Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 8 | 10 | 9 | 15.65 |
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. |
|---|---|---|---|---|---|---|---|---|
| CKHDMJND_25 | 194658 | 195827 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| CKHDMJND_80 | 48360 | 50930 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| CKHDMJND_78 | 28034 | 28627 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| CKHDMJND_127 | 21171 | 21509 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| CKHDMJND_127 | 20854 | 21171 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| CKHDMJND_106 | 7390 | 8244 | aadK | ARO:3002627 | aadK | 89.79 | 100.00 | AL009126.1 |
| CKHDMJND_74 | 1855 | 3483 | vmlR | ARO:3004476 | vmlR | 97.60 | 99.09 | 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. |
|---|---|---|---|---|---|---|---|
| CKHDMJND_106 | 7390 | 8244 | aadK | Streptomycin | 89.72 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|
| CKHDMJND_74 | 1855 | 3480 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 97.60 | 98.90 | WP_003234144.1 |
| CKHDMJND_122 | 155 | 673 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 91.91 | 100.00 | WP_003242546.1 |
| CKHDMJND_106 | 7393 | 8244 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 89.79 | 100.00 | WP_003229862.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| CKHDMJND_33 | 32622 | 33263 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| CKHDMJND_76 | 10010 | 10948 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| CKHDMJND_76 | 6327 | 7112 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| CKHDMJND_126 | 7253 | 8433 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 99.92 | NP_391471 |
| CKHDMJND_126 | 6789 | 7238 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| CKHDMJND_76 | 7138 | 8334 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| CKHDMJND_134 | 44 | 1807 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| CKHDMJND_76 | 8363 | 9982 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.89 | 100.00 | NP_391078 |
| CKHDMJND_76 | 10968 | 18104 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.88 | 100.00 | NP_391076 |
| CKHDMJND_126 | 5629 | 6770 | capA | 0.0 | Capsule | Immune modulation | 98.34 | 99.91 | NP_391469 |
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 |
|---|---|---|---|---|---|---|---|---|
| CKHDMJND_20 | 34928 | 36064 | tufA | 0.0 | elongation factor Tu | 85.22 | 95.69 | AHM69299 |
| CKHDMJND_1 | 4249 | 5118 | pdxS | 4.37e-152 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CKHDMJND_72 | 103639 | 102863 | CodY | 2.26e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CKHDMJND_24 | 36211 | 35642 | ClpP | 8.29e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CKHDMJND_18 | 166325 | 166717 | spxA1 | 1.24e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CKHDMJND_18 | 166325 | 166717 | spx | 7.40e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CKHDMJND_19 | 20532 | 20774 | SpoVG | 1.02e-38 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CKHDMJND_40 | 9822 | 10019 | CspA | 1.39e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CKHDMJND_33 | 44491 | 44685 | CspD | 3.59e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| CKHDMJND_46 | 2306 | 2500 | CspB | 3.07e-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. |
|---|---|---|---|---|---|---|
| CKHDMJND_129 | 2948 | 3135 | Col(SD853) | 188 / 194 | 82.98 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| CKHDMJND_1 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_2 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_15 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_17 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_18 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_19 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_20 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_21 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_22 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_23 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_24 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_25 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_26 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_27 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_28 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_29 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_30 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_31 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_32 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_33 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_34 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_35 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_36 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_37 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_38 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_39 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_40 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_41 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_42 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_44 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_45 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_46 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_47 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_50 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_51 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_52 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_55 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_56 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_60 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_61 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_68 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_69 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_72 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_73 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_74 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_75 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_76 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_77 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_78 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_79 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_80 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_81 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_82 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_83 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_84 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_85 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_86 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_87 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_88 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_89 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_90 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_91 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_94 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_104 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_106 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_107 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_108 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_109 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_110 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_111 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_112 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_113 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_114 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_121 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_122 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_123 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_124 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_125 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_126 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_127 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_128 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_129 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_130 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_131 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_132 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_133 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_134 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_135 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_136 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_137 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_138 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_139 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_140 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_141 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_142 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_143 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_144 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_145 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_146 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_147 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_148 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_149 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_150 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_151 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_152 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_153 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_154 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_155 | 1.0 | 0.0 | 1.0 |
| CKHDMJND_156 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_157 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_160 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_161 | 0.0 | 1.0 | 0.0 |
| CKHDMJND_166 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CKHDMJND_21 | 5527 | 27399 | False | Myoviridae | VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| CKHDMJND_36 | 3790 | 24006 | False | Siphoviridae | VOG4841, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG1266, VOG9583, VOG0704, VOG4586, VOG0541, VOG5910, VOG0801, VOG4772, VOG4626, VOG4612, VOG6243 |
| CKHDMJND_109 | 2407 | 20034 | False | Siphoviridae | VOG0198, VOG7983, VOG0796, VOG10227, VOG0691, VOG0692, VOG9317, VOG4572, VOG2621, VOG0695, VOG0696, VOG0697, VOG0698, VOG10044, VOG0701, VOG9745, VOG4605, VOG4599 |
| CKHDMJND_121 | 11493 | 20870 | False | Siphoviridae | VOG0275, VOG4602, VOG4662, VOG9667, VOG9667, VOG0650, VOG4552, VOG4600, VOG1309, VOG4566 |
| CKHDMJND_127 | 51362 | 76712 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490 |
Phigaro v2.4.0 (Database: Jan. 2024 release)