Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 9 | 18.71 |
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. |
|---|---|---|---|---|---|---|---|---|
| NADAGIKK_46 | 179581 | 180783 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| NADAGIKK_46 | 161221 | 162075 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| NADAGIKK_5 | 151310 | 151627 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| NADAGIKK_5 | 150972 | 151310 | ykkC | ARO:3003063 | ykkC | 97.32 | 100.00 | AL009126.1 |
| NADAGIKK_39 | 125704 | 126297 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| NADAGIKK_53 | 103203 | 104372 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NADAGIKK_39 | 75306 | 76745 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| NADAGIKK_39 | 62490 | 63410 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| NADAGIKK_33 | 29149 | 30795 | vmlR | ARO:3004476 | vmlR | 98.36 | 100.18 | NC_000964.3 |
| NADAGIKK_52 | 27384 | 29954 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 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. |
|---|---|---|---|---|---|---|---|
| NADAGIKK_7 | 54340 | 55716 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| NADAGIKK_39 | 62490 | 63410 | mph(K) | Spiramycin, Telithromycin | 99.67 | 100.00 | NC_000964 |
| NADAGIKK_46 | 161221 | 162073 | aadK | Streptomycin | 98.83 | 99.77 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| NADAGIKK_39 | 62490 | 63407 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| NADAGIKK_7 | 54343 | 55716 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| NADAGIKK_33 | 29149 | 30792 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.36 | 100.00 | WP_003234144.1 |
| NADAGIKK_46 | 161221 | 162072 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| NADAGIKK_7 | 51819 | 52337 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| NADAGIKK_8 | 10949 | 13546 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.17 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NADAGIKK_53 | 303111 | 303752 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| NADAGIKK_58 | 24223 | 25404 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NADAGIKK_58 | 23759 | 24208 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| NADAGIKK_3 | 51994 | 52779 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| NADAGIKK_3 | 48158 | 49096 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.47 | 100.00 | NP_391077 |
| NADAGIKK_58 | 22598 | 23740 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| NADAGIKK_3 | 41002 | 48138 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.31 | 100.00 | NP_391076 |
| NADAGIKK_3 | 50772 | 51968 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| NADAGIKK_3 | 49124 | 50743 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.89 | 100.00 | NP_391078 |
| NADAGIKK_13 | 6498 | 8261 | dep/capD | 0.0 | Capsule | Immune modulation | 98.70 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| NADAGIKK_41 | 31676 | 32812 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NADAGIKK_62 | 11241 | 10372 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NADAGIKK_1 | 2604 | 1828 | CodY | 1.09e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NADAGIKK_17 | 130701 | 130132 | ClpP | 1.14e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NADAGIKK_5 | 100 | 492 | spxA1 | 1.69e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NADAGIKK_5 | 100 | 492 | spx | 1.01e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NADAGIKK_20 | 20498 | 20740 | SpoVG | 7.49e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NADAGIKK_33 | 79189 | 78992 | CspA | 3.62e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NADAGIKK_53 | 291150 | 290956 | CspD | 2.20e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| NADAGIKK_72 | 85887 | 86081 | CspB | 1.09e-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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NADAGIKK_1 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_2 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_3 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_4 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_5 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_6 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_7 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_8 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_10 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_13 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_14 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_15 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_16 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_17 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_18 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_19 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_20 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_21 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_22 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_23 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_24 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_25 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_27 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_28 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_29 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_31 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_32 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_33 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_34 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_35 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_37 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_38 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_39 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_40 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_41 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_42 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_43 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_44 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_45 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_46 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_47 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_48 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_49 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_50 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_51 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_52 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_53 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_54 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_55 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_56 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_57 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_58 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_59 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_60 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_61 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_62 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_63 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_64 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_65 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_67 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_68 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_69 | 1.0 | 0.0 | 1.0 |
| NADAGIKK_70 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_71 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_72 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_73 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_74 | 0.0 | 1.0 | 0.0 |
| NADAGIKK_75 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NADAGIKK_5 | 93965 | 120013 | 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 |
| NADAGIKK_14 | 6249 | 23568 | False | Myoviridae | VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| NADAGIKK_34 | 9409 | 13860 | False | Unknown | VOG4714, VOG2352, VOG3851, VOG5668, VOG2725, VOG4549 |
| NADAGIKK_69 | 15129 | 38778 | False | Siphoviridae | VOG3616, VOG1024, VOG10944, VOG9244, VOG4599, VOG4605, VOG6163, VOG5852, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG4544, VOG4581, VOG0221 |
Phigaro v2.4.0 (Database: Jan. 2024 release)