Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 10 | 10 | 9 | 16.76 |
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. |
|---|---|---|---|---|---|---|---|---|
| NHAKPCLB_7 | 62273 | 62590 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| NHAKPCLB_7 | 61935 | 62273 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| NHAKPCLB_45 | 60973 | 62175 | blt | ARO:3003006 | blt | 98.00 | 100.00 | L32599.1 |
| NHAKPCLB_28 | 47644 | 49083 | lmrB | ARO:3002813 | lmrB | 99.58 | 100.42 | JYFL01000006.1 |
| NHAKPCLB_45 | 44224 | 45078 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| NHAKPCLB_28 | 34829 | 35749 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| NHAKPCLB_29 | 27256 | 29826 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.53 | 100.00 | AL009126.3 |
| NHAKPCLB_60 | 19004 | 19597 | tmrB | ARO:3003059 | tmrB | 99.49 | 100.00 | AL009126.3 |
| NHAKPCLB_50 | 5829 | 7475 | vmlR | ARO:3004476 | vmlR | 98.36 | 100.18 | 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. |
|---|---|---|---|---|---|---|---|
| NHAKPCLB_45 | 44224 | 45078 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| NHAKPCLB_28 | 34829 | 35749 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| NHAKPCLB_28 | 34829 | 35737 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| NHAKPCLB_45 | 44224 | 45075 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| NHAKPCLB_50 | 5832 | 7475 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.36 | 100.00 | WP_003234144.1 |
| NHAKPCLB_6 | 51079 | 51597 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| NHAKPCLB_14 | 29667 | 30848 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| NHAKPCLB_2 | 112948 | 113733 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| NHAKPCLB_14 | 28042 | 29184 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| NHAKPCLB_2 | 101956 | 109092 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.30 | 100.00 | NP_391076 |
| NHAKPCLB_30 | 19837 | 21600 | dep/capD | 0.0 | Capsule | Immune modulation | 99.04 | 100.00 | NP_389723 |
| NHAKPCLB_2 | 109112 | 110050 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.04 | 100.00 | NP_391077 |
| NHAKPCLB_2 | 111726 | 112922 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| NHAKPCLB_38 | 144133 | 144774 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| NHAKPCLB_14 | 29203 | 29652 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| NHAKPCLB_2 | 110078 | 111697 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.73 | 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 |
|---|---|---|---|---|---|---|---|---|
| NHAKPCLB_24 | 31853 | 32989 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NHAKPCLB_26 | 4326 | 5195 | pdxS | 1.98e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| NHAKPCLB_19 | 93966 | 93190 | CodY | 1.99e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NHAKPCLB_42 | 4413 | 4982 | ClpP | 2.96e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NHAKPCLB_25 | 23413 | 23805 | spxA1 | 4.12e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NHAKPCLB_25 | 23413 | 23805 | spx | 2.46e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NHAKPCLB_31 | 34800 | 34558 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NHAKPCLB_62 | 10981 | 11178 | CspA | 2.22e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NHAKPCLB_38 | 132903 | 132709 | CspD | 1.09e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| NHAKPCLB_5 | 13906 | 14100 | CspB | 4.22e-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. |
|---|---|---|---|---|---|---|
| NHAKPCLB_36 | 558 | 725 | Col(SD853) | 168 / 194 | 86.90 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NHAKPCLB_1 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_2 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_3 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_4 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_5 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_6 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_7 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_8 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_9 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_10 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_11 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_12 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_13 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_14 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_15 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_16 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_17 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_18 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_19 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_20 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_21 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_22 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_23 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_24 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_25 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_26 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_27 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_28 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_29 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_30 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_31 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_32 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_33 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_34 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_35 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_36 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_37 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_38 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_40 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_41 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_42 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_43 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_44 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_45 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_46 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_47 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_48 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_49 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_50 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_51 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_52 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_53 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_54 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_55 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_56 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_57 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_58 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_59 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_60 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_61 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_62 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_63 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_64 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_65 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_66 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_67 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_69 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_70 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_72 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_74 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_76 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_77 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_78 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_79 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_81 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_82 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_86 | 1.0 | 0.0 | 1.0 |
| NHAKPCLB_87 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_88 | 0.0 | 1.0 | 0.0 |
| NHAKPCLB_89 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NHAKPCLB_7 | 5788 | 32471 | False | Myoviridae | VOG9667, VOG3490, VOG0189, VOG4843, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| NHAKPCLB_13 | 8196 | 18726 | True | Siphoviridae | VOG6587, VOG0189, VOG4566, VOG7581, VOG9667, VOG9667, VOG1563, VOG0275, VOG0275 |
Phigaro v2.4.0 (Database: Jan. 2024 release)