unipept 2.1.1 → 2.2.2

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Files changed (55) hide show
  1. checksums.yaml +4 -4
  2. data/.github/dependabot.yml +9 -0
  3. data/.github/workflows/ci.yml +6 -27
  4. data/.rakeTasks +7 -0
  5. data/.rubocop.yml +2 -0
  6. data/.ruby-version +1 -1
  7. data/CITATION.cff +30 -0
  8. data/Gemfile +2 -2
  9. data/Gemfile.lock +60 -41
  10. data/README.md +2 -2
  11. data/Rakefile +4 -4
  12. data/VERSION +1 -1
  13. data/lib/batch_iterator.rb +16 -0
  14. data/lib/commands/prot2pept.rb +1 -2
  15. data/lib/commands/unipept/api_runner.rb +10 -12
  16. data/lib/commands/unipept/config.rb +1 -1
  17. data/lib/commands/unipept/pept2taxa.rb +1 -5
  18. data/lib/commands/unipept/taxa2tree.rb +74 -0
  19. data/lib/commands/unipept.rb +25 -1
  20. data/lib/commands/uniprot.rb +4 -5
  21. data/lib/configuration.rb +6 -7
  22. data/lib/formatters.rb +108 -36
  23. data/lib/server_message.rb +2 -4
  24. data/test/commands/unipept/test_api_runner.rb +8 -7
  25. data/test/commands/unipept/test_config.rb +1 -1
  26. data/test/commands/unipept/test_pept2ec.rb +11 -11
  27. data/test/commands/unipept/test_pept2funct.rb +15 -15
  28. data/test/commands/unipept/test_pept2go.rb +10 -10
  29. data/test/commands/unipept/test_pept2interpro.rb +26 -26
  30. data/test/commands/unipept/test_pept2lca.rb +2 -2
  31. data/test/commands/unipept/test_pept2prot.rb +2 -2
  32. data/test/commands/unipept/test_pept2taxa.rb +2 -4
  33. data/test/commands/unipept/test_peptinfo.rb +16 -16
  34. data/test/commands/unipept/test_taxa2lca.rb +2 -2
  35. data/test/commands/unipept/test_taxa2tree.rb +68 -0
  36. data/test/commands/unipept/test_taxonomy.rb +2 -2
  37. data/test/helper.rb +10 -0
  38. data/test/support/api_stub.rb +60 -0
  39. data/test/support/resources/pept2ec.json +55 -0
  40. data/test/support/resources/pept2funct.json +73 -0
  41. data/test/support/resources/pept2go.json +43 -0
  42. data/test/support/resources/pept2interpro.json +43 -0
  43. data/test/support/resources/pept2lca.json +14 -0
  44. data/test/support/resources/pept2prot.json +422 -0
  45. data/test/support/resources/pept2taxa.json +194 -0
  46. data/test/support/resources/peptinfo.json +70 -0
  47. data/test/support/resources/taxa2tree.json +194 -0
  48. data/test/support/resources/taxonomy.json +22 -0
  49. data/test/test_configuration.rb +1 -1
  50. data/test/test_formatters.rb +5 -5
  51. data/test/test_output_writer.rb +1 -1
  52. data/test/test_server_message.rb +2 -2
  53. data/test.taxa +4 -0
  54. data/unipept.gemspec +32 -21
  55. metadata +26 -9
data/test/support/resources/pept2funct.json ADDED
@@ -0,0 +1,73 @@
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+ [
2
+ {
3
+ "peptide": "AALTER",
4
+ "total_protein_count": 7,
5
+ "ec": [
6
+ {
7
+ "ec_number": "3.1.3.3",
8
+ "protein_count": 2
9
+ },
10
+ {
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+ "ec_number": "6.3.2.13",
12
+ "protein_count": 2
13
+ }
14
+ ],
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+ "go": [
16
+ {
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+ "go_term": "GO:0000287",
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+ "protein_count": 5
19
+ },
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+ {
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+ "go_term": "GO:0005737",
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+ "protein_count": 5
23
+ }
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+ ],
25
+ "ipr": [
26
+ {
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+ "code": "IPR013221",
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+ "protein_count": 2
29
+ }
30
+ ]
31
+ },
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+ {
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+ "peptide": "AALER",
34
+ "total_protein_count": 208,
35
+ "ec": [
36
+ {
37
+ "ec_number": "6.1.1.16",
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+ "protein_count": 44
39
+ },
40
+ {
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+ "ec_number": "2.7.7.38",
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+ "protein_count": 13
43
+ }
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+ ],
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+ "go": [
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+ {
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+ "go_term": "GO:0005737",
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+ "protein_count": 106
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+ },
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+ {
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+ "go_term": "GO:0005524",
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+ "protein_count": 75
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+ }
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+ ],
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+ "ipr": [
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+ {
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+ "code": "IPR014729",
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+ "protein_count": 48
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+ },
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+ {
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+ "code": "IPR009080",
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+ "protein_count": 45
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+ }
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+ ]
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+ },
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+ {
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+ "peptide": "AAEVALVGTEK",
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+ "total_protein_count": 0,
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+ "ec": [],
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+ "go": [],
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+ "ipr": []
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+ }
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+ ]
data/test/support/resources/pept2go.json ADDED
@@ -0,0 +1,43 @@
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+ [
2
+ {
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+ "peptide": "AALTER",
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+ "total_protein_count": 7,
5
+ "go": [
6
+ {
7
+ "go_term": "GO:0000287",
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+ "protein_count": 5
9
+ },
10
+ {
