Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 9 | 18.03 |
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. |
|---|---|---|---|---|---|---|---|---|
| ALMECFFD_95 | 122054 | 122647 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| ALMECFFD_12 | 108838 | 109155 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| ALMECFFD_12 | 108500 | 108838 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| ALMECFFD_95 | 71494 | 72933 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.42 | JYFL01000006.1 |
| ALMECFFD_3 | 59292 | 60461 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| ALMECFFD_95 | 58679 | 59599 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
| ALMECFFD_56 | 47408 | 49051 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| ALMECFFD_69 | 27368 | 29938 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| ALMECFFD_4 | 5176 | 6030 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| ALMECFFD_25 | 2128 | 3330 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
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. |
|---|---|---|---|---|---|---|---|
| ALMECFFD_4 | 5178 | 6030 | aadK | Streptomycin | 99.30 | 99.77 | M26879 |
| ALMECFFD_95 | 58679 | 59599 | mph(K) | Spiramycin, Telithromycin | 98.70 | 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. |
|---|---|---|---|---|---|---|---|---|
| ALMECFFD_95 | 58679 | 59596 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| ALMECFFD_4 | 5179 | 6030 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| ALMECFFD_56 | 47411 | 49051 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| ALMECFFD_27 | 5369 | 5887 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| ALMECFFD_38 | 60695 | 63292 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.83 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| ALMECFFD_38 | 10156 | 11919 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| ALMECFFD_9 | 20308 | 21246 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| ALMECFFD_9 | 18661 | 20280 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.81 | 100.00 | NP_391078 |
| ALMECFFD_9 | 16625 | 17410 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| ALMECFFD_99 | 30675 | 31316 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| ALMECFFD_97 | 24692 | 25873 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| ALMECFFD_97 | 25888 | 26337 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| ALMECFFD_9 | 17436 | 18632 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| ALMECFFD_97 | 26356 | 27498 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| ALMECFFD_9 | 21266 | 28402 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391076 |
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 |
|---|---|---|---|---|---|---|---|---|
| ALMECFFD_18 | 31691 | 32827 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| ALMECFFD_20 | 4269 | 5138 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| ALMECFFD_93 | 191396 | 190620 | CodY | 2.31e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| ALMECFFD_100 | 234241 | 234810 | ClpP | 1.62e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| ALMECFFD_41 | 37418 | 37026 | spxA1 | 2.38e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| ALMECFFD_41 | 37418 | 37026 | spx | 1.42e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| ALMECFFD_35 | 34772 | 34530 | SpoVG | 6.14e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| ALMECFFD_57 | 862 | 665 | CspA | 2.08e-33 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| ALMECFFD_99 | 43277 | 43471 | CspD | 1.05e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| ALMECFFD_42 | 34675 | 34869 | CspB | 6.23e-28 | cold shock protein | 83.08 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| ALMECFFD_1 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_2 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_3 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_4 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_5 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_6 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_8 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_9 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_10 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_11 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_12 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_13 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_14 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_15 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_16 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_17 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_18 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_19 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_20 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_21 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_22 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_23 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_25 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_26 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_27 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_28 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_29 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_31 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_32 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_33 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_35 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_36 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_37 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_38 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_39 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_40 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_41 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_42 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_43 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_44 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_45 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_46 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_48 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_49 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_50 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_51 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_52 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_53 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_55 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_56 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_57 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_58 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_59 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_60 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_61 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_63 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_64 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_65 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_67 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_68 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_69 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_70 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_71 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_72 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_73 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_74 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_76 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_77 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_78 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_79 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_80 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_81 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_82 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_83 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_84 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_85 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_87 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_88 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_89 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_90 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_91 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_92 | 1.0 | 0.0 | 1.0 |
| ALMECFFD_93 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_94 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_95 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_96 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_97 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_98 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_99 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_100 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_101 | 0.0 | 1.0 | 0.0 |
| ALMECFFD_102 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| ALMECFFD_12 | 53035 | 78649 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| ALMECFFD_94 | 4534 | 25652 | False | Siphoviridae | VOG0641, VOG7896, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581 |
Phigaro v2.4.0 (Database: Jan. 2024 release)