unipept 2.1.1 → 2.2.0
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- checksums.yaml +4 -4
- data/.rakeTasks +7 -0
- data/VERSION +1 -1
- data/lib/batch_iterator.rb +16 -0
- data/lib/commands/unipept.rb +25 -1
- data/lib/commands/unipept/api_runner.rb +3 -1
- data/lib/commands/unipept/taxa2tree.rb +74 -0
- data/lib/formatters.rb +104 -32
- data/test.taxa +4 -0
- data/test/commands/unipept/test_pept2ec.rb +9 -9
- data/test/commands/unipept/test_pept2funct.rb +13 -13
- data/test/commands/unipept/test_pept2go.rb +8 -8
- data/test/commands/unipept/test_pept2interpro.rb +24 -24
- data/test/commands/unipept/test_peptinfo.rb +14 -14
- data/test/commands/unipept/test_taxa2tree.rb +68 -0
- data/test/helper.rb +10 -0
- data/test/support/api_stub.rb +60 -0
- data/test/support/resources/pept2ec.json +55 -0
- data/test/support/resources/pept2funct.json +73 -0
- data/test/support/resources/pept2go.json +43 -0
- data/test/support/resources/pept2interpro.json +43 -0
- data/test/support/resources/pept2lca.json +14 -0
- data/test/support/resources/pept2prot.json +422 -0
- data/test/support/resources/pept2taxa.json +194 -0
- data/test/support/resources/peptinfo.json +70 -0
- data/test/support/resources/taxa2tree.json +194 -0
- data/test/support/resources/taxonomy.json +22 -0
- data/unipept.gemspec +18 -3
- metadata +17 -2
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"code": "IPR023214",
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"peptide": "VAQFLL",
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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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"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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"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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"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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"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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"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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"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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"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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"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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"peptide": "ENFVYIAK",
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"protein_name": "14_3_3 domain-containing protein",
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"taxon_id": 55188
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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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"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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"peptide": "ENFVYIAK",
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"protein_name": "14_3_3 domain-containing protein",
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"uniprot_id": "A0A1S4A416",
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"protein_name": "14-3-3 protein 9-like",
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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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"protein_name": "14_3_3 domain-containing protein",