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+ "go_term": "GO:0005737",
12
+ "protein_count": 5
13
+ },
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+ {
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+ "go_term": "GO:0042803",
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+ "protein_count": 1
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+ }
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+ ]
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+ },
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+ {
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+ "peptide": "AALER",
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+ "total_protein_count": 208,
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+ "go": [
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+ {
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+ "go_term": "GO:0005737",
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+ "protein_count": 106
27
+ },
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+ {
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+ "go_term": "GO:0005524",
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+ "protein_count": 75
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+ },
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+ {
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+ "go_term": "GO:0008270",
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+ "protein_count": 48
35
+ }
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+ ]
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+ },
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+ {
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+ "peptide": "AAEVALVGTEK",
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+ "total_protein_count": 0,
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+ "go": []
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+ }
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+ ]
data/test/support/resources/pept2interpro.json ADDED
@@ -0,0 +1,43 @@
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+ [
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+ {
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+ "peptide": "AALTER",
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+ "total_protein_count": 7,
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+ "ipr": [
6
+ {
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+ "code": "IPR013221",
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+ "protein_count": 2
9
+ },
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+ {
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+ "code": "IPR036565",
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+ "protein_count": 2
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+ },
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+ {
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+ "code": "IPR023214",
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+ "protein_count": 2
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+ }
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+ ]
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+ },
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+ {
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+ "peptide": "AALER",
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+ "total_protein_count": 208,
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+ "ipr": [
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+ {
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+ "code": "IPR014729",
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+ "protein_count": 48
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+ },
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+ {
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+ "code": "IPR009080",
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+ "protein_count": 45
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+ },
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+ {
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+ "code": "IPR015803",
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+ "protein_count": 44
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+ }
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+ ]
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+ },
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+ {
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+ "peptide": "VAQFLL",
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+ "total_protein_count": 0,
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+ "ipr": []
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+ }
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+ ]
data/test/support/resources/pept2lca.json ADDED
@@ -0,0 +1,14 @@
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+ [
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+ {
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+ "peptide": "AALTER",
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+ "taxon_id": 1,
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+ "taxon_name": "root",
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+ "taxon_rank": "no rank"
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+ },
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+ {
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+ "peptide": "AALER",
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+ "taxon_id": 1,
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+ "taxon_name": "root",
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+ "taxon_rank": "no rank"
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+ }
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+ ]
data/test/support/resources/pept2prot.json ADDED
@@ -0,0 +1,422 @@
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+ [
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "P42654",
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+ "protein_name": "14-3-3-like protein B",
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+ "taxon_id": 3906
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "Q96453",
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+ "protein_name": "14-3-3-like protein D",
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+ "taxon_id": 3847
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "C6TH93",
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+ "protein_name": "Casparian strip membrane protein 4",
