Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 15 | 10 | 9 | 20.15 |
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. |
|---|---|---|---|---|---|---|---|---|
| PHKPHGCG_7 | 66758 | 67096 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| PHKPHGCG_7 | 66441 | 66758 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| PHKPHGCG_26 | 36229 | 37431 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| PHKPHGCG_22 | 18424 | 19857 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.00 | JYFL01000006.1 |
| PHKPHGCG_26 | 17813 | 18667 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| PHKPHGCG_10 | 9453 | 12023 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| PHKPHGCG_13 | 9122 | 10291 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| PHKPHGCG_47 | 2662 | 4041 | tet(K) | ARO:3000178 | tet(K) | 100.00 | 100.00 | S67449.1 |
| PHKPHGCG_52 | 339 | 986 | Staphylococcus intermedius chloramphenicol acetyltransferase | ARO:3004457 | Sint_ACT_CHL | 98.14 | 100.00 | M64281.1 |
| PHKPHGCG_67 | 166 | 903 | ErmB | ARO:3000375 | ErmB | 98.78 | 98.79 | AF242872.1 |
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. |
|---|---|---|---|---|---|---|---|
| PHKPHGCG_52 | 339 | 986 | cat(pC221) | Chloramphenicol | 100.00 | 100.00 | X02529 |
| PHKPHGCG_67 | 166 | 903 | erm(B) | Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | U18931 |
| PHKPHGCG_47 | 2662 | 4041 | tet(K) | Doxycycline, Tetracycline | 100.00 | 100.00 | U38656 |
| PHKPHGCG_17 | 34712 | 36088 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.77 | 100.00 | D12567 |
| PHKPHGCG_26 | 17813 | 18665 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| PHKPHGCG_15 | 97260 | 98179 | 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. |
|---|---|---|---|---|---|---|---|---|
| PHKPHGCG_52 | 339 | 983 | catA | type A-7 chloramphenicol O-acetyltransferase | EXACTX | 100.00 | 100.00 | WP_002489529.1 |
| PHKPHGCG_67 | 169 | 903 | erm(B) | 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) | EXACTX | 100.00 | 100.00 | WP_002292226.1 |
| PHKPHGCG_47 | 2665 | 4041 | tet(K) | tetracycline efflux MFS transporter Tet(K) | EXACTX | 100.00 | 100.00 | WP_000492283.1 |
| PHKPHGCG_245 | 2 | 424 | sat4 | streptothricin N-acetyltransferase Sat4 | PARTIAL_CONTIG_ENDX | 100.00 | 78.33 | WP_000627290.1 |
| PHKPHGCG_17 | 34712 | 36085 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| PHKPHGCG_18 | 49254 | 50894 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 97.62 | 100.00 | WP_003234144.1 |
| PHKPHGCG_26 | 17813 | 18664 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| PHKPHGCG_17 | 38063 | 38581 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PHKPHGCG_2 | 143040 | 143978 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| PHKPHGCG_3 | 310695 | 311876 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| PHKPHGCG_3 | 312359 | 313501 | capA | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391469 |
| PHKPHGCG_3 | 311891 | 312340 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| PHKPHGCG_2 | 146865 | 147650 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| PHKPHGCG_12 | 76024 | 77787 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| PHKPHGCG_2 | 135884 | 143020 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.78 | 100.00 | NP_391076 |
| PHKPHGCG_2 | 145643 | 146839 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| PHKPHGCG_8 | 32583 | 33224 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 97.82 | 100.00 | NP_390062 |
| PHKPHGCG_2 | 144006 | 145625 | 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 |
|---|---|---|---|---|---|---|---|---|
| PHKPHGCG_21 | 28134 | 26998 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| PHKPHGCG_37 | 11392 | 10523 | pdxS | 1.97e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| PHKPHGCG_1 | 150526 | 151302 | CodY | 3.02e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PHKPHGCG_5 | 150573 | 150004 | ClpP | 1.43e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PHKPHGCG_16 | 38967 | 38575 | spxA1 | 5.78e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PHKPHGCG_16 | 38967 | 38575 | spx | 3.45e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PHKPHGCG_169 | 293 | 628 | mazF | 7.01e-66 | endoribonuclease | 86.61 | 93.33 | BAF68246 |
| PHKPHGCG_25 | 20633 | 20875 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PHKPHGCG_447 | 253 | 59 | CspA | 5.57e-34 | cold shock protein | 80.00 | 98.48 | CAA62903 |
| PHKPHGCG_8 | 45076 | 45270 | CspD | 3.85e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| PHKPHGCG_8 | 45076 | 45273 | CspB | 7.99e-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. |
|---|---|---|---|---|---|---|
| PHKPHGCG_41 | 6359 | 6552 | Col(SD853) | 194 / 194 | 100.00 | NC015392 |
| PHKPHGCG_47 | 170 | 708 | rep7a | 539 / 570 | 100.00 | SAU38656 |
| PHKPHGCG_49 | 3063 | 4112 | rep21 | 1050 / 1050 | 98.86 | AM990995 |
| PHKPHGCG_49 | 1 | 855 | rep19c | 855 / 972 | 94.85 | AP012467 |
| PHKPHGCG_45 | 4626 | 5254 | repUS65 | 629 / 984 | 91.73 | AL592102 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| PHKPHGCG_1 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_2 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_3 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_4 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_5 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_6 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_7 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_8 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_9 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_10 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_11 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_12 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_13 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_14 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_15 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_16 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_17 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_18 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_19 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_20 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_21 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_22 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_23 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_24 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_25 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_26 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_27 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_28 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_29 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_30 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_31 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_32 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_33 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_34 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_35 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_36 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_37 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_38 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_39 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_40 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_41 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_42 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_43 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_44 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_45 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_46 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_47 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_48 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_49 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_50 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_51 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_52 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_53 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_55 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_56 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_57 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_58 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_59 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_60 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_61 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_62 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_63 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_65 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_67 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_69 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_70 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_71 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_72 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_73 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_74 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_75 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_76 | 1.0 | 0.0 | 1.0 |
| PHKPHGCG_77 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_78 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_79 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_80 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_81 | 0.0 | 1.0 | 0.0 |
| PHKPHGCG_82 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PHKPHGCG_1 | 269632 | 290765 | False | Siphoviridae | VOG0054, VOG8632, VOG10230, VOG5070, VOG9712, VOG5042, VOG3389, VOG5035, VOG4910, VOG9312, VOG0275, VOG7930, VOG8610, VOG7895, VOG3390, VOG7718 |
| PHKPHGCG_2 | 9615 | 31893 | False | Siphoviridae | VOG4574, VOG0136, VOG0753, VOG10940, VOG5535, VOG4599, VOG4605, VOG4545, VOG1323, VOG0725, VOG2621, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG3480, VOG1329, VOG4555, VOG7363, VOG4564, VOG0720, VOG0796 |
| PHKPHGCG_2 | 39182 | 45652 | False | Unknown | VOG0044, VOG0189, VOG1309, VOG4600, VOG1720 |
| PHKPHGCG_5 | 167428 | 187884 | False | Siphoviridae | VOG3699, VOG2613, VOG0692, VOG9317, VOG4319, VOG11074, VOG0083, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0753, VOG4574, VOG0602 |
| PHKPHGCG_7 | 95402 | 122172 | False | Myoviridae | VOG4707, VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)