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. |
|---|---|---|---|---|---|---|---|---|
| NEHPIGDC_5 | 581873 | 582727 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| NEHPIGDC_5 | 563139 | 564341 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| NEHPIGDC_4 | 439295 | 439612 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NEHPIGDC_4 | 438957 | 439295 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NEHPIGDC_5 | 361461 | 362630 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| NEHPIGDC_3 | 258603 | 261173 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| NEHPIGDC_1 | 200751 | 202376 | vmlR | ARO:3004476 | vmlR | 98.15 | 98.90 | NC_000964.3 |
| NEHPIGDC_7 | 153356 | 153949 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| NEHPIGDC_7 | 102836 | 104275 | lmrB | ARO:3002813 | lmrB | 98.95 | 100.42 | JYFL01000006.1 |
| NEHPIGDC_7 | 90020 | 90940 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| NEHPIGDC_5 | 581875 | 582727 | aadK | Streptomycin | 99.30 | 99.77 | M26879 |
| NEHPIGDC_2 | 34683 | 36059 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.06 | 100.00 | D12567 |
| NEHPIGDC_7 | 90020 | 90940 | mph(K) | Spiramycin, Telithromycin | 98.26 | 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. |
|---|---|---|---|---|---|---|---|---|
| NEHPIGDC_2 | 34683 | 36056 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| NEHPIGDC_5 | 581876 | 582727 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| NEHPIGDC_7 | 90020 | 90937 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| NEHPIGDC_1 | 200754 | 202376 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.15 | 98.90 | WP_003234144.1 |
| NEHPIGDC_2 | 38012 | 38530 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| NEHPIGDC_5 | 54461 | 57058 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.29 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NEHPIGDC_5 | 162072 | 162713 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| NEHPIGDC_2 | 529625 | 530806 | capB | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | NP_391471 |
| NEHPIGDC_2 | 944583 | 945368 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| NEHPIGDC_2 | 530821 | 531270 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| NEHPIGDC_5 | 8262 | 10025 | dep/capD | 0.0 | Capsule | Immune modulation | 99.43 | 100.00 | NP_389723 |
| NEHPIGDC_2 | 948266 | 949204 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| NEHPIGDC_2 | 531289 | 532431 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| NEHPIGDC_2 | 945394 | 946590 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| NEHPIGDC_2 | 949224 | 956360 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.33 | 100.00 | NP_391076 |
| NEHPIGDC_2 | 946619 | 948238 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.04 | 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 |
|---|---|---|---|---|---|---|---|---|
| NEHPIGDC_8 | 31692 | 32828 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NEHPIGDC_11 | 4250 | 5119 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NEHPIGDC_4 | 750991 | 751767 | CodY | 8.53e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NEHPIGDC_2 | 692976 | 692407 | ClpP | 6.36e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NEHPIGDC_4 | 289132 | 289524 | spxA1 | 6.71e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NEHPIGDC_4 | 289132 | 289524 | spx | 4.00e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NEHPIGDC_6 | 20679 | 20921 | SpoVG | 7.54e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NEHPIGDC_1 | 147354 | 147551 | CspA | 1.00e-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 |
|---|---|---|---|
| NEHPIGDC_1 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_2 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_3 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_4 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_5 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_6 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_7 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_8 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_10 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_11 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_12 | 0.0 | 1.0 | 0.0 |
| NEHPIGDC_13 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NEHPIGDC_4 | 383008 | 409152 | 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 |
| NEHPIGDC_5 | 749054 | 775446 | False | Siphoviridae | VOG7531, VOG0705, VOG6116, VOG8440, VOG0602, VOG4574, VOG0753, VOG4705, VOG4626, VOG4619, VOG0801, VOG6163, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5601, VOG4553, VOG4573, VOG4556, VOG4544, VOG4581, VOG4841, VOG0531, VOG6081 |
| NEHPIGDC_5 | 795894 | 810932 | False | Siphoviridae | VOG5543, VOG0422, VOG0982, VOG0026, VOG6497, VOG10937, VOG5753, VOG9761, VOG7255, VOG0052, VOG1563, VOG11003, VOG2215, VOG4551, VOG0025 |
Phigaro v2.4.0 (Database: Jan. 2024 release)