Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| CKHNPDEH_13 | 716568 | 717737 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| CKHNPDEH_13 | 494216 | 495418 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| CKHNPDEH_13 | 475855 | 476709 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| CKHNPDEH_12 | 425602 | 425919 | ykkD | ARO:3003064 | ykkD | 100.00 | 100.00 | AL009126.1 |
| CKHNPDEH_12 | 425264 | 425602 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CKHNPDEH_15 | 276601 | 279171 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| CKHNPDEH_14 | 259323 | 260243 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| CKHNPDEH_14 | 245989 | 247428 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| CKHNPDEH_14 | 196332 | 196925 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| CKHNPDEH_18 | 47432 | 49075 | vmlR | ARO:3004476 | vmlR | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| CKHNPDEH_13 | 475855 | 476709 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| CKHNPDEH_14 | 259323 | 260243 | mph(K) | Spiramycin, Telithromycin | 100.00 | 100.00 | NC_000964 |
| CKHNPDEH_11 | 36437 | 37813 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| CKHNPDEH_13 | 475855 | 476706 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| CKHNPDEH_14 | 259326 | 260243 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| CKHNPDEH_11 | 39813 | 40331 | satA | streptothricin N-acetyltransferase SatA | EXACTX | 100.00 | 100.00 | WP_003242546.1 |
| CKHNPDEH_11 | 36437 | 37810 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| CKHNPDEH_18 | 47435 | 49075 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| CKHNPDEH_16 | 192871 | 195465 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CKHNPDEH_11 | 526531 | 527673 | capA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391469 |
| CKHNPDEH_11 | 524867 | 526048 | capB | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391471 |
| CKHNPDEH_11 | 526063 | 526512 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| CKHNPDEH_16 | 240360 | 242123 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| CKHNPDEH_11 | 933400 | 934185 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| CKHNPDEH_11 | 937083 | 938021 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391077 |
| CKHNPDEH_11 | 934211 | 935407 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391079 |
| CKHNPDEH_11 | 935436 | 937055 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391078 |
| CKHNPDEH_11 | 938041 | 945177 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391076 |
| CKHNPDEH_13 | 916442 | 917083 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
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 |
|---|---|---|---|---|---|---|---|---|
| CKHNPDEH_19 | 28088 | 26952 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CKHNPDEH_2 | 4326 | 5195 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CKHNPDEH_12 | 738866 | 739642 | CodY | 8.25e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CKHNPDEH_11 | 679461 | 678892 | ClpP | 6.30e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CKHNPDEH_12 | 276441 | 276833 | spxA1 | 2.45e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| CKHNPDEH_1 | 20849 | 21091 | SpoVG | 7.55e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CKHNPDEH_18 | 1960 | 2157 | CspA | 3.38e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CKHNPDEH_13 | 904480 | 904286 | CspD | 5.93e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| CKHNPDEH_1 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_2 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_3 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_4 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_7 | 1.0 | 0.0 | 1.0 |
| CKHNPDEH_11 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_12 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_13 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_14 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_15 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_16 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_17 | 1.0 | 0.0 | 1.0 |
| CKHNPDEH_18 | 0.0 | 1.0 | 0.0 |
| CKHNPDEH_19 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CKHNPDEH_12 | 369317 | 395425 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| CKHNPDEH_13 | 315176 | 349427 | False | Siphoviridae | VOG7438, VOG1047, VOG0021, VOG1565, VOG0026, VOG4609, VOG0327, VOG4548, VOG0198, VOG4841, VOG4581, VOG1886, VOG3644, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG4545, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5008, VOG0641, VOG4574 |
| CKHNPDEH_13 | 514970 | 545347 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| CKHNPDEH_17 | 8761 | 32410 | False | Siphoviridae | VOG3616, VOG1024, VOG10944, VOG9244, VOG4599, VOG4605, VOG6163, VOG5852, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG4544, VOG4581, VOG0221 |
| CKHNPDEH_17 | 59390 | 73116 | False | Unknown | VOG5292, VOG4549, VOG2725, VOG3531, VOG3851, VOG2352, VOG4714, VOG4561, VOG1198, VOG0397, VOG2352, VOG11080 |
Phigaro v2.4.0 (Database: Jan. 2024 release)