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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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"uniprot_id": "A0A445HTA3",
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"protein_name": "14-3-3-like protein D isoform C",
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"protein_name": "14-3-3-like protein D",
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"uniprot_id": "A0A2K3PKW1",
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"protein_name": "14-3-3-like protein d-like",
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"protein_name": "14-3-3 protein",
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"uniprot_id": "A0A5B6YWQ8",
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"protein_name": "Putative 14-3-3-like protein D",
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|
+
"uniprot_id": "A0A1S3WXS1",
|
|
161
|
+
"protein_name": "14-3-3 protein 9-like isoform X2",
|
|
162
|
+
"taxon_id": 4097
|
|
163
|
+
},
|
|
164
|
+
{
|
|
165
|
+
"peptide": "ENFVYIAK",
|
|
166
|
+
"uniprot_id": "A0A1U7VVV5",
|
|
167
|
+
"protein_name": "14-3-3 protein 9-like isoform X1",
|
|
168
|
+
"taxon_id": 4096
|
|
169
|
+
},
|
|
170
|
+
{
|
|
171
|
+
"peptide": "ENFVYIAK",
|
|
172
|
+
"uniprot_id": "A0A2H3Y4D2",
|
|
173
|
+
"protein_name": "14-3-3-like protein D isoform X2",
|
|
174
|
+
"taxon_id": 42345
|
|
175
|
+
},
|
|
176
|
+
{
|
|
177
|
+
"peptide": "ENFVYIAK",
|
|
178
|
+
"uniprot_id": "A0A5B6YWR0",
|
|
179
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
180
|
+
"taxon_id": 16924
|
|
181
|
+
},
|
|
182
|
+
{
|
|
183
|
+
"peptide": "ENFVYIAK",
|
|
184
|
+
"uniprot_id": "A0A067GE20",
|
|
185
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
186
|
+
"taxon_id": 2711
|
|
187
|
+
},
|
|
188
|
+
{
|
|
189
|
+
"peptide": "ENFVYIAK",
|
|
190
|
+
"uniprot_id": "A0A5B6Z3E6",
|
|
191
|
+
"protein_name": "Putative 14-3-3-like protein D isoform X2",
|
|
192
|
+
"taxon_id": 16924
|
|
193
|
+
},
|
|
194
|
+
{
|
|
195
|
+
"peptide": "ENFVYIAK",
|
|
196
|
+
"uniprot_id": "A0A5J5A2G8",
|
|
197
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
198
|
+
"taxon_id": 561372
|
|
199
|
+
},
|
|
200
|
+
{
|
|
201
|
+
"peptide": "ENFVYIAK",
|
|
202
|
+
"uniprot_id": "A0A445IC54",
|
|
203
|
+
"protein_name": "14-3-3-like protein D isoform C",
|
|
204
|
+
"taxon_id": 3848
|
|
205
|
+
},
|
|
206
|
+
{
|
|
207
|
+
"peptide": "ENFVYIAK",
|
|
208
|
+
"uniprot_id": "E1U3Z1",
|
|
209
|
+
"protein_name": "14-3-3-like protein B",
|
|
210
|
+
"taxon_id": 3827
|
|
211
|
+
},
|
|
212
|
+
{
|
|
213
|
+
"peptide": "ENFVYIAK",
|
|
214
|
+
"uniprot_id": "I1M3M0",
|
|
215
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
216
|
+
"taxon_id": 3847
|
|
217
|
+
},
|
|
218
|
+
{
|
|
219
|
+
"peptide": "ENFVYIAK",
|
|
220
|
+
"uniprot_id": "A0A0R0HF31",
|
|
221
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
222
|
+
"taxon_id": 3847
|
|
223
|
+
},
|
|
224
|
+
{
|
|
225
|
+
"peptide": "ENFVYIAK",
|
|
226
|
+
"uniprot_id": "A0A2H3ZH40",
|
|
227
|
+
"protein_name": "14-3-3-like protein D isoform X2",
|
|
228
|
+
"taxon_id": 42345
|
|
229
|
+
},
|
|
230
|
+
{
|
|
231
|
+
"peptide": "ENFVYIAK",
|
|
232
|
+
"uniprot_id": "A0A5B7A4U9",
|
|
233
|
+
"protein_name": "Putative 14-3-3 domain-containing protein",
