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. |
|---|---|---|---|---|---|---|---|---|
| HAKLOADF_7 | 1730678 | 1731532 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| HAKLOADF_7 | 1711932 | 1713134 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| HAKLOADF_7 | 1516087 | 1517256 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| HAKLOADF_7 | 434101 | 434418 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| HAKLOADF_7 | 433763 | 434101 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| HAKLOADF_3 | 340944 | 341864 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| HAKLOADF_3 | 327623 | 329062 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| HAKLOADF_3 | 277947 | 278540 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| HAKLOADF_4 | 265210 | 267780 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| HAKLOADF_3 | 28901 | 30529 | vmlR | ARO:3004476 | vmlR | 97.97 | 99.09 | 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. |
|---|---|---|---|---|---|---|---|
| HAKLOADF_7 | 1730678 | 1731532 | aadK | Streptomycin | 99.18 | 100.00 | M26879 |
| HAKLOADF_3 | 340944 | 341864 | mph(K) | Spiramycin, Telithromycin | 98.37 | 100.00 | NC_000964 |
| HAKLOADF_9 | 36307 | 37683 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.26 | 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. |
|---|---|---|---|---|---|---|---|---|
| HAKLOADF_7 | 1730681 | 1731532 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| HAKLOADF_3 | 340947 | 341864 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| HAKLOADF_9 | 36307 | 37680 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.25 | 100.00 | WP_063856081.1 |
| HAKLOADF_3 | 28901 | 30526 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 97.97 | 98.90 | WP_003234144.1 |
| HAKLOADF_9 | 39627 | 40145 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.33 | 100.00 | WP_003242546.1 |
| HAKLOADF_7 | 1195404 | 1198001 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.94 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HAKLOADF_9 | 943192 | 944130 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| HAKLOADF_9 | 941545 | 943164 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.81 | 100.00 | NP_391078 |
| HAKLOADF_9 | 525620 | 526801 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| HAKLOADF_9 | 939509 | 940294 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| HAKLOADF_9 | 526816 | 527265 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| HAKLOADF_7 | 1315921 | 1316562 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| HAKLOADF_7 | 1140579 | 1142342 | dep/capD | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_389723 |
| HAKLOADF_9 | 527284 | 528426 | capA | 0.0 | Capsule | Immune modulation | 99.12 | 100.00 | NP_391469 |
| HAKLOADF_9 | 944150 | 951286 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.12 | 100.00 | NP_391076 |
| HAKLOADF_9 | 940320 | 941516 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
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 |
|---|---|---|---|---|---|---|---|---|
| HAKLOADF_1 | 31671 | 32807 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| HAKLOADF_6 | 11120 | 10251 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HAKLOADF_7 | 775611 | 776387 | CodY | 1.79e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HAKLOADF_9 | 684433 | 683864 | ClpP | 6.33e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HAKLOADF_7 | 274605 | 274997 | spxA1 | 1.41e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HAKLOADF_7 | 274605 | 274997 | spx | 8.41e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HAKLOADF_5 | 20513 | 20755 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HAKLOADF_3 | 83537 | 83340 | 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 |
|---|---|---|---|
| HAKLOADF_1 | 0.0 | 1.0 | 0.0 |
| HAKLOADF_3 | 0.0 | 1.0 | 0.0 |
| HAKLOADF_4 | 0.0 | 1.0 | 0.0 |
| HAKLOADF_5 | 0.0 | 1.0 | 0.0 |
| HAKLOADF_6 | 0.0 | 1.0 | 0.0 |
| HAKLOADF_7 | 0.0 | 1.0 | 0.0 |
| HAKLOADF_8 | 0.0 | 1.0 | 0.0 |
| HAKLOADF_9 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HAKLOADF_7 | 377954 | 403947 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| HAKLOADF_7 | 977212 | 1002371 | False | Siphoviridae | VOG0275, VOG3691, VOG0083, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG9583, VOG0704, VOG4586, VOG0541, VOG5910, VOG0083, VOG0801, VOG4772, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641 |
| HAKLOADF_7 | 1901637 | 1924715 | False | Myoviridae | VOG6116, VOG4574, VOG0641, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720 |
Phigaro v2.4.0 (Database: Jan. 2024 release)