Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 5 | 17.15 |
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. |
|---|---|---|---|---|---|---|---|---|
| NPCOODPO_2 | 2542647 | 2543567 | mphK | ARO:3004541 | mphK | 98.02 | 100.00 | CP010314.1 |
| NPCOODPO_2 | 2529317 | 2530750 | lmrB | ARO:3002813 | lmrB | 100.00 | 100.00 | JYFL01000006.1 |
| NPCOODPO_2 | 2479593 | 2480186 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| NPCOODPO_2 | 2233539 | 2235182 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| NPCOODPO_2 | 1940387 | 1942957 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| NPCOODPO_2 | 1457612 | 1457950 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NPCOODPO_2 | 1457295 | 1457612 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NPCOODPO_2 | 333894 | 335063 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| NPCOODPO_2 | 162807 | 164009 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| NPCOODPO_2 | 145888 | 146742 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| NPCOODPO_2 | 145888 | 146740 | aadK | Streptomycin | 98.94 | 99.77 | M26879 |
| NPCOODPO_2 | 2845618 | 2846994 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.91 | 100.00 | D12567 |
| NPCOODPO_2 | 2542647 | 2543567 | mph(K) | Spiramycin, Telithromycin | 97.61 | 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. |
|---|---|---|---|---|---|---|---|---|
| NPCOODPO_2 | 145888 | 146739 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| NPCOODPO_2 | 2845618 | 2846991 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| NPCOODPO_2 | 2233539 | 2235179 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| NPCOODPO_2 | 2542659 | 2543567 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.02 | 99.02 | WP_003246254.1 |
| NPCOODPO_2 | 2848947 | 2849465 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| NPCOODPO_2 | 643474 | 646071 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NPCOODPO_3 | 483896 | 484681 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| NPCOODPO_3 | 480060 | 480998 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| NPCOODPO_3 | 472904 | 480040 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.78 | 100.00 | NP_391076 |
| NPCOODPO_2 | 3330528 | 3331709 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NPCOODPO_3 | 481026 | 482645 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391078 |
| NPCOODPO_2 | 3331724 | 3332173 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| NPCOODPO_2 | 693690 | 695453 | dep/capD | 0.0 | Capsule | Immune modulation | 99.43 | 100.00 | NP_389723 |
| NPCOODPO_3 | 482674 | 483870 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391079 |
| NPCOODPO_2 | 534389 | 535030 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| NPCOODPO_2 | 3332192 | 3333334 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
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 |
|---|---|---|---|---|---|---|---|---|
| NPCOODPO_2 | 2684615 | 2683479 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NPCOODPO_2 | 2798352 | 2797483 | pdxS | 4.82e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| NPCOODPO_2 | 1144334 | 1143558 | CodY | 3.00e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NPCOODPO_2 | 3490914 | 3490345 | ClpP | 2.23e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NPCOODPO_1 | 21945 | 21751 | CspB | 2.20e-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. |
|---|---|---|---|---|---|---|
| NPCOODPO_6 | 13244 | 13430 | Col(SD853) | 187 / 194 | 88.24 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NPCOODPO_1 | 0.0 | 1.0 | 0.0 |
| NPCOODPO_2 | 0.0 | 1.0 | 0.0 |
| NPCOODPO_3 | 0.0 | 1.0 | 0.0 |
| NPCOODPO_4 | 0.0 | 1.0 | 0.0 |
| NPCOODPO_5 | 0.0 | 1.0 | 0.0 |
| NPCOODPO_6 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NPCOODPO_2 | 474 | 17396 | False | Siphoviridae | VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG7896, VOG0641, VOG4574 |
| NPCOODPO_2 | 857507 | 860719 | False | Unknown | VOG4551, VOG0025 |
| NPCOODPO_2 | 927488 | 942659 | False | Unknown | VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG5070 |
| NPCOODPO_2 | 1487441 | 1514929 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| NPCOODPO_3 | 368022 | 372832 | False | Siphoviridae | VOG4555, VOG0720, VOG5023 |
| NPCOODPO_3 | 553424 | 568395 | False | Siphoviridae | VOG0136, VOG5221, VOG7896, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4619, VOG4772, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG4589 |
| NPCOODPO_5 | 5972 | 30534 | False | Siphoviridae | VOG0044, VOG0198, VOG0713, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG6163, VOG0801, VOG4619, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG7896, VOG5221 |
Phigaro v2.4.0 (Database: Jan. 2024 release)