protvista-uniprot 2.10.9 → 2.10.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (16) hide show
  1. package/dist/es/config.json +281 -240
  2. package/dist/es/protvista-alphafold-confidence.d.ts +23 -0
  3. package/dist/es/protvista-alphafold-confidence.js +21 -0
  4. package/dist/es/protvista-alphafold-confidence.js.map +1 -0
  5. package/dist/es/protvista-uniprot.d.ts +26 -3
  6. package/dist/es/protvista-uniprot.js +80 -20
  7. package/dist/es/protvista-uniprot.js.map +1 -1
  8. package/dist/es/styles/protvista-styles.js +14 -0
  9. package/dist/es/styles/protvista-styles.js.map +1 -1
  10. package/dist/protvista-uniprot.js +18 -18
  11. package/dist/protvista-uniprot.js.map +1 -1
  12. package/package.json +13 -12
  13. package/src/config.json +283 -241
  14. package/src/protvista-alphafold-confidence.ts +49 -0
  15. package/src/protvista-uniprot.ts +148 -56
  16. package/src/styles/protvista-styles.ts +14 -0
package/dist/es/config.json CHANGED
@@ -1,14 +1,14 @@
1
1
  {
2
2
  "categories": [
3
3
  {
4
- "name": "DOMAINS_AND_SITES",
5
- "label": "Domains & sites",
4
+ "name": "MOLECULE_PROCESSING",
5
+ "label": "Molecule processing",
6
6
  "trackType": "protvista-track",
7
7
  "tracks": [
8
8
  {
9
- "name": "domain",
10
- "label": "Domain",
11
- "filter": "DOMAIN",
9
+ "name": "signal",
10
+ "label": "Signal peptide",
11
+ "filter": "SIGNAL",
12
12
  "trackType": "protvista-track",
13
13
  "data": [
14
14
  {
@@ -16,12 +16,12 @@
16
16
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
17
17
  }
18
18
  ],
19
- "tooltip": "Specific combination of secondary structures organized into a characteristic three-dimensional structure or fold"
19
+ "tooltip": "N-terminal signal peptide"
20
20
  },
21
21
  {
22
- "name": "region",
23
- "label": "Region",
24
- "filter": "REGION",
22
+ "name": "chain",
23
+ "label": "Chain",
24
+ "filter": "CHAIN",
25
25
  "trackType": "protvista-track",
26
26
  "data": [
27
27
  {
@@ -29,12 +29,12 @@
29
29
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
30
30
  }
31
31
  ],
32
- "tooltip": "Regions in multifunctional enzymes or fusion proteins, or characteristics of a region, e.g., protein-protein interactions mediation"
32
+ "tooltip": "(aka mature region). This describes the extent of a polypeptide chain in the mature protein following processing"
33
33
  },
34
34
  {
35
- "name": "motif",
36
- "label": "Motif",
37
- "filter": "MOTIF",
35
+ "name": "transit",
36
+ "label": "Transit peptide",
37
+ "filter": "TRANSIT",
38
38
  "trackType": "protvista-track",
39
39
  "data": [
40
40
  {
@@ -42,12 +42,12 @@
42
42
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
43
43
  }
44
44
  ],
45
- "tooltip": "Short conserved sequence motif of biological significance"
45
+ "tooltip": "This describes the extent of a transit peptide"
46
46
  },
47
47
  {
48
- "name": "metal",
49
- "label": "Metal binding",
50
- "filter": "METAL",
48
+ "name": "init_met",
49
+ "label": "Initiator methionine",
50
+ "filter": "INIT_MET",
51
51
  "trackType": "protvista-track",
52
52
  "data": [
53
53
  {
@@ -55,12 +55,12 @@
55
55
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
56
56
  }
57
57
  ],
58
- "tooltip": "Binding site for a metal ion"
58
+ "tooltip": "This indicates that the initiator methionine is cleaved from the mature protein"
59
59
  },
60
60
  {
61
- "name": "site",
62
- "label": "Site",
63
- "filter": "SITE",
61
+ "name": "propep",
62
+ "label": "Propeptide",
63
+ "filter": "PROPEP",
64
64
  "trackType": "protvista-track",
65
65
