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. |
|---|---|---|---|---|---|---|---|---|
| HFAPHBKH_15 | 101670 | 101987 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| HFAPHBKH_15 | 101332 | 101670 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| HFAPHBKH_35 | 55566 | 56420 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| HFAPHBKH_11 | 40914 | 41834 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| HFAPHBKH_11 | 27580 | 29019 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.42 | JYFL01000006.1 |
| HFAPHBKH_2 | 18978 | 19571 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| HFAPHBKH_23 | 13029 | 14675 | vmlR | ARO:3004476 | vmlR | 98.36 | 100.18 | NC_000964.3 |
| HFAPHBKH_36 | 8686 | 9888 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| HFAPHBKH_10 | 144 | 2714 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
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. |
|---|---|---|---|---|---|---|---|
| HFAPHBKH_29 | 16399 | 17536 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 99.21 | 82.64 | X08034 |
| HFAPHBKH_35 | 55566 | 56420 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| HFAPHBKH_11 | 40914 | 41834 | 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. |
|---|---|---|---|---|---|---|---|---|
| HFAPHBKH_11 | 40926 | 41834 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| HFAPHBKH_35 | 55566 | 56417 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| HFAPHBKH_23 | 13032 | 14675 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.36 | 100.00 | WP_003234144.1 |
| HFAPHBKH_29 | 16382 | 17536 | tet(L) | tetracycline efflux MFS transporter Tet(L) | PARTIALX | 97.66 | 84.06 | WP_003242953.1 |
| HFAPHBKH_29 | 14414 | 14932 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| HFAPHBKH_40 | 135139 | 137736 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HFAPHBKH_1 | 21893 | 23074 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| HFAPHBKH_1 | 23557 | 24699 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| HFAPHBKH_6 | 6420 | 7205 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| HFAPHBKH_40 | 82301 | 84064 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| HFAPHBKH_6 | 10092 | 11030 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.94 | 100.00 | NP_391077 |
| HFAPHBKH_26 | 143840 | 144481 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| HFAPHBKH_1 | 23089 | 23538 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| HFAPHBKH_6 | 11050 | 18186 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.61 | 100.00 | NP_391076 |
| HFAPHBKH_6 | 7231 | 8427 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| HFAPHBKH_6 | 8445 | 10064 | 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 |
|---|---|---|---|---|---|---|---|---|
| HFAPHBKH_30 | 27938 | 26802 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| HFAPHBKH_53 | 4491 | 5360 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HFAPHBKH_12 | 98117 | 97341 | CodY | 1.74e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HFAPHBKH_1 | 167675 | 167106 | ClpP | 1.74e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HFAPHBKH_3 | 42097 | 41705 | spxA1 | 4.17e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HFAPHBKH_3 | 42097 | 41705 | spx | 2.48e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HFAPHBKH_13 | 11198 | 11440 | SpoVG | 6.22e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HFAPHBKH_5 | 33196 | 32999 | CspA | 1.66e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| HFAPHBKH_26 | 132611 | 132417 | CspD | 1.45e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| HFAPHBKH_44 | 1499 | 1693 | CspB | 2.89e-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. |
|---|---|---|---|---|---|---|
| HFAPHBKH_43 | 4946 | 5139 | Col(SD853) | 194 / 194 | 97.94 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| HFAPHBKH_1 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_2 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_3 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_4 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_5 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_6 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_7 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_8 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_9 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_10 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_11 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_12 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_13 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_15 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_16 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_17 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_18 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_19 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_20 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_21 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_22 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_23 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_24 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_25 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_26 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_27 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_28 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_29 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_30 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_31 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_32 | 1.0 | 0.0 | 1.0 |
| HFAPHBKH_33 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_34 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_35 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_36 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_37 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_38 | 1.0 | 0.0 | 1.0 |
| HFAPHBKH_39 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_40 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_41 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_42 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_43 | 1.0 | 0.0 | 1.0 |
| HFAPHBKH_44 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_45 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_47 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_48 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_49 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_50 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_51 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_53 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_55 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_56 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_57 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_58 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_59 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_60 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_61 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_62 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_63 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_64 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_65 | 1.0 | 0.0 | 1.0 |
| HFAPHBKH_66 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_67 | 1.0 | 0.0 | 1.0 |
| HFAPHBKH_68 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_69 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_71 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_72 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_73 | 1.0 | 0.0 | 1.0 |
| HFAPHBKH_74 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_75 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_76 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_77 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_79 | 0.0 | 1.0 | 0.0 |
| HFAPHBKH_80 | 1.0 | 0.0 | 1.0 |
| HFAPHBKH_82 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HFAPHBKH_1 | 256765 | 260933 | False | Siphoviridae | VOG0275, VOG1563, VOG9667, VOG9667, VOG7581 |
| HFAPHBKH_1 | 265293 | 286408 | False | Siphoviridae | VOG0397, VOG6581, VOG0198, VOG0275, VOG9029, VOG4841, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG9583, VOG4586, VOG0541, VOG5910, VOG0801 |
| HFAPHBKH_15 | 45192 | 71868 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| HFAPHBKH_60 | 1 | 25608 | False | Siphoviridae | VOG4612, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG2935, VOG4544, VOG4581, VOG4556, VOG4841, VOG0531, VOG0198, VOG5395, VOG0044, VOG5607, VOG2752, VOG4606 |
Phigaro v2.4.0 (Database: Jan. 2024 release)