Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| NNKFPLML_19 | 753368 | 754537 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NNKFPLML_19 | 532043 | 533245 | blt | ARO:3003006 | blt | 99.00 | 100.00 | L32599.1 |
| NNKFPLML_19 | 513663 | 514517 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| NNKFPLML_17 | 431750 | 432067 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NNKFPLML_17 | 431412 | 431750 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NNKFPLML_8 | 256119 | 258689 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| NNKFPLML_9 | 155150 | 155743 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| NNKFPLML_9 | 104629 | 106068 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| NNKFPLML_9 | 91816 | 92736 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
| NNKFPLML_5 | 29258 | 30901 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| NNKFPLML_9 | 91816 | 92736 | mph(K) | Spiramycin, Telithromycin | 99.35 | 100.00 | NC_000964 |
| NNKFPLML_19 | 513663 | 514517 | aadK | Streptomycin | 98.71 | 100.00 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| NNKFPLML_9 | 91816 | 92733 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| NNKFPLML_19 | 513663 | 514514 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| NNKFPLML_5 | 29258 | 30898 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| NNKFPLML_15 | 38306 | 38824 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.64 | 100.00 | WP_003242546.1 |
| NNKFPLML_11 | 63228 | 65825 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.65 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NNKFPLML_15 | 530732 | 531913 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NNKFPLML_15 | 953975 | 954760 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| NNKFPLML_19 | 951205 | 951846 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.69 | 100.00 | NP_390062 |
| NNKFPLML_15 | 954786 | 955982 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.33 | 100.00 | NP_391079 |
| NNKFPLML_11 | 8984 | 10747 | dep/capD | 0.0 | Capsule | Immune modulation | 99.32 | 100.00 | NP_389723 |
| NNKFPLML_15 | 531928 | 532377 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| NNKFPLML_15 | 532396 | 533538 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| NNKFPLML_15 | 958616 | 965752 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.72 | 100.00 | NP_391076 |
| NNKFPLML_15 | 957658 | 958596 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391077 |
| NNKFPLML_15 | 956011 | 957630 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.41 | 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 |
|---|---|---|---|---|---|---|---|---|
| NNKFPLML_7 | 28242 | 27106 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NNKFPLML_4 | 11475 | 10606 | pdxS | 1.18e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NNKFPLML_17 | 743166 | 743942 | CodY | 8.34e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NNKFPLML_3 | 376176 | 376745 | ClpP | 4.24e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NNKFPLML_17 | 278079 | 278471 | spxA1 | 6.56e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NNKFPLML_17 | 278079 | 278471 | spx | 3.91e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NNKFPLML_6 | 34901 | 34659 | SpoVG | 7.56e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NNKFPLML_5 | 79315 | 79118 | CspA | 9.79e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NNKFPLML_19 | 939973 | 939779 | CspD | 2.79e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| NNKFPLML_19 | 939973 | 939776 | CspB | 5.78e-27 | cold shock protein | 80.30 | 100.00 | 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 |
|---|---|---|---|
| NNKFPLML_3 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_4 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_5 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_6 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_7 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_8 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_9 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_10 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_11 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_12 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_13 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_14 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_15 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_16 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_17 | 0.0 | 1.0 | 0.0 |
| NNKFPLML_19 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NNKFPLML_17 | 375557 | 401547 | 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 |
| NNKFPLML_19 | 279788 | 307292 | False | Siphoviridae | VOG0189, VOG0025, VOG4551, VOG2215, VOG11003, VOG1563, VOG0052, VOG7255, VOG5753, VOG10937, VOG6497, VOG0026, VOG0422, VOG5543, VOG1093, VOG0371, VOG3212, VOG1838, VOG4730, VOG2368, VOG4562, VOG0085, VOG1638, VOG4561, VOG4724, VOG1298, VOG0020, VOG4567, VOG0052, VOG9755, VOG4799 |
| NNKFPLML_19 | 310951 | 341345 | False | Siphoviridae | VOG0101, VOG11003, VOG0274, VOG9437, VOG1183, VOG4841, VOG4581, VOG4544, VOG4556, VOG4573, VOG4553, VOG5601, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4626, VOG4705, VOG0753, VOG4666, VOG0602, VOG8440, VOG6116, VOG0705 |
| NNKFPLML_19 | 552807 | 582843 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862 |
| NNKFPLML_19 | 973690 | 993736 | False | Unknown | VOG10230, VOG8440, VOG5070, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG0275, VOG7930, VOG8610, VOG7895 |
| NNKFPLML_19 | 1049568 | 1054730 | False | Unknown | VOG6211, VOG0322, VOG7476, VOG0025 |
Phigaro v2.4.0 (Database: Jan. 2024 release)