Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 11 | 9 | 18.60 |
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. |
|---|---|---|---|---|---|---|---|---|
| NEEPCCMD_2 | 426691 | 428334 | vmlR | ARO:3004476 | vmlR | 98.72 | 100.00 | NC_000964.3 |
| NEEPCCMD_3 | 192390 | 193592 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| NEEPCCMD_3 | 174019 | 174873 | aadK | ARO:3002627 | aadK | 99.30 | 100.00 | AL009126.1 |
| NEEPCCMD_2 | 150922 | 151515 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| NEEPCCMD_2 | 100428 | 101861 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.00 | JYFL01000006.1 |
| NEEPCCMD_2 | 87615 | 88535 | mphK | ARO:3004541 | mphK | 99.02 | 100.00 | CP010314.1 |
| NEEPCCMD_8 | 40246 | 40584 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NEEPCCMD_8 | 39929 | 40246 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NEEPCCMD_56 | 5937 | 7106 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NEEPCCMD_32 | 966 | 3536 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 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. |
|---|---|---|---|---|---|---|---|
| NEEPCCMD_3 | 174019 | 174871 | aadK | Streptomycin | 98.94 | 99.77 | M26879 |
| NEEPCCMD_2 | 87615 | 88535 | mph(K) | Spiramycin, Telithromycin | 98.59 | 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. |
|---|---|---|---|---|---|---|---|---|
| NEEPCCMD_3 | 174019 | 174870 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 99.30 | 100.00 | WP_003229862.1 |
| NEEPCCMD_2 | 87615 | 88532 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.02 | 100.00 | WP_003246254.1 |
| NEEPCCMD_2 | 426694 | 428334 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.72 | 100.00 | WP_003234144.1 |
| NEEPCCMD_1 | 17342 | 17860 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| NEEPCCMD_23 | 10816 | 13413 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.71 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NEEPCCMD_1 | 493043 | 494224 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NEEPCCMD_62 | 4420 | 6183 | dep/capD | 0.0 | Capsule | Immune modulation | 99.72 | 100.00 | NP_389723 |
| NEEPCCMD_1 | 494707 | 495849 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| NEEPCCMD_31 | 1531 | 2172 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| NEEPCCMD_4 | 164953 | 165891 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| NEEPCCMD_1 | 494239 | 494688 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| NEEPCCMD_4 | 161270 | 162055 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| NEEPCCMD_4 | 165911 | 173047 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.23 | 100.00 | NP_391076 |
| NEEPCCMD_4 | 162081 | 163277 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| NEEPCCMD_4 | 163306 | 164925 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.39 | 100.00 | NP_391078 |
| NEEPCCMD_127 | 229 | 486 | isdG | 1.71e-122 | NEAT-type hemophore-mediated heme uptake system | Nutritional/Metabolic factor | 97.29 | 79.63 | WP_000587815 |
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 |
|---|---|---|---|---|---|---|---|---|
| NEEPCCMD_21 | 31799 | 32935 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NEEPCCMD_47 | 11245 | 10376 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NEEPCCMD_19 | 37755 | 36979 | CodY | 5.22e-126 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NEEPCCMD_13 | 30545 | 29976 | ClpP | 4.57e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NEEPCCMD_5 | 93417 | 93025 | spxA1 | 1.71e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NEEPCCMD_5 | 93417 | 93025 | spx | 1.02e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NEEPCCMD_22 | 20605 | 20847 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NEEPCCMD_2 | 378060 | 378257 | CspA | 1.98e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NEEPCCMD_31 | 14136 | 14330 | CspD | 2.02e-29 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| NEEPCCMD_9 | 32471 | 32277 | CspB | 8.65e-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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NEEPCCMD_1 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_2 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_3 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_4 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_5 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_6 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_7 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_8 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_9 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_10 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_11 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_12 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_13 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_14 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_15 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_16 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_17 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_18 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_19 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_20 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_21 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_22 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_23 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_24 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_25 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_26 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_27 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_28 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_29 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_30 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_31 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_32 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_33 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_34 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_35 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_36 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_37 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_38 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_39 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_40 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_41 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_42 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_43 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_44 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_45 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_46 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_47 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_48 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_49 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_50 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_51 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_52 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_53 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_54 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_55 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_56 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_57 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_58 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_59 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_60 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_61 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_62 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_63 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_64 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_65 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_66 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_67 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_68 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_69 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_70 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_71 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_72 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_73 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_74 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_76 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_77 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_78 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_79 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_80 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_81 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_82 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_83 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_84 | 0.0 | 1.0 | 0.0 |
| NEEPCCMD_85 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_86 | 1.0 | 0.0 | 1.0 |
| NEEPCCMD_88 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NEEPCCMD_8 | 69794 | 95766 | False | Myoviridae | VOG0136, VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490 |
| NEEPCCMD_16 | 29474 | 37277 | False | Myoviridae | VOG9867, VOG7134, VOG10940, VOG5721, VOG5779 |
| NEEPCCMD_17 | 11653 | 14600 | False | Unknown | VOG6464 |
Phigaro v2.4.0 (Database: Jan. 2024 release)