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. |
|---|---|---|---|---|---|---|---|---|
| IDMHIPAH_8 | 84865 | 85203 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| IDMHIPAH_8 | 84548 | 84865 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| IDMHIPAH_18 | 59486 | 62056 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| IDMHIPAH_19 | 40969 | 41889 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| IDMHIPAH_17 | 28800 | 30446 | vmlR | ARO:3004476 | vmlR | 98.36 | 100.18 | NC_000964.3 |
| IDMHIPAH_19 | 27635 | 29074 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.42 | JYFL01000006.1 |
| IDMHIPAH_5 | 24049 | 24903 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| IDMHIPAH_47 | 18944 | 19537 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| IDMHIPAH_5 | 6952 | 8154 | blt | ARO:3003006 | blt | 98.00 | 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. |
|---|---|---|---|---|---|---|---|
| IDMHIPAH_5 | 24049 | 24903 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| IDMHIPAH_19 | 40969 | 41889 | 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. |
|---|---|---|---|---|---|---|---|---|
| IDMHIPAH_19 | 40981 | 41889 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| IDMHIPAH_5 | 24052 | 24903 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| IDMHIPAH_17 | 28800 | 30443 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.36 | 100.00 | WP_003234144.1 |
| IDMHIPAH_16 | 51047 | 51565 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| IDMHIPAH_3 | 160061 | 161242 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| IDMHIPAH_10 | 6413 | 7198 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| IDMHIPAH_3 | 161725 | 162867 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| IDMHIPAH_10 | 11054 | 18190 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.30 | 100.00 | NP_391076 |
| IDMHIPAH_46 | 19804 | 21567 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| IDMHIPAH_10 | 10096 | 11034 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.04 | 100.00 | NP_391077 |
| IDMHIPAH_10 | 7224 | 8420 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| IDMHIPAH_20 | 42336 | 42977 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| IDMHIPAH_3 | 161257 | 161706 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| IDMHIPAH_10 | 8449 | 10068 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.73 | 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 |
|---|---|---|---|---|---|---|---|---|
| IDMHIPAH_24 | 28111 | 26975 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| IDMHIPAH_51 | 4356 | 5225 | pdxS | 1.96e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| IDMHIPAH_1 | 116449 | 117225 | CodY | 1.73e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| IDMHIPAH_32 | 45175 | 44606 | ClpP | 2.96e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| IDMHIPAH_22 | 23391 | 23783 | spxA1 | 4.13e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| IDMHIPAH_22 | 23391 | 23783 | spx | 2.46e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| IDMHIPAH_29 | 34758 | 34516 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| IDMHIPAH_17 | 76436 | 76239 | CspA | 3.90e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| IDMHIPAH_20 | 31106 | 30912 | CspD | 4.65e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| IDMHIPAH_33 | 32111 | 31917 | CspB | 4.55e-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. |
|---|---|---|---|---|---|---|
| IDMHIPAH_61 | 1537 | 1704 | Col(SD853) | 168 / 194 | 86.90 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| IDMHIPAH_1 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_2 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_3 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_4 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_5 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_6 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_7 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_8 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_9 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_10 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_11 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_12 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_13 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_14 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_15 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_16 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_17 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_18 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_19 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_20 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_21 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_22 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_23 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_24 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_25 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_26 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_27 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_28 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_29 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_30 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_31 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_32 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_33 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_34 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_35 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_36 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_37 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_38 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_39 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_40 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_41 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_42 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_43 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_44 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_45 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_46 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_47 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_48 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_49 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_50 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_51 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_52 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_53 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_54 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_55 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_56 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_57 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_58 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_59 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_60 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_61 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_62 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_63 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_64 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_65 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_66 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_67 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_68 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_69 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_70 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_72 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_73 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_75 | 1.0 | 0.0 | 1.0 |
| IDMHIPAH_76 | 0.0 | 1.0 | 0.0 |
| IDMHIPAH_77 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| IDMHIPAH_8 | 114667 | 141350 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4843, VOG0189, VOG3490 |
| IDMHIPAH_12 | 93780 | 105473 | True | Siphoviridae | VOG3490, VOG0275, VOG0275, VOG1563, VOG9667, VOG9667, VOG7581, VOG4566, VOG0189, VOG6587, VOG1336 |
| IDMHIPAH_31 | 92 | 26938 | False | Siphoviridae | VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3644, VOG4544, VOG4581, VOG7403, VOG4841, VOG0198, VOG7372, VOG2752, VOG4606, VOG1227, VOG1936, VOG0535, VOG0650 |
Phigaro v2.4.0 (Database: Jan. 2024 release)