Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| JMNKFAJP_5 | 610317 | 610655 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| JMNKFAJP_5 | 610000 | 610317 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| JMNKFAJP_3 | 606432 | 607286 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| JMNKFAJP_3 | 587697 | 588899 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| JMNKFAJP_2 | 399987 | 401633 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| JMNKFAJP_3 | 363162 | 364331 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| JMNKFAJP_2 | 153068 | 153661 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| JMNKFAJP_2 | 102544 | 103983 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| JMNKFAJP_2 | 89730 | 90650 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| JMNKFAJP_6 | 27410 | 29980 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| JMNKFAJP_4 | 36215 | 37591 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.93 | 100.00 | X08034 |
| JMNKFAJP_2 | 89730 | 90650 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| JMNKFAJP_3 | 606434 | 607286 | 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. |
|---|---|---|---|---|---|---|---|---|
| JMNKFAJP_4 | 36215 | 37588 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| JMNKFAJP_2 | 89730 | 90647 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| JMNKFAJP_2 | 399990 | 401633 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| JMNKFAJP_3 | 606435 | 607286 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| JMNKFAJP_4 | 39544 | 40062 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| JMNKFAJP_3 | 55962 | 58559 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| JMNKFAJP_4 | 508525 | 509706 | capB | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_391471 |
| JMNKFAJP_9 | 101923 | 109059 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.55 | 100.00 | NP_391076 |
| JMNKFAJP_3 | 163778 | 164419 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| JMNKFAJP_9 | 112915 | 113700 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| JMNKFAJP_9 | 109079 | 110017 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| JMNKFAJP_4 | 510189 | 511331 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| JMNKFAJP_4 | 509721 | 510170 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| JMNKFAJP_3 | 9109 | 10872 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
| JMNKFAJP_9 | 111693 | 112889 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.66 | 100.00 | NP_391079 |
| JMNKFAJP_9 | 110045 | 111664 | 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 |
|---|---|---|---|---|---|---|---|---|
| JMNKFAJP_7 | 31693 | 32829 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| JMNKFAJP_13 | 4441 | 5310 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| JMNKFAJP_5 | 300264 | 299488 | CodY | 8.23e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| JMNKFAJP_4 | 663659 | 663090 | ClpP | 5.24e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| JMNKFAJP_5 | 801242 | 800850 | spxA1 | 6.47e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| JMNKFAJP_5 | 801242 | 800850 | spx | 3.86e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| JMNKFAJP_11 | 20749 | 20991 | SpoVG | 7.54e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| JMNKFAJP_2 | 353166 | 353363 | CspA | 1.86e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| JMNKFAJP_8 | 33289 | 33095 | CspB | 5.76e-28 | cold shock protein | 83.08 | 98.48 | 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 |
|---|---|---|---|
| JMNKFAJP_2 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_3 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_4 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_5 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_6 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_7 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_8 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_9 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_11 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_12 | 1.0 | 0.0 | 1.0 |
| JMNKFAJP_13 | 0.0 | 1.0 | 0.0 |
| JMNKFAJP_14 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JMNKFAJP_3 | 541248 | 570853 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG4693, VOG0189, VOG11060, VOG1309 |
| JMNKFAJP_3 | 737182 | 773262 | False | Siphoviridae | VOG4615, VOG0136, VOG5221, VOG4705, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581, VOG4841, VOG0198, VOG4548, VOG0327, VOG4609, VOG0026, VOG1565, VOG0021, VOG1047 |
| JMNKFAJP_3 | 818826 | 843243 | False | Myoviridae | VOG5826, VOG0221, VOG6116, VOG6422, VOG4574, VOG0641, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555 |
| JMNKFAJP_5 | 641645 | 668569 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| JMNKFAJP_5 | 729462 | 749110 | False | Siphoviridae | VOG4599, VOG4605, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG5872, VOG1329, VOG4555, VOG4564, VOG0720 |
| JMNKFAJP_5 | 759594 | 762972 | False | Siphoviridae | VOG4603, VOG4552, VOG2687, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)