  "data": [
66
66
  {
@@ -68,12 +68,12 @@
68
68
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
69
69
  }
70
70
  ],
71
- "tooltip": "Any interesting single amino acid site on the sequence"
71
+ "tooltip": "Part of a protein that is cleaved during maturation or activation"
72
72
  },
73
73
  {
74
- "name": "repeat",
75
- "label": "Repeat",
76
- "filter": "REPEAT",
74
+ "name": "peptide",
75
+ "label": "Peptide",
76
+ "filter": "PEPTIDE",
77
77
  "trackType": "protvista-track",
78
78
  "data": [
79
79
  {
@@ -81,12 +81,19 @@
81
81
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
82
82
  }
83
83
  ],
84
- "tooltip": "Repeated sequence motifs or repeated domains within the protein"
85
- },
84
+ "tooltip": "The position and length of an active peptide in the mature protein"
85
+ }
86
+ ]
87
+ },
88
+ {
89
+ "name": "SEQUENCE_INFORMATION",
90
+ "label": "Sequence information",
91
+ "trackType": "protvista-track",
92
+ "tracks": [
86
93
  {
87
- "name": "ca_bind",
88
- "label": "Calcium binding",
89
- "filter": "CA_BIND",
94
+ "name": "compbias",
95
+ "label": "Compositional bias",
96
+ "filter": "COMPBIAS",
90
97
  "trackType": "protvista-track",
91
98
  "data": [
92
99
  {
@@ -94,12 +101,12 @@
94
101
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
95
102
  }
96
103
  ],
97
- "tooltip": "Calcium-binding regions, such as the EF-hand motif"
104
+ "tooltip": "Position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions"
98
105
  },
99
106
  {
100
- "name": "dna_bind",
101
- "label": "DNA binding",
102
- "filter": "DNA_BIND",
107
+ "name": "conflict",
108
+ "label": "Sequence conflict",
109
+ "filter": "CONFLICT",
103
110
  "trackType": "protvista-track",
104
111
  "data": [
105
112
  {
@@ -107,71 +114,71 @@
107
114
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
108
115
  }
109
116
  ],
110
- "tooltip": "DNA-binding domains such as AP2/ERF domain, the ETS domain, the Fork-Head domain, the HMG box and the Myb domain"
117
+ "tooltip": "Sequence discrepancies of unknown origin"
111
118
  },
112
119
  {
113
- "name": "zn_fing",
114
- "label": "Zinc finger",
115
- "filter": "ZN_FING",
120
+ "name": "non_cons",
121
+ "filter": "NON_CONS",
116
122
  "trackType": "protvista-track",
123
+ "label": "Non-adjacent residues",
117
124
  "data": [
118
125
  {
119
126
  "adapter": "protvista-feature-adapter",
120
127
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
121
128
  }
122
129
  ],
123
- "tooltip": "Small, functional, independently folded domain that coordinates one or more zinc ions"
130
+ "tooltip": "Indicates that two residues in a sequence are not consecutive and that there is an undetermined number of unsequenced residues between them"
124
131
  },
125
132
  {
126
- "name": "np_bind",
127
- "label": "Nucleotide binding",
128
- "filter": "NP_BIND",
133
+ "name": "non_ter",
134
+ "filter": "NON_TER",
129
135
  "trackType": "protvista-track",
136
+ "label": "Non-terminal residue",
130
137
  "data": [
131
138
  {
132
139
  "adapter": "protvista-feature-adapter",
133
140
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
134
141
  }
135
142
  ],
136
- "tooltip": "(aka flavin-binding). Region in the protein which binds nucleotide phosphates"
143
+ "tooltip": "The sequence is incomplete. The residue is not the terminal residue of the complete protein"
137
144
  },
138
145
  {
139
- "name": "binding",
140
- "label": "Binding site",
141
- "filter": "BINDING",
146
+ "name": "unsure",
147
+ "filter": "UNSURE",
142
148
  "trackType": "protvista-track",
