spxA1 | 6.25e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| LNCJCNME_2 | 703510 | 703118 | spx | 3.73e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| LNCJCNME_10 | 34684 | 34442 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| LNCJCNME_3 | 79027 | 78830 | CspA | 1.90e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| LNCJCNME_7 | 50364 | 50170 | CspD | 5.76e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| LNCJCNME_7 | 50364 | 50167 | CspB | 1.19e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
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 |
|---|---|---|---|
| LNCJCNME_1 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_2 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_3 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_4 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_5 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_6 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_7 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_8 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_9 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_10 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_11 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_12 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_13 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_14 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_15 | 0.0 | 1.0 | 0.0 |
| LNCJCNME_16 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LNCJCNME_2 | 533227 | 559539 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| LNCJCNME_2 | 626302 | 649639 | False | Myoviridae | VOG4574, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG1643, VOG4572, VOG4555, VOG0720, VOG10227, VOG0796 |
| LNCJCNME_2 | 660703 | 666504 | False | Unknown | VOG8233, VOG4552, VOG8241, VOG9667, VOG9667, VOG9576 |
| LNCJCNME_4 | 161633 | 191669 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862 |
Phigaro v2.4.0 (Database: Jan. 2024 release)