Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 10 | 10 | 9 | 16.76 |
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. |
|---|---|---|---|---|---|---|---|---|
| PCADNPNA_18 | 61079 | 62281 | blt | ARO:3003006 | blt | 98.00 | 100.00 | L32599.1 |
| PCADNPNA_18 | 44330 | 45184 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| PCADNPNA_6 | 41013 | 41933 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| PCADNPNA_12 | 40711 | 41049 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| PCADNPNA_12 | 40394 | 40711 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PCADNPNA_6 | 27679 | 29118 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.42 | JYFL01000006.1 |
| PCADNPNA_14 | 27473 | 30043 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| PCADNPNA_50 | 18944 | 19537 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| PCADNPNA_42 | 5731 | 7377 | vmlR | ARO:3004476 | vmlR | 98.36 | 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. |
|---|---|---|---|---|---|---|---|
| PCADNPNA_18 | 44330 | 45184 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| PCADNPNA_6 | 41013 | 41933 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| PCADNPNA_6 | 41025 | 41933 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| PCADNPNA_18 | 44330 | 45181 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| PCADNPNA_42 | 5734 | 7377 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.36 | 100.00 | WP_003234144.1 |
| PCADNPNA_13 | 40684 | 41202 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PCADNPNA_1 | 29917 | 31098 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| PCADNPNA_25 | 23059 | 23844 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PCADNPNA_1 | 28292 | 29434 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| PCADNPNA_25 | 27700 | 34836 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.30 | 100.00 | NP_391076 |
| PCADNPNA_49 | 1501 | 3264 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| PCADNPNA_25 | 26742 | 27680 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.04 | 100.00 | NP_391077 |
| PCADNPNA_25 | 23870 | 25066 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| PCADNPNA_3 | 143949 | 144590 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| PCADNPNA_1 | 29453 | 29902 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| PCADNPNA_25 | 25095 | 26714 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.73 | 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 |
|---|---|---|---|---|---|---|---|---|
| PCADNPNA_24 | 32051 | 33187 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PCADNPNA_52 | 4356 | 5225 | pdxS | 1.96e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| PCADNPNA_2 | 93912 | 93136 | CodY | 1.99e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PCADNPNA_34 | 4454 | 5023 | ClpP | 2.96e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PCADNPNA_21 | 41557 | 41165 | spxA1 | 4.13e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PCADNPNA_21 | 41557 | 41165 | spx | 2.46e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PCADNPNA_31 | 20607 | 20849 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PCADNPNA_32 | 13827 | 14024 | CspA | 2.35e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PCADNPNA_3 | 132719 | 132525 | CspD | 1.09e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PCADNPNA_37 | 14011 | 14205 | CspB | 4.23e-28 | 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. |
|---|---|---|---|---|---|---|
| PCADNPNA_62 | 3734 | 3901 | Col(SD853) | 168 / 194 | 86.90 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| PCADNPNA_1 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_2 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_3 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_4 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_5 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_6 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_7 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_8 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_9 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_10 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_11 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_12 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_13 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_14 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_15 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_16 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_17 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_18 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_19 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_20 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_21 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_22 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_23 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_24 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_25 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_26 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_27 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_28 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_29 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_30 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_31 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_32 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_33 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_34 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_35 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_36 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_37 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_38 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_39 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_40 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_41 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_42 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_43 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_44 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_45 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_46 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_47 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_48 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_49 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_50 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_51 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_52 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_53 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_54 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_55 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_56 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_57 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_58 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_59 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_60 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_61 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_62 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_63 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_64 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_65 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_66 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_67 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_68 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_69 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_70 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_71 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_72 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_73 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_74 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_75 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_76 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_79 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_80 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_81 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_82 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_84 | 1.0 | 0.0 | 1.0 |
| PCADNPNA_85 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_86 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_87 | 0.0 | 1.0 | 0.0 |
| PCADNPNA_89 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PCADNPNA_11 | 92652 | 103182 | True | Siphoviridae | VOG3490, VOG0275, VOG0275, VOG1563, VOG9667, VOG9667, VOG7581, VOG4566, VOG0189, VOG6587 |
| PCADNPNA_12 | 70513 | 97196 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4843, VOG0189, VOG3490 |
| PCADNPNA_33 | 92 | 26938 | False | Siphoviridae | VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3644, VOG4544, VOG4581, VOG7403, VOG4841, VOG0198, VOG7372, VOG2752, VOG4606, VOG1227, VOG1936, VOG0535, VOG0650 |
Phigaro v2.4.0 (Database: Jan. 2024 release)