149
+ "label": "Sequence uncertainty",
143
150
  "data": [
144
151
  {
145
152
  "adapter": "protvista-feature-adapter",
146
153
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
147
154
  }
148
155
  ],
149
- "tooltip": "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)"
156
+ "tooltip": "Regions of a sequence for which the authors are unsure about the sequence assignment"
150
157
  },
151
158
  {
152
- "name": "act_site",
153
- "label": "Active site",
154
- "filter": "ACT_SITE",
159
+ "name": "non_std",
160
+ "filter": "NON_STD",
155
161
  "trackType": "protvista-track",
162
+ "label": "Non-standard residue",
156
163
  "data": [
157
164
  {
158
165
  "adapter": "protvista-feature-adapter",
159
166
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
160
167
  }
161
168
  ],
162
- "tooltip": "Amino acid(s) directly involved in the activity of an enzyme"
169
+ "tooltip": "Non-standard amino acids (selenocysteine and pyrrolysine)"
163
170
  }
164
171
  ]
165
172
  },
166
173
  {
167
- "name": "MOLECULE_PROCESSING",
168
- "label": "Molecule processing",
174
+ "name": "TOPOLOGY",
175
+ "label": "Topology",
169
176
  "trackType": "protvista-track",
170
177
  "tracks": [
171
178
  {
172
- "name": "signal",
173
- "label": "Signal peptide",
174
- "filter": "SIGNAL",
179
+ "name": "topo_dom",
180
+ "label": "Topological domain",
181
+ "filter": "TOPO_DOM",
175
182
  "trackType": "protvista-track",
176
183
  "data": [
177
184
  {
@@ -179,12 +186,12 @@
179
186
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
180
187
  }
181
188
  ],
182
- "tooltip": "N-terminal signal peptide"
189
+ "tooltip": "Location of non-membrane regions of membrane-spanning proteins"
183
190
  },
184
191
  {
185
- "name": "chain",
186
- "label": "Chain",
187
- "filter": "CHAIN",
192
+ "name": "transmem",
193
+ "label": "Transmembrane",
194
+ "filter": "TRANSMEM",
188
195
  "trackType": "protvista-track",
189
196
  "data": [
190
197
  {
@@ -192,12 +199,12 @@
192
199
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
193
200
  }
194
201
  ],
195
- "tooltip": "(aka mature region). This describes the extent of a polypeptide chain in the mature protein following processing"
202
+ "tooltip": "Extent of a membrane-spanning region"
196
203
  },
197
204
  {
198
- "name": "transit",
199
- "label": "Transit peptide",
200
- "filter": "TRANSIT",
205
+ "name": "intramem",
206
+ "label": "Intramembrane",
207
+ "filter": "INTRAMEM",
201
208
  "trackType": "protvista-track",
202
209
  "data": [
203
210
  {
@@ -205,12 +212,19 @@
205
212
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
206
213
  }
207
214
  ],
208
- "tooltip": "This describes the extent of a transit peptide"
209
- },
215
+ "tooltip": "Extent of a region located in a membrane without crossing it"
216
+ }
217
+ ]
218
+ },
219
+ {
220
+ "name": "DOMAINS",
221
+ "label": "Domains",
222
+ "trackType": "protvista-track",
223
+ "tracks": [
210
224
  {
211
- "name": "init_met",
212
- "label": "Initiator methionine",
213
- "filter": "INIT_MET",
225
+ "name": "domain",
226
+ "label": "Domain",
227
+ "filter": "DOMAIN",
214
228
  "trackType": "protvista-track",
215
229
  "data": [
216
230
  {
@@ -218,45 +232,24 @@
218
232
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
219
233
  }
220
234
  ],
221
- "tooltip": "This indicates that the initiator methionine is cleaved from the mature protein"
235
+ "tooltip": "Specific combination of secondary structures organized into a characteristic three-dimensional structure or fold"
