Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| NPEPGNMH_3 | 678313 | 679482 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NPEPGNMH_2 | 591792 | 592130 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NPEPGNMH_2 | 591475 | 591792 | ykkD | ARO:3003064 | ykkD | 100.00 | 100.00 | AL009126.1 |
| NPEPGNMH_3 | 455959 | 457161 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| NPEPGNMH_3 | 437598 | 438452 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| NPEPGNMH_4 | 276660 | 279230 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| NPEPGNMH_6 | 163018 | 163611 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| NPEPGNMH_6 | 112515 | 113954 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| NPEPGNMH_6 | 99700 | 100620 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| NPEPGNMH_8 | 29251 | 30894 | vmlR | ARO:3004476 | vmlR | 100.00 | 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. |
|---|---|---|---|---|---|---|---|
| NPEPGNMH_3 | 437598 | 438452 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| NPEPGNMH_6 | 99700 | 100620 | mph(K) | Spiramycin, Telithromycin | 100.00 | 100.00 | NC_000964 |
| NPEPGNMH_1 | 1008757 | 1010133 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 100.00 | 100.00 | X08034 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| NPEPGNMH_3 | 437598 | 438449 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| NPEPGNMH_6 | 99700 | 100617 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| NPEPGNMH_1 | 1006239 | 1006757 | satA | streptothricin N-acetyltransferase SatA | EXACTX | 100.00 | 100.00 | WP_003242546.1 |
| NPEPGNMH_1 | 1008760 | 1010133 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| NPEPGNMH_8 | 29251 | 30891 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| NPEPGNMH_5 | 192930 | 195524 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NPEPGNMH_1 | 519262 | 520404 | capA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391469 |
| NPEPGNMH_1 | 520887 | 522068 | capB | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391471 |
| NPEPGNMH_1 | 520423 | 520872 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| NPEPGNMH_5 | 240419 | 242182 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| NPEPGNMH_1 | 112916 | 113701 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| NPEPGNMH_1 | 109080 | 110018 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391077 |
| NPEPGNMH_1 | 111694 | 112890 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391079 |
| NPEPGNMH_1 | 110046 | 111665 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391078 |
| NPEPGNMH_1 | 101924 | 109060 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391076 |
| NPEPGNMH_3 | 878201 | 878842 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
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 |
|---|---|---|---|---|---|---|---|---|
| NPEPGNMH_9 | 31719 | 32855 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NPEPGNMH_11 | 4392 | 5261 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NPEPGNMH_2 | 278506 | 277730 | CodY | 8.25e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NPEPGNMH_1 | 367642 | 368211 | ClpP | 6.29e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NPEPGNMH_2 | 740957 | 740565 | spxA1 | 2.45e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| NPEPGNMH_10 | 20889 | 21131 | SpoVG | 7.56e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NPEPGNMH_8 | 76373 | 76176 | CspA | 3.38e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NPEPGNMH_3 | 866238 | 866044 | CspD | 5.70e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
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 |
|---|---|---|---|
| NPEPGNMH_1 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_2 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_3 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_4 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_5 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_6 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_7 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_8 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_9 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_10 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_11 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_12 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_13 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_14 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_15 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_16 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_17 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_18 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_19 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_20 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_21 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_23 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_24 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_25 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_26 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_27 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_28 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_29 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_30 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_31 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_32 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_34 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_35 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_36 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_37 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_38 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_39 | 0.0 | 1.0 | 0.0 |
| NPEPGNMH_41 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_42 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_43 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_44 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_45 | 1.0 | 0.0 | 1.0 |
| NPEPGNMH_46 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NPEPGNMH_2 | 621969 | 648077 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| NPEPGNMH_3 | 476716 | 507090 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG8642, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
Phigaro v2.4.0 (Database: Jan. 2024 release)