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comparison test-data/rp_003_0131.xml @ 0:98d925a75257 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 23 Nov 2021 13:45:45 +0000
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-1:000000000000 0:98d925a75257
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="d5d4a5735e41ff2b063def8c757236e2e1a0f63c1dfee8baf1e79e81ce759172" id="RP_model_003_0131" name="003_0131" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
4 <listOfCompartments>
5 <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
6 <annotation>
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8 <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
9 <bqbiol:is>
10 <rdf:Bag>
11 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
12 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
13 <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
14 <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
15 <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
16 <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
17 <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
18 </rdf:Bag>
19 </bqbiol:is>
20 </rdf:Description>
21 </rdf:RDF>
22 </annotation>
23 </compartment>
24 </listOfCompartments>
25 <listOfSpecies>
26 <species metaid="_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a" id="MNXM36" name="MNXM36" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
27 <annotation>
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38 <brsynth:inchikey/>
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44 <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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55 <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
56 <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
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80 <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
81 <annotation>
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91 <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
92 <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
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98 <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
99 <annotation>
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109 <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
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117 <annotation>
118 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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125 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
126 <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([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]"/>
127 <brsynth:inchi value="InChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)"/>
128 <brsynth:inchikey value="VWFJDQUYCIWHTN-UHFFFAOYSA-N"/>
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130 </rdf:BRSynth>
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133 </species>
134 <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
135 <annotation>
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145 <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
146 <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
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148 </rdf:BRSynth>
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152 <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
153 <annotation>
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161 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
162 <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]"/>
163 <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
164 <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
165 </brsynth:brsynth>
166 </rdf:BRSynth>
167 </rdf:RDF>
168 </annotation>
169 </species>
170 </listOfSpecies>
171 <listOfParameters>
172 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
173 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
174 </listOfParameters>
175 <listOfReactions>
176 <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
177 <annotation>
178 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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180 <bqbiol:is>
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185 </rdf:Description>
186 <rdf:BRSynth rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
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189 <brsynth:rp2_transfo_id value="TRS_0_0_1"/>
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193 <brsynth:tmpl_rxn_ids>
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196 <brsynth:rule_score value="0.7358363677022237"/>
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203 <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
204 <speciesReference species="MNXM8975" stoichiometry="4" constant="true"/>
205 </listOfReactants>
206 <listOfProducts>
207 <speciesReference species="MNXM36" stoichiometry="4" constant="true"/>
208 <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
209 </listOfProducts>
210 </reaction>
211 <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
212 <annotation>
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218 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.99"/>
219 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.96"/>
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223 <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
