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. |
|---|---|---|---|---|---|---|---|---|
| AMJBDFML_3 | 629717 | 630886 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| AMJBDFML_3 | 456328 | 457530 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| AMJBDFML_2 | 439356 | 439673 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| AMJBDFML_2 | 439018 | 439356 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| AMJBDFML_3 | 437960 | 438814 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| AMJBDFML_4 | 430168 | 431811 | vmlR | ARO:3004476 | vmlR | 98.72 | 100.00 | NC_000964.3 |
| AMJBDFML_6 | 158554 | 161124 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| AMJBDFML_4 | 154880 | 155473 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| AMJBDFML_4 | 104359 | 105792 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| AMJBDFML_4 | 91543 | 92463 | mphK | ARO:3004541 | mphK | 98.37 | 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. |
|---|---|---|---|---|---|---|---|
| AMJBDFML_9 | 34770 | 36146 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 100.00 | 100.00 | X08034 |
| AMJBDFML_3 | 437960 | 438814 | aadK | Streptomycin | 98.71 | 100.00 | M26879 |
| AMJBDFML_4 | 91543 | 92463 | 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. |
|---|---|---|---|---|---|---|---|---|
| AMJBDFML_9 | 34770 | 36143 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| AMJBDFML_4 | 430171 | 431811 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.72 | 100.00 | WP_003234144.1 |
| AMJBDFML_3 | 437960 | 438811 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| AMJBDFML_4 | 91543 | 92460 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| AMJBDFML_9 | 38145 | 38663 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| AMJBDFML_7 | 92495 | 95092 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.29 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| AMJBDFML_3 | 829636 | 830277 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| AMJBDFML_1 | 414529 | 415710 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| AMJBDFML_1 | 869693 | 870478 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| AMJBDFML_1 | 873376 | 874314 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| AMJBDFML_1 | 874334 | 881470 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.41 | 100.00 | NP_391076 |
| AMJBDFML_1 | 415725 | 416174 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| AMJBDFML_1 | 416193 | 417335 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| AMJBDFML_1 | 870504 | 871700 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| AMJBDFML_7 | 143220 | 144983 | dep/capD | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_389723 |
| AMJBDFML_1 | 871729 | 873348 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.33 | 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 |
|---|---|---|---|---|---|---|---|---|
| AMJBDFML_10 | 31764 | 32900 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| AMJBDFML_12 | 4356 | 5225 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| AMJBDFML_2 | 749454 | 750230 | CodY | 7.70e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| AMJBDFML_1 | 577861 | 577292 | ClpP | 5.91e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| AMJBDFML_2 | 289229 | 289621 | spxA1 | 6.05e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| AMJBDFML_2 | 289229 | 289621 | spx | 3.61e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| AMJBDFML_11 | 20605 | 20847 | SpoVG | 7.53e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| AMJBDFML_4 | 381775 | 381972 | CspA | 1.99e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| AMJBDFML_3 | 817671 | 817477 | CspD | 5.24e-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. |
|---|---|---|---|---|---|---|
| AMJBDFML_16 | 5956 | 6143 | Col(SD853) | 188 / 194 | 94.68 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| AMJBDFML_1 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_2 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_3 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_4 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_5 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_6 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_7 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_8 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_9 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_10 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_11 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_12 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_13 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_14 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_15 | 0.0 | 1.0 | 0.0 |
| AMJBDFML_16 | 1.0 | 0.0 | 1.0 |
| AMJBDFML_17 | 1.0 | 0.0 | 1.0 |
| AMJBDFML_20 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| AMJBDFML_1 | 767121 | 801828 | False | Siphoviridae | VOG4602, VOG9667, VOG5353, VOG0181, VOG4556, VOG0787, VOG1638, VOG4552, VOG4566, VOG9600, VOG0025, VOG1884, VOG0198, VOG0275, VOG9029, VOG4841, VOG0713, VOG4581, VOG1886, VOG3607, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG9583, VOG0704, VOG4586, VOG0541, VOG5910, VOG0801, VOG4772, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG7896 |
| AMJBDFML_2 | 383085 | 409215 | 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 |
| AMJBDFML_8 | 90251 | 114929 | False | Siphoviridae | VOG4574, VOG0136, VOG0753, VOG4728, VOG5535, VOG4599, VOG4605, VOG4545, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG3480, VOG2621, VOG1329, VOG4555, VOG4564, VOG0720, VOG10227, VOG0796, VOG0198 |
Phigaro v2.4.0 (Database: Jan. 2024 release)