Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 9 | 18.03 |
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. |
|---|---|---|---|---|---|---|---|---|
| HGDKEKEP_47 | 109517 | 110950 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.00 | JYFL01000006.1 |
| HGDKEKEP_76 | 85360 | 87930 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| HGDKEKEP_19 | 53555 | 54475 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| HGDKEKEP_48 | 48085 | 48423 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| HGDKEKEP_48 | 47768 | 48085 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| HGDKEKEP_47 | 46431 | 47024 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| HGDKEKEP_31 | 28735 | 30378 | vmlR | ARO:3004476 | vmlR | 98.32 | 100.00 | NC_000964.3 |
| HGDKEKEP_66 | 18785 | 19954 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| HGDKEKEP_30 | 7706 | 8557 | aadK | ARO:3002627 | aadK | 98.24 | 99.65 | AL009126.1 |
| HGDKEKEP_104 | 6846 | 8048 | blt | ARO:3003006 | blt | 99.25 | 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. |
|---|---|---|---|---|---|---|---|
| HGDKEKEP_30 | 7706 | 8557 | aadK | Streptomycin | 98.48 | 99.65 | M26879 |
| HGDKEKEP_19 | 53555 | 54475 | 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. |
|---|---|---|---|---|---|---|---|---|
| HGDKEKEP_19 | 53555 | 54463 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| HGDKEKEP_30 | 7709 | 8557 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| HGDKEKEP_31 | 28735 | 30375 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 96.71 | 99.82 | WP_003234144.1 |
| HGDKEKEP_2 | 17249 | 17641 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 91.60 | 75.72 | WP_003242546.1 |
| HGDKEKEP_22 | 71026 | 73623 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.48 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HGDKEKEP_128 | 2075 | 3256 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| HGDKEKEP_8 | 36215 | 37000 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| HGDKEKEP_128 | 450 | 1592 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| HGDKEKEP_22 | 18176 | 19939 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| HGDKEKEP_8 | 32390 | 33328 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.94 | 100.00 | NP_391077 |
| HGDKEKEP_64 | 1403 | 2044 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| HGDKEKEP_128 | 1611 | 2060 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| HGDKEKEP_8 | 34993 | 36189 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.75 | 100.00 | NP_391079 |
| HGDKEKEP_8 | 25234 | 32370 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.56 | 100.00 | NP_391076 |
| HGDKEKEP_8 | 33356 | 34975 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.28 | 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 |
|---|---|---|---|---|---|---|---|---|
| HGDKEKEP_18 | 28039 | 26903 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| HGDKEKEP_46 | 4250 | 5119 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HGDKEKEP_5 | 82620 | 81844 | CodY | 1.27e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HGDKEKEP_10 | 93967 | 94536 | ClpP | 8.35e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HGDKEKEP_1 | 41581 | 41189 | spxA1 | 3.26e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HGDKEKEP_1 | 41581 | 41189 | spx | 1.95e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HGDKEKEP_34 | 20642 | 20884 | SpoVG | 6.46e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HGDKEKEP_35 | 75818 | 76015 | CspA | 3.36e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| HGDKEKEP_64 | 13275 | 13469 | CspD | 5.60e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| HGDKEKEP_17 | 25091 | 24897 | CspB | 6.82e-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. |
|---|---|---|---|---|---|---|
| HGDKEKEP_49 | 1685 | 2179 | rep21 | 495 / 717 | 90.51 | FR821780 |
| HGDKEKEP_49 | 3811 | 3975 | Col(SD853) | 165 / 194 | 86.06 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| HGDKEKEP_1 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_2 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_3 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_4 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_5 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_6 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_7 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_8 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_9 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_10 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_11 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_13 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_15 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_16 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_17 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_18 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_19 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_20 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_21 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_22 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_23 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_24 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_25 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_26 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_27 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_28 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_29 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_30 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_31 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_32 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_33 | 1.0 | 0.0 | 1.0 |
| HGDKEKEP_34 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_35 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_36 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_37 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_38 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_39 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_40 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_41 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_42 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_43 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_44 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_45 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_46 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_47 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_48 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_49 | 1.0 | 0.0 | 1.0 |
| HGDKEKEP_50 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_51 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_52 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_53 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_54 | 1.0 | 0.0 | 1.0 |
| HGDKEKEP_55 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_56 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_57 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_58 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_59 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_60 | 1.0 | 0.0 | 1.0 |
| HGDKEKEP_61 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_62 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_63 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_64 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_65 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_66 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_67 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_68 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_69 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_70 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_71 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_72 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_73 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_74 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_75 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_76 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_77 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_78 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_79 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_80 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_81 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_82 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_83 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_84 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_85 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_86 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_87 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_88 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_89 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_90 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_91 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_92 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_93 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_94 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_95 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_96 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_97 | 1.0 | 0.0 | 1.0 |
| HGDKEKEP_98 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_99 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_100 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_101 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_102 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_103 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_104 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_105 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_106 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_107 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_108 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_109 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_110 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_111 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_113 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_114 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_115 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_116 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_117 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_118 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_119 | 1.0 | 0.0 | 1.0 |
| HGDKEKEP_120 | 1.0 | 0.0 | 1.0 |
| HGDKEKEP_123 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_124 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_126 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_127 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_128 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_129 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_130 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_131 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_132 | 1.0 | 0.0 | 1.0 |
| HGDKEKEP_133 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_134 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_137 | 0.0 | 1.0 | 0.0 |
| HGDKEKEP_138 | 1.0 | 0.0 | 1.0 |
| HGDKEKEP_139 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HGDKEKEP_10 | 3991 | 10406 | True | Siphoviridae | VOG1563, VOG0275, VOG0275 |
| HGDKEKEP_43 | 2211 | 24528 | False | Myoviridae | VOG0720, VOG4555, VOG4553, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG5008, VOG0753, VOG0136, VOG4574, VOG10547 |
| HGDKEKEP_48 | 77887 | 105329 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG6875, VOG0189, VOG3490, VOG9667 |
| HGDKEKEP_56 | 466 | 32909 | False | Siphoviridae | VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841, VOG0713, VOG0198, VOG1985, VOG4693, VOG0189, VOG4566, VOG0186, VOG8233, VOG4603, VOG4552, VOG0650, VOG9667, VOG9667, VOG4602, VOG0275 |
Phigaro v2.4.0 (Database: Jan. 2024 release)