Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 4 | 16.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| NOGEOMFM_1 | 2741113 | 2741967 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| NOGEOMFM_1 | 2721940 | 2723142 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| NOGEOMFM_1 | 2492350 | 2493519 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NOGEOMFM_1 | 1356816 | 1357133 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NOGEOMFM_1 | 1356478 | 1356816 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NOGEOMFM_1 | 893339 | 895909 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| NOGEOMFM_1 | 591381 | 593024 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| NOGEOMFM_1 | 286733 | 288166 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| NOGEOMFM_1 | 273917 | 274837 | mphK | ARO:3004541 | mphK | 97.71 | 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. |
|---|---|---|---|---|---|---|---|
| NOGEOMFM_1 | 4213105 | 4214481 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| NOGEOMFM_1 | 2741115 | 2741967 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| NOGEOMFM_1 | 273917 | 274837 | mph(K) | Spiramycin, Telithromycin | 97.50 | 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. |
|---|---|---|---|---|---|---|---|---|
| NOGEOMFM_1 | 4213108 | 4214481 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| NOGEOMFM_1 | 591384 | 593024 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| NOGEOMFM_1 | 273917 | 274834 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| NOGEOMFM_1 | 2741116 | 2741967 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| NOGEOMFM_1 | 4210588 | 4211106 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| NOGEOMFM_1 | 2054019 | 2056616 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NOGEOMFM_1 | 2293164 | 2293805 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| NOGEOMFM_1 | 3719760 | 3720941 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| NOGEOMFM_1 | 2003994 | 2005757 | dep/capD | 0.0 | Capsule | Immune modulation | 99.49 | 100.00 | NP_389723 |
| NOGEOMFM_1 | 3305241 | 3306026 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| NOGEOMFM_1 | 3301405 | 3302343 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| NOGEOMFM_1 | 3304019 | 3305215 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| NOGEOMFM_1 | 3294251 | 3301385 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.06 | 99.97 | NP_391076 |
| NOGEOMFM_1 | 3718135 | 3719277 | capA | 0.0 | Capsule | Immune modulation | 98.95 | 100.00 | NP_391469 |
| NOGEOMFM_1 | 3719296 | 3719745 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| NOGEOMFM_1 | 3302371 | 3303990 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 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 |
|---|---|---|---|---|---|---|---|---|
| NOGEOMFM_1 | 132399 | 133535 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NOGEOMFM_1 | 18665 | 19534 | pdxS | 3.15e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NOGEOMFM_1 | 1666714 | 1667490 | CodY | 3.44e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NOGEOMFM_1 | 3558406 | 3558975 | ClpP | 2.55e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
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 |
|---|---|---|---|
| NOGEOMFM_1 | 0.0 | 1.0 | 0.0 |
| NOGEOMFM_2 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NOGEOMFM_1 | 1299005 | 1326668 | 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 |
| NOGEOMFM_1 | 2167801 | 2180094 | False | Siphoviridae | VOG1198, VOG0918, VOG4551, VOG0025, VOG7476, VOG0322, VOG6211, VOG4908 |
| NOGEOMFM_1 | 2224157 | 2252279 | False | Siphoviridae | VOG10940, VOG7134, VOG9867, VOG6036, VOG5495, VOG9219, VOG9713, VOG6940, VOG5534, VOG7718, VOG4705, VOG8610, VOG0275, VOG9667, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG7900, VOG4574 |
| NOGEOMFM_1 | 2670519 | 2688830 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
| NOGEOMFM_2 | 9761 | 32859 | False | Siphoviridae | VOG0221, VOG4581, VOG5819, VOG1886, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5852, VOG6163, VOG4605, VOG4599, VOG9244, VOG10944, VOG1024 |
| NOGEOMFM_2 | 52154 | 70267 | False | Siphoviridae | VOG11080, VOG2352, VOG0397, VOG1198, VOG4561, VOG4714, VOG2352, VOG3851, VOG2725, VOG4549, VOG5292, VOG1574, VOG0918, VOG4551 |
Phigaro v2.4.0 (Database: Jan. 2024 release)