Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| OMFNGPGA_1 | 1657145 | 1657483 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| OMFNGPGA_1 | 1656828 | 1657145 | ykkD | ARO:3003064 | ykkD | 100.00 | 100.00 | AL009126.1 |
| OMFNGPGA_1 | 672583 | 673752 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| OMFNGPGA_1 | 498264 | 499466 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| OMFNGPGA_1 | 479903 | 480757 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| OMFNGPGA_4 | 108893 | 109813 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| OMFNGPGA_4 | 95559 | 96998 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| OMFNGPGA_8 | 47482 | 49125 | vmlR | ARO:3004476 | vmlR | 100.00 | 100.00 | NC_000964.3 |
| OMFNGPGA_4 | 45902 | 46495 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| OMFNGPGA_3 | 27546 | 30116 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
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. |
|---|---|---|---|---|---|---|---|
| OMFNGPGA_1 | 479903 | 480757 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| OMFNGPGA_4 | 108893 | 109813 | mph(K) | Spiramycin, Telithromycin | 100.00 | 100.00 | NC_000964 |
| OMFNGPGA_2 | 36557 | 37933 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 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. |
|---|---|---|---|---|---|---|---|---|
| OMFNGPGA_1 | 479903 | 480754 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| OMFNGPGA_4 | 108896 | 109813 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| OMFNGPGA_2 | 39933 | 40451 | satA | streptothricin N-acetyltransferase SatA | EXACTX | 100.00 | 100.00 | WP_003242546.1 |
| OMFNGPGA_2 | 36557 | 37930 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| OMFNGPGA_8 | 47485 | 49125 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| OMFNGPGA_1 | 980070 | 982664 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| OMFNGPGA_2 | 526536 | 527678 | capA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391469 |
| OMFNGPGA_2 | 524872 | 526053 | capB | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391471 |
| OMFNGPGA_2 | 526068 | 526517 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| OMFNGPGA_1 | 1027559 | 1029322 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| OMFNGPGA_2 | 969974 | 970759 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| OMFNGPGA_2 | 973657 | 974595 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391077 |
| OMFNGPGA_2 | 970785 | 971981 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391079 |
| OMFNGPGA_2 | 972010 | 973629 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391078 |
| OMFNGPGA_2 | 974615 | 981751 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391076 |
| OMFNGPGA_1 | 872457 | 873098 | 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 |
|---|---|---|---|---|---|---|---|---|
| OMFNGPGA_9 | 28208 | 27072 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| OMFNGPGA_12 | 4392 | 5261 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| OMFNGPGA_1 | 1343881 | 1343105 | CodY | 1.69e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| OMFNGPGA_2 | 679290 | 678721 | ClpP | 6.52e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| OMFNGPGA_1 | 1806298 | 1805906 | spxA1 | 5.01e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| OMFNGPGA_10 | 20899 | 21141 | SpoVG | 7.57e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| OMFNGPGA_8 | 2010 | 2207 | CspA | 3.38e-32 | 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. |
|---|---|---|---|---|---|---|
| OMFNGPGA_14 | 7080 | 7266 | Col(SD853) | 187 / 194 | 88.24 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| OMFNGPGA_1 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_2 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_3 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_4 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_5 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_6 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_7 | 1.0 | 0.0 | 1.0 |
| OMFNGPGA_8 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_9 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_10 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_11 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_12 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_13 | 0.0 | 1.0 | 0.0 |
| OMFNGPGA_14 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| OMFNGPGA_1 | 322179 | 348601 | False | Siphoviridae | VOG0044, VOG0198, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5008, VOG0641 |
| OMFNGPGA_1 | 1687322 | 1713430 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| OMFNGPGA_2 | 773807 | 778589 | False | Siphoviridae | VOG0275, VOG1563, VOG9667 |
| OMFNGPGA_2 | 783933 | 810400 | False | Siphoviridae | VOG0044, VOG6581, VOG0198, VOG0275, VOG1837, VOG0531, VOG4841, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641, VOG4707 |
| OMFNGPGA_7 | 7865 | 11507 | False | Siphoviridae | VOG1574, VOG0918 |
| OMFNGPGA_7 | 30305 | 56804 | False | Siphoviridae | VOG4724, VOG0018, VOG9096, VOG0221, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5852, VOG6163, VOG4605, VOG4599, VOG9244, VOG10944, VOG1024 |
| OMFNGPGA_11 | 13717 | 43661 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309 |
Phigaro v2.4.0 (Database: Jan. 2024 release)