222
236
  },
223
237
  {
224
- "name": "propep",
225
- "label": "Propeptide",
226
- "filter": "PROPEP",
238
+ "name": "InterPro representative domain",
239
+ "label": "InterPro Representative Domain",
227
240
  "trackType": "protvista-track",
228
241
  "data": [
229
242
  {
230
- "adapter": "protvista-feature-adapter",
231
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
243
+ "adapter": "protvista-interpro-adapter",
244
+ "url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/{accession}?type=domain&page_size=100"
232
245
  }
233
246
  ],
234
- "tooltip": "Part of a protein that is cleaved during maturation or activation"
247
+ "tooltip": "InterPro representative domains"
235
248
  },
236
249
  {
237
- "name": "peptide",
238
- "label": "Peptide",
239
- "filter": "PEPTIDE",
240
- "trackType": "protvista-track",
241
- "data": [
242
- {
243
- "adapter": "protvista-feature-adapter",
244
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
245
- }
246
- ],
247
- "tooltip": "The position and length of an active peptide in the mature protein"
248
- }
249
- ]
250
- },
251
- {
252
- "name": "PTM",
253
- "label": "PTM",
254
- "trackType": "protvista-track",
255
- "tracks": [
256
- {
257
- "name": "mod_res",
258
- "label": "Modified residue",
259
- "filter": "MOD_RES",
250
+ "name": "region",
251
+ "label": "Region",
252
+ "filter": "REGION",
260
253
  "trackType": "protvista-track",
261
254
  "data": [
262
255
  {
@@ -264,25 +257,12 @@
264
257
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
265
258
  }
266
259
  ],
267
- "tooltip": "Modified residues such as phosphorylation, acetylation, acylation, methylation"
268
- },
269
- {
270
- "name": "mod_res_ls",
271
- "label": "Modified residue (large scale data)",
272
- "filter": "MOD_RES_LS",
273
- "trackType": "protvista-track",
274
- "data": [
275
- {
276
- "adapter": "protvista-proteomics-ptm-adapter",
277
- "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
278
- }
279
- ],
280
- "tooltip": "Modified residues from Large scale studies"
260
+ "tooltip": "Regions in multifunctional enzymes or fusion proteins, or characteristics of a region, e.g., protein-protein interactions mediation"
281
261
  },
282
262
  {
283
- "name": "carbohyd",
284
- "label": "Glycosylation",
285
- "filter": "CARBOHYD",
263
+ "name": "repeat",
264
+ "label": "Repeat",
265
+ "filter": "REPEAT",
286
266
  "trackType": "protvista-track",
287
267
  "data": [
288
268
  {
@@ -290,12 +270,12 @@
290
270
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
291
271
  }
292
272
  ],
293
- "tooltip": "Covalently attached glycan group(s)"
273
+ "tooltip": "Repeated sequence motifs or repeated domains within the protein"
294
274
  },
295
275
  {
296
- "name": "disulfid",
297
- "label": "Disulfide bond",
298
- "filter": "DISULFID",
276
+ "name": "motif",
277
+ "label": "Motif",
278
+ "filter": "MOTIF",
299
279
  "trackType": "protvista-track",
300
280
  "data": [
301
281
  {
@@ -303,12 +283,19 @@
303
283
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
304
284
  }
305
285
  ],
306
- "tooltip": "The positions of cysteine residues participating in disulphide bonds"
307
- },
286
+ "tooltip": "Short conserved sequence motif of biological significance"
287
+ }
288
+ ]
289
+ },
290
+ {
291
+ "name": "SITES",
292
+ "label": "Sites",
293
+ "trackType": "protvista-track",
294
+ "tracks": [
308
295
  {
309
- "name": "crosslnk",
310
- "label": "Cross-link",
311
- "filter": "CROSSLNK",
296
+ "name": "metal",
297
+ "label": "Metal binding",
298
