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. |
|---|---|---|---|---|---|---|---|---|
| PNEKKDIO_5 | 124823 | 127393 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PNEKKDIO_4 | 94864 | 95784 | mphK | ARO:3004541 | mphK | 98.04 | 100.00 | CP010314.1 |
| PNEKKDIO_4 | 81530 | 82969 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| PNEKKDIO_4 | 31847 | 32440 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| PNEKKDIO_38 | 31064 | 32233 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PNEKKDIO_9 | 30948 | 32591 | vmlR | ARO:3004476 | vmlR | 98.17 | 100.00 | NC_000964.3 |
| PNEKKDIO_45 | 12655 | 12972 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PNEKKDIO_45 | 12317 | 12655 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| PNEKKDIO_55 | 11585 | 12439 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| PNEKKDIO_63 | 6221 | 7423 | blt | ARO:3003006 | blt | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| PNEKKDIO_55 | 11587 | 12439 | aadK | Streptomycin | 98.71 | 99.77 | M26879 |
| PNEKKDIO_24 | 36536 | 37912 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.47 | 100.00 | D12567 |
| PNEKKDIO_4 | 94864 | 95784 | mph(K) | Spiramycin, Telithromycin | 97.94 | 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. |
|---|---|---|---|---|---|---|---|---|
| PNEKKDIO_55 | 11588 | 12439 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| PNEKKDIO_24 | 36536 | 37909 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.25 | 100.00 | WP_063856081.1 |
| PNEKKDIO_9 | 30948 | 32588 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.17 | 100.00 | WP_003234144.1 |
| PNEKKDIO_4 | 94867 | 95784 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.04 | 100.00 | WP_003246254.1 |
| PNEKKDIO_24 | 39920 | 40438 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| PNEKKDIO_16 | 40883 | 43480 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PNEKKDIO_15 | 77174 | 78793 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.81 | 100.00 | NP_391078 |
| PNEKKDIO_15 | 78821 | 79759 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.79 | 100.00 | NP_391077 |
| PNEKKDIO_20 | 64789 | 65970 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PNEKKDIO_34 | 14047 | 14688 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| PNEKKDIO_15 | 75138 | 75923 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| PNEKKDIO_15 | 79779 | 86915 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.27 | 100.00 | NP_391076 |
| PNEKKDIO_17 | 78504 | 80267 | dep/capD | 0.0 | Capsule | Immune modulation | 99.26 | 100.00 | NP_389723 |
| PNEKKDIO_20 | 63164 | 64306 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| PNEKKDIO_20 | 64325 | 64774 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| PNEKKDIO_15 | 75949 | 77145 | 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 |
|---|---|---|---|---|---|---|---|---|
| PNEKKDIO_36 | 8385 | 9521 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PNEKKDIO_57 | 4548 | 5417 | pdxS | 9.99e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PNEKKDIO_6 | 95385 | 96161 | CodY | 1.13e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PNEKKDIO_8 | 106132 | 106701 | ClpP | 8.12e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PNEKKDIO_10 | 29081 | 28689 | spxA1 | 7.84e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PNEKKDIO_10 | 29081 | 28689 | spx | 4.67e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PNEKKDIO_30 | 35186 | 34944 | SpoVG | 7.00e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PNEKKDIO_9 | 85587 | 85390 | CspA | 5.41e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PNEKKDIO_34 | 2084 | 1890 | CspD | 2.33e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PNEKKDIO_3 | 23206 | 23012 | CspB | 1.58e-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 |
|---|---|---|---|
| PNEKKDIO_1 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_2 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_3 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_4 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_5 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_6 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_7 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_8 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_9 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_10 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_11 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_12 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_13 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_14 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_15 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_16 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_17 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_18 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_19 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_20 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_21 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_22 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_23 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_24 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_25 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_26 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_27 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_28 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_29 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_30 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_31 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_32 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_33 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_34 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_35 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_36 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_37 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_38 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_39 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_40 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_41 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_42 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_43 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_44 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_45 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_46 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_47 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_48 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_49 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_50 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_51 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_52 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_53 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_54 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_55 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_56 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_57 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_58 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_59 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_60 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_61 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_62 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_63 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_64 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_65 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_66 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_67 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_68 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_69 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_70 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_71 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_72 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_73 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_74 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_75 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_76 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_77 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_78 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_79 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_80 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_81 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_82 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_83 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_84 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_85 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_86 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_87 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_88 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_89 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_91 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_92 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_93 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_95 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_96 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_97 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_98 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_99 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_100 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_101 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_102 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_103 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_104 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_105 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_106 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_107 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_108 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_109 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_111 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_112 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_113 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_115 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_116 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_117 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_118 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_119 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_120 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_121 | 1.0 | 0.0 | 1.0 |
| PNEKKDIO_122 | 0.0 | 1.0 | 0.0 |
| PNEKKDIO_123 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PNEKKDIO_22 | 19048 | 41560 | False | Siphoviridae | VOG4574, VOG0136, VOG0753, VOG5535, VOG4599, VOG4605, VOG4545, VOG0725, VOG2621, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG3480, VOG1329, VOG4555, VOG4564, VOG0720, VOG10227, VOG0796 |
| PNEKKDIO_44 | 17477 | 28058 | False | Myoviridae | VOG4705, VOG4612, VOG5384, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865 |
Phigaro v2.4.0 (Database: Jan. 2024 release)