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+ "taxon_id": 3847
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A2Z6PAC3",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 3900
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5B7A3K5",
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+ "protein_name": "Putative 14-3-3-like protein D isoform X1",
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+ "taxon_id": 16924
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A396GNG6",
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+ "protein_name": "Putative 14-3-3 protein",
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+ "taxon_id": 3880
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A072VBW0",
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+ "protein_name": "Putative 14-3-3 protein",
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+ "taxon_id": 3880
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "I1LUM3",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 3847
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A1S3WXW9",
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+ "protein_name": "14-3-3 protein 9-like isoform X1",
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+ "taxon_id": 4097
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A2H5N535",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 55188
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A438E5J2",
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+ "protein_name": "14-3-3-like protein D",
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+ "taxon_id": 29760
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A445HT97",
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+ "protein_name": "14-3-3-like protein D isoform A",
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+ "taxon_id": 3848
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5J5A607",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 561372
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A1S4A416",
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+ "protein_name": "14-3-3 protein 9-like",
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+ "taxon_id": 4097
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A1U7VM87",
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+ "protein_name": "14-3-3 protein 9-like isoform X2",
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+ "taxon_id": 4096
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A2N9J4Q3",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 28930
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A445IBP6",
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+ "protein_name": "14-3-3-like protein D isoform A",
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+ "taxon_id": 3848
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A445HTA3",
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+ "protein_name": "14-3-3-like protein D isoform C",
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+ "taxon_id": 3848
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "T2DN83",
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+ "protein_name": "14-3-3-like protein D",
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+ "taxon_id": 3885
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A445CI86",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 3818
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A444Y3Q8",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 3818
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A2K3PKW1",
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+ "protein_name": "14-3-3-like protein d-like",
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+ "taxon_id": 57577
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A200QJZ5",
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+ "protein_name": "14-3-3 protein",
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+ "taxon_id": 56857
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5B6YWQ8",
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+ "protein_name": "Putative 14-3-3-like protein D",
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+ "taxon_id": 16924
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5J5A796",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 561372
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "C6TM63",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 3847
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A1S3WXS1",
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+ "protein_name": "14-3-3 protein 9-like isoform X2",
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+ "taxon_id": 4097
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A1U7VVV5",
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+ "protein_name": "14-3-3 protein 9-like isoform X1",
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+ "taxon_id": 4096
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A2H3Y4D2",
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+ "protein_name": "14-3-3-like protein D isoform X2",
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+ "taxon_id": 42345
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5B6YWR0",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 16924
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A067GE20",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 2711
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5B6Z3E6",
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+ "protein_name": "Putative 14-3-3-like protein D isoform X2",
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+ "taxon_id": 16924
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5J5A2G8",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 561372
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A445IC54",
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+ "protein_name": "14-3-3-like protein D isoform C",
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+ "taxon_id": 3848
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "E1U3Z1",
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+ "protein_name": "14-3-3-like protein B",
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+ "taxon_id": 3827
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "I1M3M0",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 3847
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A0R0HF31",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 3847