+ "filter": "METAL",
312
299
  "trackType": "protvista-track",
313
300
  "data": [
314
301
  {
@@ -316,12 +303,12 @@
316
303
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
317
304
  }
318
305
  ],
319
- "tooltip": "Covalent linkages of various types formed between two proteins or between two parts of the same protein"
306
+ "tooltip": "Binding site for a metal ion"
320
307
  },
321
308
  {
322
- "name": "lipid",
323
- "label": "Lipidation",
324
- "filter": "LIPID",
309
+ "name": "site",
310
+ "label": "Site",
311
+ "filter": "SITE",
325
312
  "trackType": "protvista-track",
326
313
  "data": [
327
314
  {
@@ -329,19 +316,12 @@
329
316
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
330
317
  }
331
318
  ],
332
- "tooltip": "Covalently attached lipid group(s)"
333
- }
334
- ]
335
- },
336
- {
337
- "name": "SEQUENCE_INFORMATION",
338
- "label": "Sequence information",
339
- "trackType": "protvista-track",
340
- "tracks": [
319
+ "tooltip": "Any interesting single amino acid site on the sequence"
320
+ },
341
321
  {
342
- "name": "compbias",
343
- "label": "Compositional bias",
344
- "filter": "COMPBIAS",
322
+ "name": "ca_bind",
323
+ "label": "Calcium binding",
324
+ "filter": "CA_BIND",
345
325
  "trackType": "protvista-track",
346
326
  "data": [
347
327
  {
@@ -349,12 +329,12 @@
349
329
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
350
330
  }
351
331
  ],
352
- "tooltip": "Position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions"
332
+ "tooltip": "Calcium-binding regions, such as the EF-hand motif"
353
333
  },
354
334
  {
355
- "name": "conflict",
356
- "label": "Sequence conflict",
357
- "filter": "CONFLICT",
335
+ "name": "dna_bind",
336
+ "label": "DNA binding",
337
+ "filter": "DNA_BIND",
358
338
  "trackType": "protvista-track",
359
339
  "data": [
360
340
  {
@@ -362,71 +342,71 @@
362
342
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
363
343
  }
364
344
  ],
365
- "tooltip": "Sequence discrepancies of unknown origin"
345
+ "tooltip": "DNA-binding domains such as AP2/ERF domain, the ETS domain, the Fork-Head domain, the HMG box and the Myb domain"
366
346
  },
367
347
  {
368
- "name": "non_cons",
369
- "filter": "NON_CONS",
348
+ "name": "zn_fing",
349
+ "label": "Zinc finger",
350
+ "filter": "ZN_FING",
370
351
  "trackType": "protvista-track",
371
- "label": "Non-adjacent residues",
372
352
  "data": [
373
353
  {
374
354
  "adapter": "protvista-feature-adapter",
375
355
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
376
356
  }
377
357
  ],
378
- "tooltip": "Indicates that two residues in a sequence are not consecutive and that there is an undetermined number of unsequenced residues between them"
358
+ "tooltip": "Small, functional, independently folded domain that coordinates one or more zinc ions"
379
359
  },
380
360
  {
381
- "name": "non_ter",
382
- "filter": "NON_TER",
361
+ "name": "np_bind",
362
+ "label": "Nucleotide binding",
363
+ "filter": "NP_BIND",
383
364
  "trackType": "protvista-track",
384
- "label": "Non-terminal residue",
385
365
  "data": [
386
366
  {
387
367
  "adapter": "protvista-feature-adapter",
388
368
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
389
369
  }
390
370
  ],
391
- "tooltip": "The sequence is incomplete. The residue is not the terminal residue of the complete protein"
371
+ "tooltip": "(aka flavin-binding). Region in the protein which binds nucleotide phosphates"
392
372
  },
393
373
  {
394
- "name": "unsure",
395
- "filter": "UNSURE",
374
+ "name": "binding",
