Mercurial > repos > iuc > rpbasicdesign

comparison test-data/lycopene_CrtEBI_from_selenzy.xml @ 0:cdd6a526bdcf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign commit bdac148247c9c3d3da3420220d006e723c718277"
author iuc
date Wed, 30 Mar 2022 13:05:31 +0000
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-1:000000000000 0:cdd6a526bdcf
1 <?xml version="1.0" encoding="UTF-8"?>
2 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false">
3 <model metaid="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
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242 <brsynth:tmpl_rxn_ids>
243 <brsynth:MNXR111250/>
244 <brsynth:MNXR111499/>
245 <brsynth:MNXR113543/>
246 <brsynth:MNXR118024/>
247 <brsynth:MNXR139549/>
248 </brsynth:tmpl_rxn_ids>
249 <brsynth:rule_score value="0.5683242688496836"/>
250 <brsynth:idx_in_path value="2"/>
251 <brsynth:selenzy_P21683>
252 <brsynth:score value="91.9"/>
253 <brsynth:target_ID value="553"/>
254 </brsynth:selenzy_P21683>
255 <brsynth:selenzy_P21684>
256 <brsynth:score value="74.885"/>
257 <brsynth:target_ID value="553"/>
258 </brsynth:selenzy_P21684>
259 </brsynth:brsynth>
260 </rdf:BRSynth>
261 </rdf:RDF>
262 </annotation>
263 <listOfReactants>
264 <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
265 </listOfReactants>
266 <listOfProducts>
267 <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
268 <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
269 </listOfProducts>
270 </reaction>
271 <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_999999_0">
272 <annotation>
273 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
274 <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
275 <bqbiol:is>
276 <rdf:Bag>
277 <rdf:li rdf:resource="http://identifiers.org/uniprot/P21683"/>
278 <rdf:li rdf:resource="http://identifiers.org/uniprot/P21685"/>
279 <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.31"/>
280 </rdf:Bag>
281 </bqbiol:is>
282 </rdf:Description>
283 <rdf:BRSynth rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
284 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
285 <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]&gt;&gt;[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
286 <brsynth:rp2_transfo_id value="TRS_0_0_1"/>
287 <brsynth:rule_ids>
288 <brsynth:RR-02-bdf7d8715e2e4d93-16-F/>
289 </brsynth:rule_ids>
290 <brsynth:tmpl_rxn_ids>
291 <brsynth:MNXR113128/>
292 </brsynth:tmpl_rxn_ids>
293 <brsynth:rule_score value="0.7486085128675456"/>
294 <brsynth:idx_in_path value="3"/>
295 <brsynth:selenzy_P21685>
296 <brsynth:score value="81.82"/>
297 <brsynth:target_ID value="553"/>
298 </brsynth:selenzy_P21685>
299 <brsynth:selenzy_P21683>
300 <brsynth:score value="63.183"/>
301 <brsynth:target_ID value="553"/>
302 </brsynth:selenzy_P21683>
303 </brsynth:brsynth>
304 </rdf:BRSynth>
305 </rdf:RDF>
306 </annotation>
307 <listOfReactants>
308 <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
309 <speciesReference species="MNXM8975" stoichiometry="4" constant="true"/>
310 </listOfReactants>
311 <listOfProducts>
312 <speciesReference species="MNXM24" stoichiometry="4" constant="true"/>
313 <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
314 </listOfProducts>
315 </reaction>
316 </listOfReactions>
317 <groups:listOfGroups>
318 <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
319 <annotation>
320 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
321 <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
322 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
323 <brsynth:global_score value="-1"/>
324 </brsynth:brsynth>
325 </rdf:BRSynth>
326 </rdf:RDF>
327 </annotation>
328 <groups:listOfMembers>
329 <groups:member groups:idRef="rxn_1"/>
330 <groups:member groups:idRef="rxn_2"/>
331 <groups:member groups:idRef="rxn_3"/>
332 </groups:listOfMembers>
333 </groups:group>
334 <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
335 <annotation>
336 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
337 <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
338 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
339 </rdf:BRSynth>
340 </rdf:RDF>
341 </annotation>
342 <groups:listOfMembers>
343 <groups:member groups:idRef="CMPD_0000000003"/>
344 <groups:member groups:idRef="CMPD_0000000001"/>
345 </groups:listOfMembers>
346 </groups:group>
347 <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
348 <annotation>
349 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
350 <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
351 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
352 </rdf:BRSynth>
353 </rdf:RDF>
354 </annotation>
355 <groups:listOfMembers>
356 <groups:member groups:idRef="CMPD_0000000001"/>
357 <groups:member groups:idRef="MNXM132"/>
358 <groups:member groups:idRef="CMPD_0000000003"/>
359 <groups:member groups:idRef="TARGET_0000000001"/>
360 <groups:member groups:idRef="MNXM83"/>
361 </groups:listOfMembers>
362 </groups:group>
363 <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
364 <annotation>
365 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
366 <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
367 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
368 </rdf:BRSynth>
369 </rdf:RDF>
370 </annotation>
371 <groups:listOfMembers>
372 <groups:member groups:idRef="MNXM8975"/>
373 <groups:member groups:idRef="MNXM24"/>
374 <groups:member groups:idRef="MNXM11"/>
375 </groups:listOfMembers>
376 </groups:group>
377 <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
378 <annotation>
379 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
380 <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
381 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
382 </rdf:BRSynth>
383 </rdf:RDF>
384 </annotation>
385 <groups:listOfMembers>
386 <groups:member groups:idRef="MNXM83"/>
387 <groups:member groups:idRef="MNXM132"/>
388 <groups:member groups:idRef="MNXM11"/>
389 </groups:listOfMembers>
390 </groups:group>
391 </groups:listOfGroups>
392 </model>
393 </sbml>