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. |
|---|---|---|---|---|---|---|---|---|
| GMIFEMBC_33 | 751833 | 752687 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| GMIFEMBC_33 | 733128 | 734330 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| GMIFEMBC_33 | 510808 | 511977 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| GMIFEMBC_50 | 424219 | 424536 | ykkD | ARO:3003064 | ykkD | 100.00 | 100.00 | AL009126.1 |
| GMIFEMBC_50 | 423881 | 424219 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| GMIFEMBC_61 | 407987 | 409630 | vmlR | ARO:3004476 | vmlR | 100.00 | 100.00 | NC_000964.3 |
| GMIFEMBC_61 | 162919 | 163512 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| GMIFEMBC_61 | 112416 | 113855 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| GMIFEMBC_61 | 99601 | 100521 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| GMIFEMBC_72 | 27326 | 29896 | 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. |
|---|---|---|---|---|---|---|---|
| GMIFEMBC_33 | 751833 | 752687 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| GMIFEMBC_61 | 99601 | 100521 | mph(K) | Spiramycin, Telithromycin | 100.00 | 100.00 | NC_000964 |
| GMIFEMBC_83 | 90439 | 91815 | 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. |
|---|---|---|---|---|---|---|---|---|
| GMIFEMBC_33 | 751836 | 752687 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| GMIFEMBC_61 | 99601 | 100518 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| GMIFEMBC_83 | 87921 | 88439 | satA | streptothricin N-acetyltransferase SatA | EXACTX | 100.00 | 100.00 | WP_003242546.1 |
| GMIFEMBC_83 | 90442 | 91815 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| GMIFEMBC_61 | 407990 | 409630 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| GMIFEMBC_33 | 201896 | 204490 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| GMIFEMBC_40 | 555876 | 557018 | capA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391469 |
| GMIFEMBC_40 | 557501 | 558682 | capB | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391471 |
| GMIFEMBC_40 | 557037 | 557486 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| GMIFEMBC_33 | 155238 | 157001 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| GMIFEMBC_40 | 112859 | 113644 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| GMIFEMBC_33 | 311462 | 312103 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| GMIFEMBC_40 | 101867 | 109003 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.99 | 100.00 | NP_391076 |
| GMIFEMBC_40 | 109023 | 109961 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| GMIFEMBC_40 | 111637 | 112833 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.67 | 100.00 | NP_391079 |
| GMIFEMBC_40 | 109989 | 111608 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 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 |
|---|---|---|---|---|---|---|---|---|
| GMIFEMBC_94 | 28004 | 26868 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| GMIFEMBC_116 | 4308 | 5177 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| GMIFEMBC_50 | 737483 | 738259 | CodY | 7.61e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| GMIFEMBC_40 | 404264 | 404833 | ClpP | 5.74e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| GMIFEMBC_50 | 276441 | 276833 | spxA1 | 2.25e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| GMIFEMBC_105 | 34711 | 34469 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| GMIFEMBC_61 | 362515 | 362712 | CspA | 1.89e-31 | 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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| GMIFEMBC_33 | 0.0 | 1.0 | 0.0 |
| GMIFEMBC_40 | 0.0 | 1.0 | 0.0 |
| GMIFEMBC_50 | 0.0 | 1.0 | 0.0 |
| GMIFEMBC_61 | 0.0 | 1.0 | 0.0 |
| GMIFEMBC_72 | 0.0 | 1.0 | 0.0 |
| GMIFEMBC_83 | 0.0 | 1.0 | 0.0 |
| GMIFEMBC_94 | 0.0 | 1.0 | 0.0 |
| GMIFEMBC_105 | 0.0 | 1.0 | 0.0 |
| GMIFEMBC_116 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| GMIFEMBC_33 | 3200 | 26202 | False | Siphoviridae | VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641, VOG4918 |
| GMIFEMBC_33 | 683199 | 713443 | 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, VOG4600 |
| GMIFEMBC_40 | 273217 | 300468 | False | Siphoviridae | VOG4707, VOG0641, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG4544, VOG4581, VOG4841, VOG0531, VOG0275, VOG0198, VOG4567 |
| GMIFEMBC_40 | 303623 | 312231 | False | Siphoviridae | VOG4566, VOG3622, VOG9667, VOG9667, VOG1563, VOG0275 |
| GMIFEMBC_50 | 367934 | 394042 | 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 |
| GMIFEMBC_50 | 928440 | 931023 | False | Siphoviridae | VOG4602, VOG9667, VOG5353, VOG0181 |
Phigaro v2.4.0 (Database: Jan. 2024 release)