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A2H3ZH40",
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+ "protein_name": "14-3-3-like protein D isoform X2",
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+ "taxon_id": 42345
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5B7A4U9",
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+ "protein_name": "Putative 14-3-3 domain-containing protein",
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+ "taxon_id": 16924
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "M0TAI1",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 214687
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A1S4CN65",
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+ "protein_name": "14-3-3 protein 9-like isoform X2",
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+ "taxon_id": 4097
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
250
+ "uniprot_id": "A0A2H5N3C1",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 55188
253
+ },
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+ {
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+ "peptide": "ENFVYIAK",
256
+ "uniprot_id": "A0A2H3ZHX0",
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+ "protein_name": "14-3-3-like protein D isoform X1",
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+ "taxon_id": 42345
259
+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "M0TY03",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 214687
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A445CI73",
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+ "protein_name": "14_3_3 domain-containing protein",
270
+ "taxon_id": 3818
271
+ },
272
+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A3S3NBY5",
275
+ "protein_name": "14-3-3-like protein D isoform X1",
276
+ "taxon_id": 337451
277
+ },
278
+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "V4U9U4",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 85681
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A151SEM7",
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+ "protein_name": "14-3-3-like protein D",
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+ "taxon_id": 3821
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A445IBK9",
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+ "protein_name": "14-3-3-like protein D isoform D",
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+ "taxon_id": 3848
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A1S4CMF0",
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+ "protein_name": "14-3-3 protein 9-like isoform X1",
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+ "taxon_id": 4097
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A1J6KH36",
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+ "protein_name": "14-3-3 protein 9",
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+ "taxon_id": 49451
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5B7A5K1",
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+ "protein_name": "Putative 14-3-3-like protein D isoform X1",
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+ "taxon_id": 16924
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "F6H2P0",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 29760
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A1J6IP66",
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+ "protein_name": "14-3-3 protein 9",
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+ "taxon_id": 49451
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A5B7A8T8",
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+ "protein_name": "Putative 14-3-3-like protein D isoform X1",
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+ "taxon_id": 16924
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+ },
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+ {
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+ "peptide": "ENFVYIAK",
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+ "uniprot_id": "A0A0R0H7R6",
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+ "protein_name": "14_3_3 domain-containing protein",
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+ "taxon_id": 3847
337
+ },
338
+ {
339
+ "peptide": "ENFVYIAK",
340
+ "uniprot_id": "A0A067GDS1",
341
+ "protein_name": "14_3_3 domain-containing protein",
342
+ "taxon_id": 2711
343
+ },
344
+ {
345
+ "peptide": "ENFVYIAK",
346
+ "uniprot_id": "A0A445BBW8",
347
+ "protein_name": "14_3_3 domain-containing protein",
348
+ "taxon_id": 3818
349
+ },
350
+ {
351
+ "peptide": "ENFVYIAK",
352
+ "uniprot_id": "V4W919",
353
+ "protein_name": "14_3_3 domain-containing protein",
354
+ "taxon_id": 85681
355
+ },
356
+ {
357
+ "peptide": "ENFVYIAK",
358
+ "uniprot_id": "G7LIR4",
359
+ "protein_name": "General regulatory factor 2",
360
+ "taxon_id": 3880
361
+ },
362
+ {
363
+ "peptide": "ENFVYIAK",
364
+ "uniprot_id": "A0A2H3Y3V0",
365
+ "protein_name": "14-3-3-like protein D isoform X1",
366
+ "taxon_id": 42345
367
+ },
368
+ {
369
+ "peptide": "ENFVYIAK",
370
+ "uniprot_id": "A0A5J4ZBP6",
371
+ "protein_name": "14_3_3 domain-containing protein",
372
+ "taxon_id": 561372
373
+ },
374
+ {
375
+ "peptide": "EGGAGSSTGQR",
376
+ "uniprot_id": "A0A370PI74",
377
+ "protein_name": "Uncharacterized protein",
378
+ "taxon_id": 1353007
379
+ },
380
+ {
381
+ "peptide": "EGGAGSSTGQR",
382
+ "uniprot_id": "G3Y2A8",
383
+ "protein_name": "Uncharacterized protein",
384
+ "taxon_id": 380704
385
+ },
386
+ {
387
+ "peptide": "EGGAGSSTGQR",
388
+ "uniprot_id": "A0A401KHS6",
389
+ "protein_name": "Uncharacterized protein",
390
+ "taxon_id": 105351
391
+ },
392
+ {
393
+ "peptide": "EGGAGSSTGQR",
394
+ "uniprot_id": "A0A3F3RJX9",
395
+ "protein_name": "Uncharacterized protein",
396
+ "taxon_id": 5061
397
+ },
398
+ {
399
+ "peptide": "EGGAGSSTGQR",
400
+ "uniprot_id": "A0A370CDF7",
401
+ "protein_name": "Uncharacterized protein",
402
+ "taxon_id": 1353008
403
+ },
404
+ {
405
+ "peptide": "EGGAGSSTGQR",
406
+ "uniprot_id": "A0A319AT72",
407
+ "protein_name": "Uncharacterized protein",
408
+ "taxon_id": 1450533
409
+ },
410
+ {
411
+ "peptide": "EGGAGSSTGQR",
412
+ "uniprot_id": "A2QCE4",
413
+ "protein_name": "Aspergillus niger contig An02c0090, genomic contig",
414
+ "taxon_id": 425011
415
+ },
416
+ {
417
+ "peptide": "EGGAGSSTGQR",
418
+ "uniprot_id": "A0A3F3PXY4",
419
+ "protein_name": "Uncharacterized protein",
420
+ "taxon_id": 1341132
421
+ }
422
+ ]