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Table 3 Epitope prediction of HLA-II-restrict T cells using Rm39, Rm180, Rm239 and Rm76 protein sequences with TEPITOPE and NetMHCII software

From: Mining a differential sialotranscriptome of Rhipicephalus microplus guides antigen discovery to formulate a vaccine that reduces tick infestations

TEPITOPE
Native antigen (full-length sequence) No. of peptidesa No. of allelesb Scorec
Rm239 (500 amino acids) 2,023 54 31.22
Rm76 (152 amino acids) 867 54 30.85
Rm180 (186 amino acids) 105 53 43.27
Rm39 (105 amino acids) 38 34 4.05
Recombinant vaccine antigend (partial sequence) Positionf No. of allelesb Scoreg
Rm180 25 53 24.9
Rm39 69 5 0.6
30 9 2.3
Rm239 79 2 0.23
59 27 3.06
38 5 1.30
Rm76e 157 52 24.5
137 52 9.7
132 52 2.4
129 53 6.2
122 53 25.7
121 53 17.8
120 52 7.5
117 54 5.7
116 53 5.0
66 52 15.0
62 35 3.3
56 53 22.1
50 1 1.2
46 53 11.9
40 53 5.0
39 53 15.7
37 3 2.4
36 53 12.0
NetMHCII
Recombinant vaccine antigene No of peptidesh No of Allelesi Strong ligandsj
Rm180 52 10 33
Rm39 72 6
Rm239 130 14 75
Rm76 e1 138 14 166
  1. aTotal number of epitopes with positive score
  2. bA total of 54 HLA-DR alleles were used by TEPITOPE. The values refer to the number of HLA-DRB alleles that binds to predicted epitopes
  3. cThe score (ranging from negative to positive values) is a calculated value to define the binding affinity between peptide and HLA, therefore the higher the score, the higher the binding affinity. The values are expressed as the mean of scores from predicted bindings
  4. dData from sequences (partial) of recombinant proteins used in this study
  5. eRm76 was the only antigen cloned as full-length sequence
  6. fPosition of the first amino acid of the HLA class II binding peptide on the protein sequence
  7. gOnly the positive scores were considered, i.e. those with the most binding affinity properties
  8. hTotal number of possible peptides based on each protein size
  9. iA total of 14 HLA-DR alleles were used by NetMHCII v. 2.2. The values refer to the number of alleles that presents predicted ligands
  10. jThe binding affinity to HLA-DR is based on IC50 values in nM. The threshold for strong ligands is IC50 = 50. Only results for strong ligands are shown