Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 5 | 10 | 9 | 14.35 |
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. |
|---|---|---|---|---|---|---|---|---|
| JNFPGMDP_30 | 50358 | 50951 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| JNFPGMDP_15 | 39236 | 40861 | vmlR | ARO:3004476 | vmlR | 96.49 | 98.90 | NC_000964.3 |
| JNFPGMDP_93 | 38750 | 39067 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| JNFPGMDP_93 | 38412 | 38750 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| JNFPGMDP_32 | 140 | 2710 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 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. |
|---|---|---|---|---|---|---|---|
| No hit found | |||||||
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| JNFPGMDP_15 | 39239 | 40861 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 96.49 | 98.90 | WP_003234144.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| JNFPGMDP_8 | 68884 | 69669 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| JNFPGMDP_8 | 72556 | 73494 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391077 |
| JNFPGMDP_26 | 32694 | 33335 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| JNFPGMDP_86 | 8169 | 9345 | capB | 0.0 | Capsule | Immune modulation | 99.24 | 99.92 | NP_391471 |
| JNFPGMDP_58 | 20682 | 22445 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| JNFPGMDP_86 | 9828 | 10970 | capA | 0.0 | Capsule | Immune modulation | 98.86 | 100.00 | NP_391469 |
| JNFPGMDP_8 | 73514 | 80650 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.85 | 100.00 | NP_391076 |
| JNFPGMDP_8 | 70909 | 72528 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.77 | 100.00 | NP_391078 |
| JNFPGMDP_86 | 9360 | 9809 | capC | 0.0 | Capsule | Immune modulation | 98.67 | 100.00 | NP_391470 |
| JNFPGMDP_8 | 69695 | 70891 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.66 | 100.00 | NP_391079 |
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 |
|---|---|---|---|---|---|---|---|---|
| JNFPGMDP_11 | 31691 | 32827 | tufA | 0.0 | elongation factor Tu | 84.70 | 95.69 | AHM69299 |
| JNFPGMDP_55 | 11389 | 10520 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| JNFPGMDP_19 | 132889 | 133665 | CodY | 2.18e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| JNFPGMDP_7 | 74261 | 74830 | ClpP | 9.58e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| JNFPGMDP_49 | 28933 | 28541 | spxA1 | 3.33e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| JNFPGMDP_49 | 28933 | 28541 | spx | 1.99e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| JNFPGMDP_20 | 34593 | 34351 | SpoVG | 1.02e-38 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| JNFPGMDP_15 | 5112 | 5309 | CspA | 2.57e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| JNFPGMDP_26 | 44567 | 44761 | CspD | 2.80e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| JNFPGMDP_13 | 200810 | 201004 | CspB | 2.12e-27 | 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. |
|---|---|---|---|---|---|---|
| JNFPGMDP_78 | 1255 | 1415 | Col(SD853) | 161 / 194 | 83.85 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| JNFPGMDP_2 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_3 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_4 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_5 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_6 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_7 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_8 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_9 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_10 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_11 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_12 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_13 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_14 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_15 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_16 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_17 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_18 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_19 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_20 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_21 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_22 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_23 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_24 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_25 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_26 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_27 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_28 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_30 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_31 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_32 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_33 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_34 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_35 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_36 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_37 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_38 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_39 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_40 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_41 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_42 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_43 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_45 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_46 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_47 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_48 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_49 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_50 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_51 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_52 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_53 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_54 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_55 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_56 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_57 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_58 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_59 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_60 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_61 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_62 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_63 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_64 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_65 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_66 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_67 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_68 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_69 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_70 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_71 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_72 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_73 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_74 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_75 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_76 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_77 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_78 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_79 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_81 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_82 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_83 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_84 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_85 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_86 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_87 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_88 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_90 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_91 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_92 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_93 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_94 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_95 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_96 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_97 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_98 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_99 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_100 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_101 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_103 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_105 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_106 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_108 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_110 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_112 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_113 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_114 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_116 | 1.0 | 0.0 | 1.0 |
| JNFPGMDP_121 | 0.0 | 1.0 | 0.0 |
| JNFPGMDP_125 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JNFPGMDP_12 | 11874 | 18744 | False | Siphoviridae | VOG0275, VOG4602, VOG4662, VOG9667, VOG9667, VOG0650, VOG4552 |
| JNFPGMDP_12 | 25272 | 45713 | False | Siphoviridae | VOG6005, VOG7983, VOG0796, VOG10227, VOG0691, VOG0692, VOG9317, VOG4572, VOG2621, VOG0695, VOG0696, VOG0697, VOG0698, VOG10044, VOG0701, VOG9745, VOG4605, VOG4599, VOG3390, VOG5535, VOG5615, VOG0753, VOG0136, VOG4574 |
| JNFPGMDP_18 | 7614 | 31197 | False | Myoviridae | VOG4574, VOG0136, VOG0753, VOG5008, VOG4705, VOG3390, VOG7718, VOG4845, VOG4691, VOG5205, VOG0573, VOG1348, VOG1433, VOG1956, VOG6163, VOG4699, VOG1352, VOG1883, VOG1881, VOG1353, VOG4623, VOG4564, VOG4553, VOG4555, VOG0720 |
| JNFPGMDP_23 | 8765 | 16968 | False | Unknown | VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490 |
| JNFPGMDP_66 | 31140 | 34889 | False | Siphoviridae | VOG0181, VOG0737, VOG4556, VOG0787, VOG1638, VOG4552 |
| JNFPGMDP_93 | 1549 | 7713 | False | Myoviridae | VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
Phigaro v2.4.0 (Database: Jan. 2024 release)