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. |
|---|---|---|---|---|---|---|---|---|
| AFOFKEHG_1 | 426663 | 426980 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| AFOFKEHG_1 | 426325 | 426663 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| AFOFKEHG_23 | 270838 | 273408 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| AFOFKEHG_12 | 173414 | 174583 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| AFOFKEHG_25 | 107998 | 108918 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| AFOFKEHG_25 | 94664 | 96103 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| AFOFKEHG_21 | 63587 | 64441 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| AFOFKEHG_25 | 44983 | 45576 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| AFOFKEHG_21 | 44882 | 46084 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| AFOFKEHG_24 | 28970 | 30613 | 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. |
|---|---|---|---|---|---|---|---|
| AFOFKEHG_21 | 63587 | 64441 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| AFOFKEHG_22 | 323084 | 324460 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.85 | 100.00 | D12567 |
| AFOFKEHG_25 | 107998 | 108918 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| AFOFKEHG_21 | 63590 | 64441 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| AFOFKEHG_22 | 323087 | 324460 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_063856081.1 |
| AFOFKEHG_24 | 28970 | 30610 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| AFOFKEHG_25 | 108001 | 108918 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| AFOFKEHG_22 | 320556 | 321074 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| AFOFKEHG_12 | 481699 | 484293 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| AFOFKEHG_12 | 529187 | 530950 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| AFOFKEHG_20 | 413414 | 414199 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| AFOFKEHG_12 | 374103 | 374744 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| AFOFKEHG_20 | 417097 | 418035 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| AFOFKEHG_20 | 414225 | 415421 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.67 | 100.00 | NP_391079 |
| AFOFKEHG_26 | 155842 | 157023 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| AFOFKEHG_20 | 415450 | 417069 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391078 |
| AFOFKEHG_20 | 418055 | 425191 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391076 |
| AFOFKEHG_26 | 157506 | 158648 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| AFOFKEHG_26 | 157038 | 157487 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| AFOFKEHG_2 | 31656 | 32792 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| AFOFKEHG_5 | 4265 | 5134 | pdxS | 2.56e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| AFOFKEHG_1 | 739985 | 740761 | CodY | 8.25e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| AFOFKEHG_20 | 120146 | 119577 | ClpP | 3.17e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| AFOFKEHG_1 | 275529 | 275921 | spxA1 | 6.49e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| AFOFKEHG_1 | 275529 | 275921 | spx | 3.87e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| AFOFKEHG_3 | 20512 | 20754 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| AFOFKEHG_24 | 76530 | 76333 | CspA | 9.36e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| AFOFKEHG_12 | 362141 | 361947 | CspD | 3.32e-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 |
|---|---|---|---|
| AFOFKEHG_1 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_2 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_3 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_4 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_5 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_6 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_7 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_8 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_9 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_10 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_11 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_12 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_13 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_20 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_21 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_22 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_23 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_24 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_25 | 0.0 | 1.0 | 0.0 |
| AFOFKEHG_26 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| AFOFKEHG_1 | 371163 | 396837 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| AFOFKEHG_4 | 7105 | 21422 | False | Myoviridae | VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG1328, VOG4567, VOG4618, VOG7983 |
| AFOFKEHG_4 | 30901 | 34852 | False | Unknown | VOG1292, VOG1309, VOG0083 |
| AFOFKEHG_20 | 313241 | 347246 | False | Siphoviridae | VOG4602, VOG9667, VOG5353, VOG0181, VOG4556, VOG0787, VOG1638, VOG4552, VOG4566, VOG9600, VOG0025, VOG1884, VOG9091, VOG4841, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG5008, VOG0641, VOG4574 |
| AFOFKEHG_21 | 7496 | 25197 | False | Myoviridae / Siphoviridae | VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309, VOG4600 |
Phigaro v2.4.0 (Database: Jan. 2024 release)