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. |
|---|---|---|---|---|---|---|---|---|
| DMJOHPCI_1 | 543275 | 544129 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| DMJOHPCI_1 | 524614 | 525816 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| DMJOHPCI_3 | 494630 | 494968 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| DMJOHPCI_3 | 494313 | 494630 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| DMJOHPCI_1 | 354518 | 355687 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| DMJOHPCI_4 | 334342 | 335262 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| DMJOHPCI_4 | 321009 | 322448 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| DMJOHPCI_4 | 271377 | 271970 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| DMJOHPCI_4 | 29203 | 30846 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
| DMJOHPCI_5 | 27451 | 30021 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 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. |
|---|---|---|---|---|---|---|---|
| DMJOHPCI_2 | 1001825 | 1003201 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.84 | 100.00 | X08034 |
| DMJOHPCI_1 | 543277 | 544129 | aadK | Streptomycin | 98.71 | 99.77 | M26879 |
| DMJOHPCI_4 | 334342 | 335262 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| DMJOHPCI_2 | 1001828 | 1003201 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_003242953.1 |
| DMJOHPCI_4 | 29203 | 30843 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| DMJOHPCI_1 | 543278 | 544129 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| DMJOHPCI_4 | 334345 | 335262 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| DMJOHPCI_2 | 999354 | 999872 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| DMJOHPCI_1 | 56925 | 59522 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| DMJOHPCI_1 | 153071 | 153712 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| DMJOHPCI_2 | 109418 | 110356 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| DMJOHPCI_2 | 516970 | 518151 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| DMJOHPCI_2 | 110384 | 112003 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.26 | 100.00 | NP_391078 |
| DMJOHPCI_2 | 113254 | 114039 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| DMJOHPCI_2 | 515345 | 516487 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| DMJOHPCI_2 | 112032 | 113228 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| DMJOHPCI_1 | 9984 | 11747 | dep/capD | 0.0 | Capsule | Immune modulation | 98.87 | 100.00 | NP_389723 |
| DMJOHPCI_2 | 102262 | 109398 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.82 | 100.00 | NP_391076 |
| DMJOHPCI_2 | 516506 | 516955 | 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 |
|---|---|---|---|---|---|---|---|---|
| DMJOHPCI_9 | 31928 | 33064 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| DMJOHPCI_14 | 4358 | 5227 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| DMJOHPCI_3 | 184769 | 183993 | CodY | 1.82e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| DMJOHPCI_2 | 375553 | 376122 | ClpP | 6.25e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| DMJOHPCI_3 | 646529 | 646137 | spxA1 | 5.88e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| DMJOHPCI_3 | 646529 | 646137 | spx | 3.51e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| DMJOHPCI_11 | 20606 | 20848 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| DMJOHPCI_4 | 77576 | 77379 | CspA | 1.88e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| DMJOHPCI_42 | 285 | 214 | Z3917 | 1.79e-06 | 83.33 | 85.71 | AE005492_1 |
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 |
|---|---|---|---|
| DMJOHPCI_1 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_2 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_3 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_4 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_5 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_6 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_7 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_8 | 1.0 | 0.0 | 1.0 |
| DMJOHPCI_9 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_10 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_11 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_12 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_13 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_14 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_15 | 0.0 | 1.0 | 0.0 |
| DMJOHPCI_17 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| DMJOHPCI_1 | 695276 | 729314 | False | Siphoviridae | VOG4972, VOG4574, VOG0641, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG4545, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3644, VOG4544, VOG4581, VOG4841, VOG0198, VOG4548, VOG0327, VOG4609, VOG0026, VOG1565, VOG0021, VOG1047, VOG7438 |
| DMJOHPCI_3 | 524452 | 552016 | 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 |
| DMJOHPCI_5 | 276093 | 299158 | False | Siphoviridae | VOG2703, VOG4574, VOG0136, VOG0753, VOG4728, VOG5535, VOG4599, VOG4605, VOG4545, VOG0725, VOG2621, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG3480, VOG1329, VOG4555, VOG4564, VOG0720, VOG10227 |
| DMJOHPCI_6 | 111275 | 144865 | False | Siphoviridae | VOG1659, VOG4918, VOG0641, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581, VOG7462, VOG6093, VOG0198, VOG1884, VOG0025, VOG9600, VOG4566 |
| DMJOHPCI_7 | 89232 | 115846 | False | Siphoviridae | VOG7134, VOG9867, VOG6036, VOG5495, VOG9219, VOG9713, VOG6940, VOG5534, VOG7718, VOG3390, VOG4705, VOG5008, VOG8610, VOG7930, VOG0275, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712 |
| DMJOHPCI_8 | 30781 | 55313 | False | Siphoviridae | VOG3616, VOG1024, VOG10944, VOG9244, VOG4599, VOG4605, VOG6163, VOG5852, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG1886, VOG5819, VOG4581, VOG0221 |
| DMJOHPCI_10 | 8338 | 34231 | False | Myoviridae | VOG7895, VOG3390, VOG7718, VOG0906, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315 |
| DMJOHPCI_10 | 45579 | 52412 | False | Siphoviridae | VOG3709, VOG11060, VOG1292, VOG1309, VOG0083, VOG1878, VOG3549 |
| DMJOHPCI_12 | 6238 | 30486 | False | Myoviridae | VOG7060, VOG0796, VOG9315, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
Phigaro v2.4.0 (Database: Jan. 2024 release)