Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 9 | 18.71 |
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. |
|---|---|---|---|---|---|---|---|---|
| HAAFFPIK_3 | 366652 | 367821 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| HAAFFPIK_6 | 280470 | 281390 | mphK | ARO:3004541 | mphK | 98.04 | 100.00 | CP010314.1 |
| HAAFFPIK_6 | 267140 | 268579 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| HAAFFPIK_2 | 225204 | 225542 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| HAAFFPIK_2 | 224887 | 225204 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| HAAFFPIK_6 | 217460 | 218053 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| HAAFFPIK_9 | 64306 | 65949 | vmlR | ARO:3004476 | vmlR | 98.17 | 100.00 | NC_000964.3 |
| HAAFFPIK_4 | 51392 | 52246 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| HAAFFPIK_4 | 32621 | 33823 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| HAAFFPIK_8 | 27375 | 29945 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 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. |
|---|---|---|---|---|---|---|---|
| HAAFFPIK_4 | 51392 | 52246 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| HAAFFPIK_6 | 280470 | 281390 | mph(K) | Spiramycin, Telithromycin | 97.94 | 100.00 | NC_000964 |
| HAAFFPIK_1 | 674655 | 676031 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 96.37 | 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. |
|---|---|---|---|---|---|---|---|---|
| HAAFFPIK_4 | 51395 | 52246 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| HAAFFPIK_9 | 64309 | 65949 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.17 | 100.00 | WP_003234144.1 |
| HAAFFPIK_6 | 280473 | 281390 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.04 | 100.00 | WP_003246254.1 |
| HAAFFPIK_1 | 674658 | 676031 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 97.16 | 100.00 | WP_063856081.1 |
| HAAFFPIK_1 | 672141 | 672659 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| HAAFFPIK_3 | 60837 | 63434 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HAAFFPIK_3 | 163859 | 164500 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| HAAFFPIK_1 | 192550 | 193731 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| HAAFFPIK_7 | 101894 | 109030 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.61 | 100.00 | NP_391076 |
| HAAFFPIK_1 | 192086 | 192535 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| HAAFFPIK_3 | 8999 | 10762 | dep/capD | 0.0 | Capsule | Immune modulation | 99.55 | 100.00 | NP_389723 |
| HAAFFPIK_7 | 109050 | 109988 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| HAAFFPIK_7 | 112886 | 113671 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| HAAFFPIK_1 | 190925 | 192067 | capA | 0.0 | Capsule | Immune modulation | 99.12 | 100.00 | NP_391469 |
| HAAFFPIK_7 | 110016 | 111635 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.01 | 100.00 | NP_391078 |
| HAAFFPIK_7 | 111664 | 112860 | 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 |
|---|---|---|---|---|---|---|---|---|
| HAAFFPIK_10 | 28147 | 27011 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| HAAFFPIK_12 | 11295 | 10426 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HAAFFPIK_5 | 294886 | 294110 | CodY | 3.14e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HAAFFPIK_1 | 33987 | 34556 | ClpP | 4.29e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HAAFFPIK_2 | 373680 | 373288 | spxA1 | 4.14e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HAAFFPIK_2 | 373680 | 373288 | spx | 2.47e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HAAFFPIK_11 | 20607 | 20849 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HAAFFPIK_9 | 5634 | 5831 | CspA | 4.10e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| HAAFFPIK_3 | 176460 | 176654 | CspD | 3.24e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| HAAFFPIK_2 | 616899 | 617093 | CspB | 5.96e-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 |
|---|---|---|---|
| HAAFFPIK_1 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_2 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_3 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_4 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_5 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_6 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_7 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_8 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_9 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_10 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_11 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_12 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_13 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_14 | 0.0 | 1.0 | 0.0 |
| HAAFFPIK_15 | 1.0 | 0.0 | 1.0 |
| HAAFFPIK_16 | 1.0 | 0.0 | 1.0 |
| HAAFFPIK_17 | 1.0 | 0.0 | 1.0 |
| HAAFFPIK_18 | 1.0 | 0.0 | 1.0 |
| HAAFFPIK_21 | 1.0 | 0.0 | 1.0 |
| HAAFFPIK_22 | 1.0 | 0.0 | 1.0 |
| HAAFFPIK_23 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HAAFFPIK_2 | 256500 | 282969 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4843, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)