375
+ "label": "Binding site",
376
+ "filter": "BINDING",
396
377
  "trackType": "protvista-track",
397
- "label": "Sequence uncertainty",
398
378
  "data": [
399
379
  {
400
380
  "adapter": "protvista-feature-adapter",
401
381
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
402
382
  }
403
383
  ],
404
- "tooltip": "Regions of a sequence for which the authors are unsure about the sequence assignment"
384
+ "tooltip": "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)"
405
385
  },
406
386
  {
407
- "name": "non_std",
408
- "filter": "NON_STD",
387
+ "name": "act_site",
388
+ "label": "Active site",
389
+ "filter": "ACT_SITE",
409
390
  "trackType": "protvista-track",
410
- "label": "Non-standard residue",
411
391
  "data": [
412
392
  {
413
393
  "adapter": "protvista-feature-adapter",
414
394
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
415
395
  }
416
396
  ],
417
- "tooltip": "Non-standard amino acids (selenocysteine and pyrrolysine)"
397
+ "tooltip": "Amino acid(s) directly involved in the activity of an enzyme"
418
398
  }
419
399
  ]
420
400
  },
421
401
  {
422
- "name": "STRUCTURAL",
423
- "label": "Structural features",
402
+ "name": "PTM",
403
+ "label": "PTM",
424
404
  "trackType": "protvista-track",
425
405
  "tracks": [
426
406
  {
427
- "name": "helix",
428
- "label": "Helix",
429
- "filter": "HELIX",
407
+ "name": "mod_res",
408
+ "label": "Modified residue",
409
+ "filter": "MOD_RES",
430
410
  "trackType": "protvista-track",
431
411
  "data": [
432
412
  {
@@ -434,25 +414,25 @@
434
414
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
435
415
  }
436
416
  ],
437
- "tooltip": "The positions of experimentally determined helical regions"
417
+ "tooltip": "Modified residues such as phosphorylation, acetylation, acylation, methylation"
438
418
  },
439
419
  {
440
- "name": "strand",
441
- "label": "Beta strand",
442
- "filter": "STRAND",
420
+ "name": "mod_res_ls",
421
+ "label": "Modified residue (large scale data)",
422
+ "filter": "MOD_RES_LS",
443
423
  "trackType": "protvista-track",
444
424
  "data": [
445
425
  {
446
- "adapter": "protvista-feature-adapter",
447
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
426
+ "adapter": "protvista-proteomics-ptm-adapter",
427
+ "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
448
428
  }
449
429
  ],
450
- "tooltip": "The positions of experimentally determined beta strands"
430
+ "tooltip": "Modified residues from Large scale studies"
451
431
  },
452
432
  {
453
- "name": "turn",
454
- "label": "Turn",
455
- "filter": "TURN",
433
+ "name": "carbohyd",
434
+ "label": "Glycosylation",
435
+ "filter": "CARBOHYD",
456
436
  "trackType": "protvista-track",
457
437
  "data": [
458
438
  {
@@ -460,12 +440,12 @@
460
440
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
461
441
  }
462
442
  ],
463
- "tooltip": "The positions of experimentally determined hydrogen-bonded turns"
443
+ "tooltip": "Covalently attached glycan group(s)"
464
444
  },
465
445
  {
466
- "name": "coiled",
467
- "label": "Coiled coil",
468
- "filter": "COILED",
446
+ "name": "disulfid",
447
+ "label": "Disulfide bond",
448
+ "filter": "DISULFID",
469
449
  "trackType": "protvista-track",
470
450
  "data": [
471
451
  {
@@ -473,38 +453,12 @@
473
453
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
474
454
  }
475
455
  ],
476
- "tooltip": "Coiled coils are built by two or more alpha-helices that wind around each other to form a supercoil"
477
- }
478
- ]
479
- },
480
- {
481