|
|
234
|
+
"taxon_id": 16924
|
|
235
|
+
},
|
|
236
|
+
{
|
|
237
|
+
"peptide": "ENFVYIAK",
|
|
238
|
+
"uniprot_id": "M0TAI1",
|
|
239
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
240
|
+
"taxon_id": 214687
|
|
241
|
+
},
|
|
242
|
+
{
|
|
243
|
+
"peptide": "ENFVYIAK",
|
|
244
|
+
"uniprot_id": "A0A1S4CN65",
|
|
245
|
+
"protein_name": "14-3-3 protein 9-like isoform X2",
|
|
246
|
+
"taxon_id": 4097
|
|
247
|
+
},
|
|
248
|
+
{
|
|
249
|
+
"peptide": "ENFVYIAK",
|
|
250
|
+
"uniprot_id": "A0A2H5N3C1",
|
|
251
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
252
|
+
"taxon_id": 55188
|
|
253
|
+
},
|
|
254
|
+
{
|
|
255
|
+
"peptide": "ENFVYIAK",
|
|
256
|
+
"uniprot_id": "A0A2H3ZHX0",
|
|
257
|
+
"protein_name": "14-3-3-like protein D isoform X1",
|
|
258
|
+
"taxon_id": 42345
|
|
259
|
+
},
|
|
260
|
+
{
|
|
261
|
+
"peptide": "ENFVYIAK",
|
|
262
|
+
"uniprot_id": "M0TY03",
|
|
263
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
264
|
+
"taxon_id": 214687
|
|
265
|
+
},
|
|
266
|
+
{
|
|
267
|
+
"peptide": "ENFVYIAK",
|
|
268
|
+
"uniprot_id": "A0A445CI73",
|
|
269
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
270
|
+
"taxon_id": 3818
|
|
271
|
+
},
|
|
272
|
+
{
|
|
273
|
+
"peptide": "ENFVYIAK",
|
|
274
|
+
"uniprot_id": "A0A3S3NBY5",
|
|
275
|
+
"protein_name": "14-3-3-like protein D isoform X1",
|
|
276
|
+
"taxon_id": 337451
|
|
277
|
+
},
|
|
278
|
+
{
|
|
279
|
+
"peptide": "ENFVYIAK",
|
|
280
|
+
"uniprot_id": "V4U9U4",
|
|
281
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
282
|
+
"taxon_id": 85681
|
|
283
|
+
},
|
|
284
|
+
{
|
|
285
|
+
"peptide": "ENFVYIAK",
|
|
286
|
+
"uniprot_id": "A0A151SEM7",
|
|
287
|
+
"protein_name": "14-3-3-like protein D",
|
|
288
|
+
"taxon_id": 3821
|
|
289
|
+
},
|
|
290
|
+
{
|
|
291
|
+
"peptide": "ENFVYIAK",
|
|
292
|
+
"uniprot_id": "A0A445IBK9",
|
|
293
|
+
"protein_name": "14-3-3-like protein D isoform D",
|
|
294
|
+
"taxon_id": 3848
|
|
295
|
+
},
|
|
296
|
+
{
|
|
297
|
+
"peptide": "ENFVYIAK",
|
|
298
|
+
"uniprot_id": "A0A1S4CMF0",
|
|
299
|
+
"protein_name": "14-3-3 protein 9-like isoform X1",
|
|
300
|
+
"taxon_id": 4097
|
|
301
|
+
},
|
|
302
|
+
{
|
|
303
|
+
"peptide": "ENFVYIAK",
|
|
304
|
+
"uniprot_id": "A0A1J6KH36",
|
|
305
|
+
"protein_name": "14-3-3 protein 9",
|
|
306
|
+
"taxon_id": 49451
|
|
307
|
+
},
|
|
308
|
+
{
|
|
309
|
+
"peptide": "ENFVYIAK",
|
|
310
|
+
"uniprot_id": "A0A5B7A5K1",
|
|
311
|
+
"protein_name": "Putative 14-3-3-like protein D isoform X1",
|
|
312
|
+
"taxon_id": 16924
|
|
313
|
+
},
|
|
314
|
+
{
|
|
315
|
+
"peptide": "ENFVYIAK",
|
|
316
|
+
"uniprot_id": "F6H2P0",
|
|
317
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
318
|
+
"taxon_id": 29760
|
|
319
|
+
},
|
|
320
|
+
{
|
|
321
|
+
"peptide": "ENFVYIAK",
|
|
322
|
+
"uniprot_id": "A0A1J6IP66",
|
|
323
|
+
"protein_name": "14-3-3 protein 9",
|
|
324
|
+
"taxon_id": 49451
|
|
325
|
+
},
|
|
326
|
+
{
|
|
327
|
+
"peptide": "ENFVYIAK",
|
|
328
|
+
"uniprot_id": "A0A5B7A8T8",
|
|
329
|
+
"protein_name": "Putative 14-3-3-like protein D isoform X1",
|
|
330
|
+
"taxon_id": 16924
|
|
331
|
+
},
|
|
332
|
+
{
|
|
333
|
+
"peptide": "ENFVYIAK",
|
|
334
|
+
"uniprot_id": "A0A0R0H7R6",
|
|
335
|
+
"protein_name": "14_3_3 domain-containing protein",
|
|
336
|
+
"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
|
+
]
|