Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 9 | 18.03 |
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. |
|---|---|---|---|---|---|---|---|---|
| PDPJIKIB_23 | 425380 | 425697 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PDPJIKIB_23 | 425042 | 425380 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PDPJIKIB_37 | 284728 | 287298 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PDPJIKIB_1 | 232285 | 233487 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| PDPJIKIB_39 | 110582 | 111502 | mphK | ARO:3004541 | mphK | 99.67 | 100.00 | CP010314.1 |
| PDPJIKIB_39 | 97252 | 98691 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| PDPJIKIB_1 | 59025 | 60194 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PDPJIKIB_39 | 47603 | 48196 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| PDPJIKIB_38 | 28915 | 30561 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| PDPJIKIB_39 | 110582 | 111502 | mph(K) | Spiramycin, Telithromycin | 99.57 | 100.00 | NC_000964 |
| PDPJIKIB_40 | 159551 | 160927 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.84 | 100.00 | D12567 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PDPJIKIB_39 | 110585 | 111502 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.67 | 100.00 | WP_003246254.1 |
| PDPJIKIB_40 | 159554 | 160927 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| PDPJIKIB_38 | 28915 | 30558 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| PDPJIKIB_40 | 157065 | 157583 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| PDPJIKIB_12 | 506680 | 509268 | rphC | rifamycin-inactivating phosphotransferase RphC | INTERNAL_STOP | 80.25 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PDPJIKIB_34 | 333005 | 333790 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| PDPJIKIB_41 | 39700 | 40149 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PDPJIKIB_41 | 40164 | 41345 | capB | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_391471 |
| PDPJIKIB_3 | 26064 | 26705 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| PDPJIKIB_41 | 38539 | 39681 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| PDPJIKIB_34 | 336688 | 337626 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| PDPJIKIB_12 | 460927 | 462690 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| PDPJIKIB_34 | 337646 | 344782 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.70 | 100.00 | NP_391076 |
| PDPJIKIB_34 | 333816 | 335012 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| PDPJIKIB_34 | 335041 | 336660 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.53 | 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 |
|---|---|---|---|---|---|---|---|---|
| PDPJIKIB_6 | 27958 | 26822 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PDPJIKIB_14 | 4305 | 5174 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PDPJIKIB_12 | 241577 | 242353 | CodY | 4.18e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PDPJIKIB_34 | 58960 | 58391 | ClpP | 2.68e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PDPJIKIB_23 | 275598 | 275990 | spxA1 | 3.12e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PDPJIKIB_23 | 275598 | 275990 | spx | 1.86e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PDPJIKIB_7 | 34740 | 34498 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PDPJIKIB_38 | 75956 | 75759 | CspA | 9.27e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PDPJIKIB_3 | 38665 | 38859 | CspD | 1.01e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PDPJIKIB_23 | 30604 | 30410 | CspB | 4.50e-27 | 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 |
|---|---|---|---|
| PDPJIKIB_1 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_2 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_3 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_4 | 1.0 | 0.0 | 1.0 |
| PDPJIKIB_5 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_6 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_7 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_8 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_9 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_10 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_11 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_12 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_13 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_14 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_15 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_16 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_17 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_18 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_19 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_20 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_21 | 1.0 | 0.0 | 1.0 |
| PDPJIKIB_22 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_23 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_24 | 1.0 | 0.0 | 1.0 |
| PDPJIKIB_25 | 1.0 | 0.0 | 1.0 |
| PDPJIKIB_34 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_37 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_38 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_39 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_40 | 0.0 | 1.0 | 0.0 |
| PDPJIKIB_41 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PDPJIKIB_4 | 23116 | 74927 | False | Myoviridae | VOG10599, VOG7848, VOG8611, VOG10598, VOG9245, VOG0058, VOG5216, VOG7814, VOG5821, VOG0678, VOG0048, VOG4570, VOG5722, VOG7724, VOG5721, VOG6031, VOG6524, VOG6246, VOG6941, VOG6036, VOG6472, VOG7629, VOG7628, VOG6940, VOG5534, VOG8610, VOG8609, VOG0275, VOG3389, VOG5242, VOG9244, VOG3432, VOG5173, VOG0647, VOG7230, VOG4615, VOG9091, VOG0703 |
| PDPJIKIB_4 | 125353 | 135072 | False | Myoviridae / Siphoviridae | VOG0154, VOG0982, VOG0677, VOG0918, VOG5263, VOG4551, VOG0025, VOG7627, VOG9220 |
| PDPJIKIB_8 | 4367 | 10796 | False | Siphoviridae | VOG3390, VOG4626, VOG9712, VOG5042 |
| PDPJIKIB_23 | 370281 | 395811 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG7895, VOG0753 |
| PDPJIKIB_34 | 437529 | 440366 | False | Unknown | VOG4600, VOG1309 |
Phigaro v2.4.0 (Database: Jan. 2024 release)