- "name": "STRUCTURE_COVERAGE",
482
- "label": "PDBe 3D structure coverage",
483
- "trackType": "protvista-track",
484
- "tracks": [
485
- {
486
- "name": "pdbe_cover",
487
- "label": "PDBe coverage",
488
- "trackType": "protvista-track",
489
- "tooltip": "PDBe 3D structure coverage",
490
- "data": [
491
- {
492
- "adapter": "protvista-structure-adapter",
493
- "url": "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
494
- }
495
- ]
496
- }
497
- ]
498
- },
499
- {
500
- "name": "TOPOLOGY",
501
- "label": "Topology",
502
- "trackType": "protvista-track",
503
- "tracks": [
456
+ "tooltip": "The positions of cysteine residues participating in disulphide bonds"
457
+ },
504
458
  {
505
- "name": "topo_dom",
506
- "label": "Topological domain",
507
- "filter": "TOPO_DOM",
459
+ "name": "crosslnk",
460
+ "label": "Cross-link",
461
+ "filter": "CROSSLNK",
508
462
  "trackType": "protvista-track",
509
463
  "data": [
510
464
  {
@@ -512,12 +466,12 @@
512
466
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
513
467
  }
514
468
  ],
515
- "tooltip": "Location of non-membrane regions of membrane-spanning proteins"
469
+ "tooltip": "Covalent linkages of various types formed between two proteins or between two parts of the same protein"
516
470
  },
517
471
  {
518
- "name": "transmem",
519
- "label": "Transmembrane",
520
- "filter": "TRANSMEM",
472
+ "name": "lipid",
473
+ "label": "Lipidation",
474
+ "filter": "LIPID",
521
475
  "trackType": "protvista-track",
522
476
  "data": [
523
477
  {
@@ -525,20 +479,26 @@
525
479
  "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
526
480
  }
527
481
  ],
528
- "tooltip": "Extent of a membrane-spanning region"
529
- },
482
+ "tooltip": "Covalently attached lipid group(s)"
483
+ }
484
+ ]
485
+ },
486
+ {
487
+ "name": "ANTIGEN",
488
+ "label": "Antigenic sequences",
489
+ "trackType": "protvista-track",
490
+ "tracks": [
530
491
  {
531
- "name": "intramem",
532
- "label": "Intramembrane",
533
- "filter": "INTRAMEM",
492
+ "name": "antigen",
493
+ "label": "Antibody binding sequences",
534
494
  "trackType": "protvista-track",
535
495
  "data": [
536
496
  {
537
497
  "adapter": "protvista-feature-adapter",
538
- "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
498
+ "url": "https://www.ebi.ac.uk/proteins/api/antigen/{accession}"
539
499
  }
540
500
  ],
541
- "tooltip": "Extent of a region located in a membrane without crossing it"
501
+ "tooltip": ""
542
502
  }
543
503
  ]
544
504
  },
@@ -562,7 +522,7 @@
562
522
  },
563
523
  {
564
524
  "name": "othermutagen",
565
- "label": "Other Mutagenesis",
525
+ "label": "Mutagenesis (large scale data)",
566
526
  "trackType": "protvista-track",
567
527
  "data": [
568
528
  {
@@ -574,6 +534,25 @@
574
534
  }
575
535
  ]
576
536
  },
537
+ {
538
+ "name": "VARIATION",
539
+ "label": "Variants",
540
+ "trackType": "protvista-variation-graph",
541
+ "tracks": [
542
+ {
543
+ "name": "variation",
544
+ "filterComponent": "protvista-filter",
545
+ "trackType": "protvista-variation",
546
+ "data": [
547
+ {
548
+ "adapter": "protvista-variation-adapter",
549
+ "url": "https://www.ebi.ac.uk/proteins/api/variation/{accession}"
550
+ }
551
+ ],
552
+ "tooltip": "Natural variant of the protein, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events"
553
+ }
554
+ ]
555
+ },
577
556
  {
578
557
  "name": "PROTEOMICS",
579
558
  "label": "Proteomics",
@@ -625,40 +604,102 @@
625
604
  ]
626
605
  },
627
606
  {
628
- "name": "ANTIGEN",
629
- "label": "Antigenic sequences",
607
