Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 10 | 10 | 9 | 16.76 |
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. |
|---|---|---|---|---|---|---|---|---|
| PMMEFHNH_6 | 65715 | 66053 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| PMMEFHNH_6 | 65398 | 65715 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PMMEFHNH_25 | 47841 | 50411 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PMMEFHNH_4 | 39512 | 40951 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.42 | JYFL01000006.1 |
| PMMEFHNH_10 | 8998 | 10167 | bmr | ARO:3003007 | bmr | 98.97 | 100.00 | M33768.1 |
| PMMEFHNH_63 | 219 | 1073 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| PMMEFHNH_16 | 79330 | 80706 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.35 | 100.00 | X08034 |
| PMMEFHNH_63 | 221 | 1073 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
| PMMEFHNH_4 | 66319 | 67238 | 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. |
|---|---|---|---|---|---|---|---|---|
| PMMEFHNH_16 | 79333 | 80706 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.13 | 100.00 | WP_003242953.1 |
| PMMEFHNH_63 | 222 | 1073 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| PMMEFHNH_22 | 44606 | 46246 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 97.62 | 100.00 | WP_003234144.1 |
| PMMEFHNH_16 | 76831 | 77349 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 92.49 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PMMEFHNH_33 | 3209 | 4390 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| PMMEFHNH_33 | 1584 | 2726 | capA | 0.0 | Capsule | Immune modulation | 99.65 | 100.00 | NP_391469 |
| PMMEFHNH_33 | 2745 | 3194 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PMMEFHNH_5 | 104102 | 104887 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| PMMEFHNH_41 | 21347 | 23110 | dep/capD | 0.0 | Capsule | Immune modulation | 99.26 | 100.00 | NP_389723 |
| PMMEFHNH_5 | 93110 | 100246 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.95 | 100.00 | NP_391076 |
| PMMEFHNH_5 | 102880 | 104076 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.75 | 100.00 | NP_391079 |
| PMMEFHNH_5 | 100266 | 101204 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.62 | 100.00 | NP_391077 |
| PMMEFHNH_5 | 101232 | 102851 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.90 | 100.00 | NP_391078 |
| PMMEFHNH_11 | 6678 | 7319 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 97.82 | 100.00 | NP_390062 |
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 |
|---|---|---|---|---|---|---|---|---|
| PMMEFHNH_21 | 27970 | 26834 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PMMEFHNH_55 | 4229 | 5098 | pdxS | 1.94e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| PMMEFHNH_1 | 196014 | 196790 | CodY | 2.52e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PMMEFHNH_2 | 161038 | 161607 | ClpP | 1.87e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PMMEFHNH_23 | 38631 | 38239 | spxA1 | 3.72e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PMMEFHNH_23 | 38631 | 38239 | spx | 2.22e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PMMEFHNH_26 | 20512 | 20754 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PMMEFHNH_59 | 10783 | 10980 | CspA | 4.81e-33 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| PMMEFHNH_11 | 19280 | 19474 | CspD | 6.46e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| PMMEFHNH_3 | 190892 | 191086 | CspB | 1.87e-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 |
|---|---|---|---|
| PMMEFHNH_1 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_2 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_3 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_4 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_5 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_6 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_7 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_8 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_9 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_10 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_11 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_12 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_13 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_14 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_15 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_16 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_17 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_18 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_19 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_20 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_21 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_22 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_23 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_24 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_25 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_26 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_27 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_28 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_29 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_30 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_31 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_32 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_33 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_34 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_35 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_36 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_37 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_38 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_39 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_40 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_41 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_42 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_43 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_44 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_45 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_46 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_47 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_48 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_49 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_50 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_51 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_52 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_53 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_54 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_55 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_56 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_57 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_58 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_59 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_60 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_61 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_62 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_63 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_64 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_65 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_66 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_67 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_68 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_69 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_70 | 1.0 | 0.0 | 1.0 |
| PMMEFHNH_71 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_72 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_73 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_74 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_76 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_77 | 1.0 | 0.0 | 1.0 |
| PMMEFHNH_79 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_80 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_81 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_82 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_83 | 1.0 | 0.0 | 1.0 |
| PMMEFHNH_84 | 0.0 | 1.0 | 0.0 |
| PMMEFHNH_85 | 1.0 | 0.0 | 1.0 |
| PMMEFHNH_86 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PMMEFHNH_6 | 96050 | 121905 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| PMMEFHNH_8 | 19349 | 40118 | False | Unknown | VOG8537, VOG10230, VOG5070, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG0275, VOG7930, VOG8610 |
| PMMEFHNH_8 | 103151 | 112976 | False | Siphoviridae | VOG0322, VOG7476, VOG0025, VOG4551, VOG0918 |
| PMMEFHNH_14 | 54935 | 78043 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227 |
| PMMEFHNH_27 | 8638 | 29320 | False | Siphoviridae | VOG0198, VOG7983, VOG0796, VOG10227, VOG0691, VOG0692, VOG9317, VOG4572, VOG2621, VOG0695, VOG0696, VOG0697, VOG6548, VOG10044, VOG0701, VOG9745, VOG4605, VOG4599, VOG5535, VOG10940, VOG0753, VOG0136 |
Phigaro v2.4.0 (Database: Jan. 2024 release)