Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 7 | 16.43 |
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. |
|---|---|---|---|---|---|---|---|---|
| NCILFEGH_10 | 689271 | 690125 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| NCILFEGH_10 | 648846 | 650048 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| NCILFEGH_10 | 468208 | 469377 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| NCILFEGH_15 | 423903 | 424220 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| NCILFEGH_15 | 423565 | 423903 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| NCILFEGH_16 | 297372 | 299942 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| NCILFEGH_17 | 212517 | 214163 | vmlR | ARO:3004476 | vmlR | 98.91 | 100.18 | NC_000964.3 |
| NCILFEGH_18 | 108611 | 109531 | mphK | ARO:3004541 | mphK | 97.06 | 100.00 | CP010314.1 |
| NCILFEGH_18 | 95281 | 96720 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.42 | JYFL01000006.1 |
| NCILFEGH_18 | 45559 | 46152 | tmrB | ARO:3003059 | tmrB | 97.97 | 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. |
|---|---|---|---|---|---|---|---|
| NCILFEGH_10 | 689271 | 690125 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| NCILFEGH_18 | 108611 | 109531 | mph(K) | Spiramycin, Telithromycin | 97.07 | 99.89 | 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. |
|---|---|---|---|---|---|---|---|---|
| NCILFEGH_17 | 212520 | 214163 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.91 | 100.00 | WP_003234144.1 |
| NCILFEGH_10 | 689274 | 690125 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| NCILFEGH_18 | 108614 | 109531 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.06 | 100.00 | WP_003246254.1 |
| NCILFEGH_10 | 175117 | 177714 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.52 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NCILFEGH_14 | 947381 | 948166 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391080 |
| NCILFEGH_14 | 536598 | 537779 | capB | 0.0 | Capsule | Immune modulation | 99.41 | 100.00 | NP_391471 |
| NCILFEGH_14 | 537794 | 538243 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| NCILFEGH_10 | 268615 | 269256 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| NCILFEGH_14 | 538262 | 539404 | capA | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_391469 |
| NCILFEGH_14 | 948192 | 949388 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| NCILFEGH_14 | 951064 | 952002 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.72 | 100.00 | NP_391077 |
| NCILFEGH_14 | 952022 | 959158 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.61 | 100.00 | NP_391076 |
| NCILFEGH_10 | 129385 | 131148 | dep/capD | 0.0 | Capsule | Immune modulation | 98.53 | 100.00 | NP_389723 |
| NCILFEGH_14 | 949417 | 951036 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.46 | 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 |
|---|---|---|---|---|---|---|---|---|
| NCILFEGH_19 | 28103 | 26967 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| NCILFEGH_21 | 4356 | 5225 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NCILFEGH_15 | 735749 | 736525 | CodY | 7.66e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NCILFEGH_14 | 694222 | 693653 | ClpP | 6.38e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NCILFEGH_15 | 275728 | 276120 | spxA1 | 6.02e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NCILFEGH_15 | 275728 | 276120 | spx | 3.59e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NCILFEGH_20 | 34709 | 34467 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NCILFEGH_17 | 155982 | 156179 | CspA | 1.05e-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 |
|---|---|---|---|
| NCILFEGH_1 | 0.0 | 1.0 | 0.0 |
| NCILFEGH_10 | 0.0 | 1.0 | 0.0 |
| NCILFEGH_14 | 0.0 | 1.0 | 0.0 |
| NCILFEGH_15 | 0.0 | 1.0 | 0.0 |
| NCILFEGH_16 | 0.0 | 1.0 | 0.0 |
| NCILFEGH_17 | 0.0 | 1.0 | 0.0 |
| NCILFEGH_18 | 0.0 | 1.0 | 0.0 |
| NCILFEGH_19 | 0.0 | 1.0 | 0.0 |
| NCILFEGH_20 | 0.0 | 1.0 | 0.0 |
| NCILFEGH_21 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NCILFEGH_15 | 367256 | 393697 | False | Myoviridae | VOG4602, VOG9667, VOG10599, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| NCILFEGH_16 | 12001 | 19590 | False | Siphoviridae | VOG0275, VOG4602, VOG9607, VOG9667, VOG4603, VOG0650, VOG4552, VOG4603 |
| NCILFEGH_16 | 27565 | 52913 | False | Siphoviridae | VOG0198, VOG0796, VOG10227, VOG0720, VOG4564, VOG4555, VOG4553, VOG1125, VOG0815, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG1323, VOG9745, VOG4605, VOG4599, VOG5535, VOG4728, VOG0641, VOG4574 |
Phigaro v2.4.0 (Database: Jan. 2024 release)