+ "name": "STRUCTURE_COVERAGE",
608
+ "label": "PDBe 3D structure coverage",
630
609
  "trackType": "protvista-track",
631
610
  "tracks": [
632
611
  {
633
- "name": "antigen",
634
- "label": "Antibody binding sequences",
612
+ "name": "pdbe_cover",
613
+ "label": "PDBe coverage",
635
614
  "trackType": "protvista-track",
615
+ "tooltip": "PDBe 3D structure coverage",
636
616
  "data": [
637
617
  {
638
- "adapter": "protvista-feature-adapter",
639
- "url": "https://www.ebi.ac.uk/proteins/api/antigen/{accession}"
618
+ "adapter": "protvista-structure-adapter",
619
+ "url": "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
620
+ }
621
+ ]
622
+ }
623
+ ]
624
+ },
625
+ {
626
+ "name": "ALPHAFOLD_CONFIDENCE",
627
+ "label": "AlphaFold",
628
+ "trackType": "protvista-coloured-sequence",
629
+ "scale": "H:90,M:70,L:50,D:0",
630
+ "color-range": "#ff7d45:0,#ffdb13:50,#65cbf3:70,#0053d6:90,#0053d6:100",
631
+ "tracks": [
632
+ {
633
+ "name": "alphafold_confidence",
634
+ "label": "AlphaFold Confidence",
635
+ "labelUrl": "https://alphafold.ebi.ac.uk/entry/{accession}",
636
+ "trackType": "protvista-coloured-sequence",
637
+ "data": [
638
+ {
639
+ "adapter": "protvista-alphafold-confidence-adapter",
640
+ "url": "https://alphafold.ebi.ac.uk/api/prediction/{accession}"
640
641
  }
641
642
  ],
642
- "tooltip": ""
643
+ "tooltip": "AlphaFold prediction confidence"
643
644
  }
644
645
  ]
645
646
  },
646
647
  {
647
- "name": "VARIATION",
648
- "label": "Variants",
649
- "trackType": "protvista-variation-graph",
648
+ "name": "STRUCTURAL",
649
+ "label": "Structural features",
650
+ "trackType": "protvista-track",
650
651
  "tracks": [
651
652
  {
652
- "name": "variation",
653
- "filterComponent": "protvista-filter",
654
- "trackType": "protvista-variation",
653
+ "name": "helix",
654
+ "label": "Helix",
655
+ "filter": "HELIX",
656
+ "trackType": "protvista-track",
655
657
  "data": [
656
658
  {
657
- "adapter": "protvista-variation-adapter",
658
- "url": "https://www.ebi.ac.uk/proteins/api/variation/{accession}"
659
+ "adapter": "protvista-feature-adapter",
660
+ "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
659
661
  }
660
662
  ],
661
- "tooltip": "Natural variant of the protein, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events"
663
+ "tooltip": "The positions of experimentally determined helical regions"
664
+ },
665
+ {
666
+ "name": "strand",
667
+ "label": "Beta strand",
668
+ "filter": "STRAND",
669
+ "trackType": "protvista-track",
670
+ "data": [
671
+ {
672
+ "adapter": "protvista-feature-adapter",
673
+ "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
674
+ }
675
+ ],
676
+ "tooltip": "The positions of experimentally determined beta strands"
677
+ },
678
+ {
679
+ "name": "turn",
680
+ "label": "Turn",
681
+ "filter": "TURN",
682
+ "trackType": "protvista-track",
683
+ "data": [
684
+ {
685
+ "adapter": "protvista-feature-adapter",
686
+ "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
687
+ }
688
+ ],
689
+ "tooltip": "The positions of experimentally determined hydrogen-bonded turns"
690
+ },
691
+ {
692
+ "name": "coiled",
693
+ "label": "Coiled coil",
694
+ "filter": "COILED",
695
+ "trackType": "protvista-track",
696
+ "data": [
697
+ {
698
+ "adapter": "protvista-feature-adapter",
699
+ "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
700
+ }
701
+ ],
702
+ "tooltip": "Coiled coils are built by two or more alpha-helices that wind around each other to form a supercoil"
662
703
  }
663
704
  ]
664
705
  }