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. |
|---|---|---|---|---|---|---|---|---|
| PGHHMJKG_34 | 85262 | 87832 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PGHHMJKG_28 | 84864 | 85202 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| PGHHMJKG_28 | 84547 | 84864 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PGHHMJKG_83 | 69105 | 70274 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PGHHMJKG_36 | 41818 | 42411 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| PGHHMJKG_46 | 22442 | 23362 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| PGHHMJKG_10 | 12927 | 14570 | vmlR | ARO:3004476 | vmlR | 98.32 | 100.00 | NC_000964.3 |
| PGHHMJKG_105 | 9382 | 10815 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.00 | JYFL01000006.1 |
| PGHHMJKG_18 | 7706 | 8557 | aadK | ARO:3002627 | aadK | 98.24 | 99.65 | AL009126.1 |
| PGHHMJKG_92 | 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. |
|---|---|---|---|---|---|---|---|
| PGHHMJKG_18 | 7706 | 8557 | aadK | Streptomycin | 98.48 | 99.65 | M26879 |
| PGHHMJKG_46 | 22442 | 23362 | 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. |
|---|---|---|---|---|---|---|---|---|
| PGHHMJKG_46 | 22442 | 23350 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| PGHHMJKG_18 | 7709 | 8557 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| PGHHMJKG_10 | 12930 | 14570 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 96.71 | 99.82 | WP_003234144.1 |
| PGHHMJKG_5 | 17436 | 17828 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 91.60 | 75.72 | WP_003242546.1 |
| PGHHMJKG_8 | 5529 | 8126 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PGHHMJKG_118 | 1857 | 3038 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| PGHHMJKG_7 | 16149 | 16934 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| PGHHMJKG_118 | 232 | 1374 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| PGHHMJKG_8 | 59213 | 60976 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| PGHHMJKG_7 | 19821 | 20759 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.94 | 100.00 | NP_391077 |
| PGHHMJKG_30 | 58845 | 59486 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| PGHHMJKG_118 | 1393 | 1842 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| PGHHMJKG_7 | 16960 | 18156 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.75 | 100.00 | NP_391079 |
| PGHHMJKG_7 | 20779 | 27915 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.57 | 100.00 | NP_391076 |
| PGHHMJKG_7 | 18174 | 19793 | 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 |
|---|---|---|---|---|---|---|---|---|
| PGHHMJKG_12 | 28149 | 27013 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PGHHMJKG_70 | 11443 | 10574 | pdxS | 1.15e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PGHHMJKG_15 | 82818 | 82042 | CodY | 1.27e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PGHHMJKG_22 | 45184 | 44615 | ClpP | 7.58e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PGHHMJKG_49 | 23484 | 23876 | spxA1 | 4.13e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PGHHMJKG_49 | 23484 | 23876 | spx | 2.46e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PGHHMJKG_31 | 26883 | 26641 | SpoVG | 6.43e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PGHHMJKG_60 | 2120 | 1923 | CspA | 3.37e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PGHHMJKG_30 | 70717 | 70911 | CspD | 9.12e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PGHHMJKG_33 | 49380 | 49574 | CspB | 7.29e-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. |
|---|---|---|---|---|---|---|
| PGHHMJKG_20 | 1170 | 1664 | rep21 | 495 / 717 | 90.51 | FR821780 |
| PGHHMJKG_20 | 3296 | 3460 | 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 |
|---|---|---|---|
| PGHHMJKG_1 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_2 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_3 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_4 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_5 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_6 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_7 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_8 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_9 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_10 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_11 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_12 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_13 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_14 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_15 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_16 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_17 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_18 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_19 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_20 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_21 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_22 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_23 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_24 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_25 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_26 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_27 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_28 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_29 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_30 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_31 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_32 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_33 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_34 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_35 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_36 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_37 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_38 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_39 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_40 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_41 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_42 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_43 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_44 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_45 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_46 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_47 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_48 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_49 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_50 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_51 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_52 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_53 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_54 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_55 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_56 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_57 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_58 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_59 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_60 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_61 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_62 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_63 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_65 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_66 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_67 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_68 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_69 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_70 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_71 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_72 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_73 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_74 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_75 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_76 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_77 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_78 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_79 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_81 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_82 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_83 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_84 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_85 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_86 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_87 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_88 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_89 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_90 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_91 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_92 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_93 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_94 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_96 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_97 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_98 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_100 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_101 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_102 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_103 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_104 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_105 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_106 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_108 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_109 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_110 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_111 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_112 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_113 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_114 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_115 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_116 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_117 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_118 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_119 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_121 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_122 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_123 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_124 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_125 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_126 | 0.0 | 1.0 | 0.0 |
| PGHHMJKG_131 | 1.0 | 0.0 | 1.0 |
| PGHHMJKG_133 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PGHHMJKG_3 | 10428 | 20341 | False | Siphoviridae | VOG6513, VOG0275, VOG4602, VOG9667, VOG9667, VOG0650, VOG4552, VOG4603, VOG8233, VOG0186 |
| PGHHMJKG_3 | 22336 | 42871 | False | Siphoviridae | VOG1985, VOG0198, VOG0713, VOG4841, VOG4581, VOG1886, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801 |
| PGHHMJKG_6 | 13367 | 39530 | False | Myoviridae | VOG0753, 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)