Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| PAAFKCII_15 | 86850 | 88289 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| PAAFKCII_21 | 83698 | 84867 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PAAFKCII_15 | 74036 | 74956 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
| PAAFKCII_37 | 70655 | 70993 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PAAFKCII_37 | 70338 | 70655 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PAAFKCII_10 | 31842 | 33488 | vmlR | ARO:3004476 | vmlR | 99.27 | 100.18 | NC_000964.3 |
| PAAFKCII_7 | 27321 | 29891 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PAAFKCII_20 | 20091 | 20684 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| PAAFKCII_39 | 10532 | 11386 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| PAAFKCII_28 | 3384 | 4586 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
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. |
|---|---|---|---|---|---|---|---|
| PAAFKCII_15 | 74036 | 74956 | mph(K) | Spiramycin, Telithromycin | 99.24 | 100.00 | NC_000964 |
| PAAFKCII_39 | 10532 | 11386 | aadK | Streptomycin | 98.48 | 100.00 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PAAFKCII_10 | 31842 | 33485 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.27 | 100.00 | WP_003234144.1 |
| PAAFKCII_15 | 74036 | 74953 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| PAAFKCII_39 | 10535 | 11386 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| PAAFKCII_22 | 21137 | 21655 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.64 | 100.00 | WP_003242546.1 |
| PAAFKCII_38 | 1219 | 3816 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PAAFKCII_18 | 164226 | 165407 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PAAFKCII_2 | 34914 | 35555 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| PAAFKCII_14 | 73157 | 74353 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.42 | 100.00 | NP_391079 |
| PAAFKCII_14 | 72346 | 73131 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| PAAFKCII_58 | 30649 | 32412 | dep/capD | 0.0 | Capsule | Immune modulation | 99.09 | 100.00 | NP_389723 |
| PAAFKCII_18 | 165890 | 167032 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| PAAFKCII_14 | 76987 | 84123 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.70 | 100.00 | NP_391076 |
| PAAFKCII_18 | 165422 | 165871 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| PAAFKCII_14 | 76029 | 76967 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.62 | 100.00 | NP_391077 |
| PAAFKCII_14 | 74382 | 76001 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| PAAFKCII_12 | 31708 | 32844 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PAAFKCII_43 | 4334 | 5203 | pdxS | 4.72e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PAAFKCII_32 | 1265 | 489 | CodY | 1.77e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PAAFKCII_8 | 141292 | 140723 | ClpP | 2.04e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PAAFKCII_19 | 37350 | 36958 | spxA1 | 1.91e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PAAFKCII_19 | 37350 | 36958 | spx | 1.14e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PAAFKCII_42 | 20549 | 20791 | SpoVG | 4.74e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PAAFKCII_10 | 79814 | 79617 | CspA | 3.83e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PAAFKCII_2 | 46786 | 46980 | CspD | 5.92e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| PAAFKCII_2 | 46786 | 46983 | CspB | 1.23e-27 | cold shock protein | 80.30 | 100.00 | 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 |
|---|---|---|---|
| PAAFKCII_1 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_2 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_3 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_4 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_5 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_6 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_7 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_8 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_9 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_10 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_12 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_13 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_14 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_15 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_16 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_17 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_18 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_19 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_20 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_21 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_22 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_23 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_24 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_25 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_26 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_28 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_29 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_30 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_31 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_32 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_33 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_34 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_35 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_36 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_37 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_38 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_39 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_40 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_41 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_42 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_43 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_44 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_45 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_46 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_47 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_49 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_50 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_51 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_52 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_53 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_54 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_55 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_57 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_58 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_59 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_60 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_61 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_62 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_63 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_65 | 0.0 | 1.0 | 0.0 |
| PAAFKCII_66 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PAAFKCII_37 | 100232 | 107307 | False | Myoviridae | VOG0136, VOG0753, VOG7895, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885 |
| PAAFKCII_45 | 53084 | 63412 | False | Siphoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749 |
Phigaro v2.4.0 (Database: Jan. 2024 release)