Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 4 | 16.88 |
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. |
|---|---|---|---|---|---|---|---|---|
| HIHHNDKO_1 | 2606214 | 2607068 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| HIHHNDKO_1 | 2587045 | 2588247 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| HIHHNDKO_1 | 2357954 | 2359123 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| HIHHNDKO_1 | 1358506 | 1358823 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| HIHHNDKO_1 | 1358168 | 1358506 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| HIHHNDKO_1 | 894972 | 897542 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| HIHHNDKO_1 | 591557 | 593200 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| HIHHNDKO_1 | 337311 | 337904 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| HIHHNDKO_1 | 286755 | 288188 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| HIHHNDKO_1 | 273939 | 274859 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| HIHHNDKO_1 | 4069586 | 4070962 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| HIHHNDKO_1 | 2606216 | 2607068 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| HIHHNDKO_1 | 273939 | 274859 | 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. |
|---|---|---|---|---|---|---|---|---|
| HIHHNDKO_1 | 4069589 | 4070962 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| HIHHNDKO_1 | 273939 | 274856 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| HIHHNDKO_1 | 591560 | 593200 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| HIHHNDKO_1 | 2606217 | 2607068 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| HIHHNDKO_1 | 4067069 | 4067587 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| HIHHNDKO_1 | 2054218 | 2056815 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HIHHNDKO_1 | 2158786 | 2159427 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| HIHHNDKO_1 | 3585106 | 3586287 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| HIHHNDKO_1 | 3170807 | 3171592 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| HIHHNDKO_1 | 3166971 | 3167909 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| HIHHNDKO_1 | 3169585 | 3170781 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| HIHHNDKO_1 | 2004137 | 2005900 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| HIHHNDKO_1 | 3159817 | 3166951 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.06 | 99.97 | NP_391076 |
| HIHHNDKO_1 | 3583481 | 3584623 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| HIHHNDKO_1 | 3584642 | 3585091 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| HIHHNDKO_1 | 3167937 | 3169556 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.46 | 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 |
|---|---|---|---|---|---|---|---|---|
| HIHHNDKO_1 | 132399 | 133535 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| HIHHNDKO_1 | 18665 | 19534 | pdxS | 3.04e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HIHHNDKO_1 | 1668403 | 1669179 | CodY | 3.32e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HIHHNDKO_1 | 3423752 | 3424321 | ClpP | 2.46e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| HIHHNDKO_1 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HIHHNDKO_1 | 1301453 | 1328680 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| HIHHNDKO_1 | 2535692 | 2554004 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
Phigaro v2.4.0 (Database: Jan. 2024 release)