Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 7 | 16.43 |
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. |
|---|---|---|---|---|---|---|---|---|
| ABCCKPFK_2 | 626872 | 628041 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| ABCCKPFK_3 | 533692 | 534030 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| ABCCKPFK_3 | 533375 | 533692 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| ABCCKPFK_2 | 456825 | 458027 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| ABCCKPFK_2 | 437825 | 438679 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| ABCCKPFK_4 | 344750 | 345670 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| ABCCKPFK_4 | 331429 | 332868 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| ABCCKPFK_4 | 281868 | 282461 | tmrB | ARO:3003059 | tmrB | 98.98 | 100.00 | AL009126.3 |
| ABCCKPFK_5 | 159359 | 161929 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| ABCCKPFK_4 | 29260 | 30903 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| ABCCKPFK_4 | 344750 | 345670 | mph(K) | Spiramycin, Telithromycin | 99.67 | 100.00 | NC_000964 |
| ABCCKPFK_2 | 437825 | 438677 | aadK | Streptomycin | 98.94 | 99.77 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| ABCCKPFK_4 | 344753 | 345670 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| ABCCKPFK_2 | 437825 | 438676 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| ABCCKPFK_4 | 29260 | 30900 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| ABCCKPFK_1 | 44304 | 44822 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| ABCCKPFK_1 | 528409 | 529590 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| ABCCKPFK_2 | 826610 | 827251 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| ABCCKPFK_1 | 954477 | 955262 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| ABCCKPFK_1 | 530073 | 531215 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| ABCCKPFK_1 | 958160 | 959098 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| ABCCKPFK_1 | 529605 | 530054 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| ABCCKPFK_1 | 959118 | 966254 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391076 |
| ABCCKPFK_1 | 955288 | 956484 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| ABCCKPFK_1 | 956513 | 958132 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.77 | 100.00 | NP_391078 |
| ABCCKPFK_2 | 990337 | 992100 | dep/capD | 0.0 | Capsule | Immune modulation | 98.70 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| ABCCKPFK_8 | 28230 | 27094 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| ABCCKPFK_11 | 4392 | 5261 | pdxS | 1.14e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| ABCCKPFK_3 | 223426 | 222650 | CodY | 7.93e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| ABCCKPFK_1 | 684398 | 683829 | ClpP | 6.42e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| ABCCKPFK_3 | 702337 | 701945 | spxA1 | 6.23e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| ABCCKPFK_3 | 702337 | 701945 | spx | 3.72e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| ABCCKPFK_9 | 20641 | 20883 | SpoVG | 7.54e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| ABCCKPFK_4 | 80556 | 80359 | CspA | 1.64e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| ABCCKPFK_1 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_2 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_3 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_4 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_5 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_6 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_7 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_8 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_9 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_10 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_11 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_12 | 0.0 | 1.0 | 0.0 |
| ABCCKPFK_13 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| ABCCKPFK_3 | 563525 | 591209 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| ABCCKPFK_6 | 92728 | 117587 | False | Myoviridae | VOG3490, VOG5284, VOG2703, VOG1993, VOG4574, VOG0136, VOG0753, VOG5008, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG4550, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555 |
| ABCCKPFK_6 | 127653 | 135117 | False | Siphoviridae | VOG0186, VOG8233, VOG4603, VOG4552, VOG0650, VOG11075, VOG9667, VOG4602 |
Phigaro v2.4.0 (Database: Jan. 2024 release)