Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 14 | 10 | 8 | 18.97 |
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. |
|---|---|---|---|---|---|---|---|---|
| EPNHKGJO_202 | 105104 | 106537 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.00 | JYFL01000006.1 |
| EPNHKGJO_72 | 100637 | 101806 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| EPNHKGJO_135 | 86862 | 87179 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| EPNHKGJO_135 | 86524 | 86862 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| EPNHKGJO_192 | 30667 | 31521 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| EPNHKGJO_192 | 11904 | 13106 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| EPNHKGJO_196 | 9312 | 11882 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| EPNHKGJO_140 | 6310 | 7155 | PC1 beta-lactamase (blaZ) | ARO:3000621 | PC1_blaZ | 96.44 | 100.00 | CP000732.1 |
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. |
|---|---|---|---|---|---|---|---|
| EPNHKGJO_140 | 6310 | 7155 | blaZ | Amoxicillin, Ampicillin, Penicillin, Piperacillin | 100.00 | 100.00 | NZ_CAVU010000015 |
| EPNHKGJO_52 | 24745 | 26121 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.77 | 100.00 | D12567 |
| EPNHKGJO_192 | 30669 | 31521 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| EPNHKGJO_202 | 78827 | 79746 | mph(K) | Spiramycin, Telithromycin | 97.61 | 99.89 | 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. |
|---|---|---|---|---|---|---|---|---|
| EPNHKGJO_140 | 6313 | 7155 | blaZ | penicillin-hydrolyzing class A beta-lactamase BlaZ | BLASTX | 99.64 | 100.00 | WP_000733289.1 |
| EPNHKGJO_140 | 9009 | 9386 | blaI | penicillinase repressor BlaI | BLASTX | 99.21 | 100.00 | WP_001284656.1 |
| EPNHKGJO_52 | 24748 | 26121 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| EPNHKGJO_74 | 9664 | 11304 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 97.62 | 100.00 | WP_003234144.1 |
| EPNHKGJO_192 | 30670 | 31521 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| EPNHKGJO_140 | 7262 | 9016 | blaR1 | beta-lactam sensor/signal transducer BlaR1 | BLASTX | 95.56 | 100.00 | WP_001096386.1 |
| EPNHKGJO_52 | 22252 | 22770 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| EPNHKGJO_44 | 99631 | 100569 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| EPNHKGJO_41 | 3229 | 4410 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| EPNHKGJO_41 | 1604 | 2746 | capA | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391469 |
| EPNHKGJO_41 | 2765 | 3214 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| EPNHKGJO_44 | 103456 | 104241 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| EPNHKGJO_87 | 43560 | 45323 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| EPNHKGJO_44 | 92475 | 99611 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.78 | 100.00 | NP_391076 |
| EPNHKGJO_44 | 102234 | 103430 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| EPNHKGJO_83 | 48177 | 48818 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 97.82 | 100.00 | NP_390062 |
| EPNHKGJO_44 | 100597 | 102216 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.78 | 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 |
|---|---|---|---|---|---|---|---|---|
| EPNHKGJO_136 | 31658 | 32794 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| EPNHKGJO_172 | 3234 | 2365 | pdxS | 7.83e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| EPNHKGJO_188 | 150418 | 151194 | CodY | 2.10e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| EPNHKGJO_203 | 6901 | 7470 | ClpP | 8.75e-101 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| EPNHKGJO_38 | 51780 | 52172 | spxA1 | 5.40e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| EPNHKGJO_38 | 51780 | 52172 | spx | 3.22e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| EPNHKGJO_82 | 34651 | 34409 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| EPNHKGJO_168 | 3980 | 4177 | CspA | 1.63e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| EPNHKGJO_83 | 36325 | 36131 | CspD | 1.62e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| EPNHKGJO_83 | 36325 | 36128 | CspB | 3.35e-28 | 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. |
|---|---|---|---|---|---|---|
| EPNHKGJO_51 | 165 | 358 | Col(SD853) | 194 / 194 | 100.00 | NC015392 |
| EPNHKGJO_140 | 17608 | 18351 | rep16 | 744 / 744 | 100.00 | BX571858 |
| EPNHKGJO_140 | 19642 | 20502 | rep5a | 861 / 861 | 100.00 | AP003139 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| EPNHKGJO_1 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_6 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_7 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_10 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_38 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_39 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_40 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_41 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_42 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_43 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_44 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_45 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_47 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_48 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_49 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_51 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_52 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_53 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_54 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_55 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_56 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_58 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_59 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_60 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_61 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_62 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_63 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_64 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_65 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_66 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_67 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_69 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_70 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_71 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_72 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_73 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_74 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_75 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_76 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_77 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_78 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_80 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_81 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_82 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_83 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_84 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_87 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_88 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_89 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_91 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_92 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_96 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_97 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_98 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_105 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_112 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_127 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_128 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_129 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_130 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_131 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_132 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_133 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_135 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_136 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_137 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_138 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_139 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_140 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_142 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_167 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_168 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_169 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_170 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_171 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_172 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_173 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_174 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_175 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_176 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_184 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_188 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_189 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_190 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_191 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_192 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_193 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_194 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_195 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_196 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_197 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_198 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_199 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_200 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_201 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_202 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_203 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_204 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_205 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_206 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_207 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_208 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_209 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_210 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_211 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_212 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_213 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_214 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_215 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_216 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_217 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_218 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_219 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_220 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_221 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_222 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_223 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_224 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_225 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_226 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_227 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_228 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_229 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_230 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_231 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_232 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_233 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_234 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_235 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_236 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_237 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_238 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_239 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_240 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_241 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_242 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_243 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_244 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_245 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_247 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_248 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_252 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_253 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_255 | 0.0 | 1.0 | 0.0 |
| EPNHKGJO_256 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_258 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_263 | 1.0 | 0.0 | 1.0 |
| EPNHKGJO_265 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| EPNHKGJO_58 | 16401 | 31447 | False | Siphoviridae | VOG6154, VOG0519, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG5660, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801 |
| EPNHKGJO_61 | 1977 | 25491 | False | Myoviridae | VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG0796, VOG4673, VOG4567, VOG4693 |
| EPNHKGJO_65 | 3372 | 11865 | False | Siphoviridae | VOG9667, VOG8241, VOG3549, VOG1878, VOG0083, VOG1309, VOG1292, VOG11060, VOG3709, VOG0025 |
| EPNHKGJO_65 | 18476 | 44233 | False | Myoviridae | VOG4618, VOG4567, VOG1328, VOG9315, VOG4773, VOG4688, VOG4685, VOG0749, VOG1581, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| EPNHKGJO_135 | 31448 | 58218 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136 |
| EPNHKGJO_195 | 7421 | 29742 | False | Siphoviridae | VOG0602, VOG4574, VOG5221, VOG4705, VOG4612, VOG4660, VOG4619, VOG0801, VOG0083, VOG11074, VOG4319, VOG9317, VOG0692, VOG2613, VOG3699, VOG5023, VOG0275 |
Phigaro v2.4.0 (Database: Jan. 2024 release)