Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| INLNBEGN_58 | 596487 | 597341 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| INLNBEGN_58 | 577818 | 579020 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| INLNBEGN_80 | 510389 | 510727 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| INLNBEGN_80 | 510072 | 510389 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| INLNBEGN_91 | 403599 | 405245 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.18 | NC_000964.3 |
| INLNBEGN_58 | 352934 | 354103 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| INLNBEGN_102 | 259270 | 261840 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| INLNBEGN_91 | 162464 | 163057 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| INLNBEGN_91 | 111987 | 113426 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| INLNBEGN_91 | 99173 | 100093 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| INLNBEGN_124 | 54028 | 55404 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.42 | 100.00 | D12567 |
| INLNBEGN_58 | 596489 | 597341 | aadK | Streptomycin | 98.71 | 99.77 | M26879 |
| INLNBEGN_91 | 99173 | 100093 | 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. |
|---|---|---|---|---|---|---|---|---|
| INLNBEGN_124 | 54031 | 55404 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.34 | 100.00 | WP_063856081.1 |
| INLNBEGN_91 | 403602 | 405245 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| INLNBEGN_58 | 596490 | 597341 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| INLNBEGN_91 | 99173 | 100090 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| INLNBEGN_124 | 51500 | 52018 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| INLNBEGN_58 | 55335 | 57932 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.48 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| INLNBEGN_69 | 109221 | 110159 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| INLNBEGN_69 | 553777 | 554958 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| INLNBEGN_69 | 110187 | 111806 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.26 | 100.00 | NP_391078 |
| INLNBEGN_69 | 113057 | 113842 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| INLNBEGN_58 | 151482 | 152123 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| INLNBEGN_69 | 552152 | 553294 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| INLNBEGN_69 | 111835 | 113031 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| INLNBEGN_58 | 8394 | 10157 | dep/capD | 0.0 | Capsule | Immune modulation | 98.87 | 100.00 | NP_389723 |
| INLNBEGN_69 | 102065 | 109201 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.82 | 100.00 | NP_391076 |
| INLNBEGN_69 | 553313 | 553762 | 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 |
|---|---|---|---|---|---|---|---|---|
| INLNBEGN_135 | 31717 | 32853 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| INLNBEGN_11 | 11283 | 10414 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| INLNBEGN_80 | 200530 | 199754 | CodY | 7.60e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| INLNBEGN_69 | 412373 | 412942 | ClpP | 5.88e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| INLNBEGN_80 | 661218 | 660826 | spxA1 | 5.98e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| INLNBEGN_80 | 661218 | 660826 | spx | 3.56e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| INLNBEGN_146 | 34655 | 34413 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| INLNBEGN_91 | 356845 | 357042 | CspA | 1.88e-31 | 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 |
|---|---|---|---|
| INLNBEGN_11 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_22 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_58 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_69 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_80 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_91 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_102 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_113 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_124 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_135 | 0.0 | 1.0 | 0.0 |
| INLNBEGN_146 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| INLNBEGN_58 | 531123 | 560972 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG0796, VOG4673, VOG4693, VOG0189, VOG11060, VOG1309 |
| INLNBEGN_58 | 776669 | 802241 | False | Myoviridae | VOG4574, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720, VOG10227, VOG0796 |
| INLNBEGN_69 | 273672 | 298940 | False | Siphoviridae | VOG4574, VOG0641, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG4544, VOG4581, VOG8909, VOG7884, VOG0275, VOG0198 |
| INLNBEGN_69 | 305610 | 310556 | False | Siphoviridae | VOG3622, VOG6495, VOG9667, VOG1563, VOG0275 |
| INLNBEGN_80 | 6982 | 9565 | False | Siphoviridae | VOG4552, VOG0181, VOG5353, VOG9667 |
| INLNBEGN_80 | 540208 | 566691 | 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 |
| INLNBEGN_113 | 112409 | 137043 | 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, VOG4841 |
Phigaro v2.4.0 (Database: Jan. 2024 release)