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226 <brsynth:rp2_transfo_id value="TRS_0_1_9"/>
227 <brsynth:rule_ids>
228 <brsynth:RR-02-bedda4e2f5001e0c-14-F/>
229 </brsynth:rule_ids>
230 <brsynth:tmpl_rxn_ids>
231 <brsynth:MNXR111250/>
232 <brsynth:MNXR111499/>
233 <brsynth:MNXR113543/>
234 <brsynth:MNXR118024/>
235 <brsynth:MNXR139549/>
236 </brsynth:tmpl_rxn_ids>
237 <brsynth:rule_score value="0.5518755963407151"/>
238 <brsynth:idx_in_path value="2"/>
239 </brsynth:brsynth>
240 </rdf:BRSynth>
241 </rdf:RDF>
242 </annotation>
243 <listOfReactants>
244 <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
245 </listOfReactants>
246 <listOfProducts>
247 <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
248 <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
249 </listOfProducts>
250 </reaction>
251 <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
252 <annotation>
253 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
254 <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
255 <bqbiol:is>
256 <rdf:Bag>
257 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.92"/>
258 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.85"/>
259 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.84"/>
260 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.31"/>
261 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.81"/>
262 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.88"/>
263 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.-"/>
264 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1"/>
265 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/>
266 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.68"/>
267 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.10"/>
268 </rdf:Bag>
269 </bqbiol:is>
270 </rdf:Description>
271 <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
272 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
273 <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([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].[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]&gt;&gt;[H]OP(=O)(O[H])OP(=O)(O[H])OC([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].O=P(O)(O)OP(=O)(O)O"/>
274 <brsynth:rp2_transfo_id value="TRS_0_2_742"/>
275 <brsynth:rule_ids>
276 <brsynth:RR-02-07adee9ac9c42c7d-14-F/>
277 <brsynth:RR-02-1494429c7e6e0694-14-F/>
278 <brsynth:RR-02-1d50852f3f343682-14-F/>
279 <brsynth:RR-02-3bf131230c6b2bf2-14-F/>
280 <brsynth:RR-02-58d0f0d25e47b74a-14-F/>
281 <brsynth:RR-02-b3db29f084fc7a81-14-F/>
282 <brsynth:RR-02-f9759fe03c57b29f-14-F/>
283 </brsynth:rule_ids>
284 <brsynth:tmpl_rxn_ids>
285 <brsynth:MNXR100137/>
286 <brsynth:MNXR112247/>
287 <brsynth:MNXR116653/>
288 <brsynth:MNXR100621/>
289 <brsynth:MNXR99634/>
290 <brsynth:MNXR112069/>
291 <brsynth:MNXR99650/>
292 <brsynth:MNXR109677/>
293 <brsynth:MNXR113141/>
294 <brsynth:MNXR105052/>
295 <brsynth:MNXR109713/>
296 <brsynth:MNXR110950/>
297 <brsynth:MNXR110952/>
298 <brsynth:MNXR112246/>
299 <brsynth:MNXR112250/>
300 <brsynth:MNXR112251/>
301 <brsynth:MNXR112252/>
302 <brsynth:MNXR116656/>
303 <brsynth:MNXR117266/>
304 <brsynth:MNXR139515/>
305 <brsynth:MNXR139637/>
306 <brsynth:MNXR112249/>
307 <brsynth:MNXR116655/>
308 <brsynth:MNXR103150/>
309 <brsynth:MNXR112248/>
310 <brsynth:MNXR116654/>
311 </brsynth:tmpl_rxn_ids>
312 <brsynth:rule_score value="0.7358363677022237"/>
313 <brsynth:idx_in_path value="1"/>
314 </brsynth:brsynth>
315 </rdf:BRSynth>
316 </rdf:RDF>
317 </annotation>
318 <listOfReactants>
319 <speciesReference species="MNXM34" stoichiometry="1" constant="true"/>
320 <speciesReference species="MNXM83" stoichiometry="1" constant="true"/>
321 </listOfReactants>
322 <listOfProducts>
323 <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
324 <speciesReference species="MNXM11" stoichiometry="1" constant="true"/>
325 </listOfProducts>
326 </reaction>
327 </listOfReactions>
328 <groups:listOfGroups>
329 <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
330 <annotation>
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332 <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
333 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
334 <brsynth:global_score value="-1"/>
335 </brsynth:brsynth>
336 </rdf:BRSynth>
337 </rdf:RDF>
338 </annotation>
339 <groups:listOfMembers>
340 <groups:member groups:idRef="rxn_1"/>
341 <groups:member groups:idRef="rxn_2"/>
342 <groups:member groups:idRef="rxn_3"/>
343 </groups:listOfMembers>
344 </groups:group>
345 <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
346 <annotation>
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348 <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
349 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
350 </rdf:BRSynth>
351 </rdf:RDF>
352 </annotation>
353 <groups:listOfMembers>
354 <groups:member groups:idRef="CMPD_0000000001"/>
355 <groups:member groups:idRef="CMPD_0000000003"/>
356 </groups:listOfMembers>
357 </groups:group>
358 <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
359 <annotation>
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361 <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
362 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
363 </rdf:BRSynth>
364 </rdf:RDF>
365 </annotation>
366 <groups:listOfMembers>
367 <groups:member groups:idRef="CMPD_0000000003"/>
368 <groups:member groups:idRef="MNXM83"/>
369 <groups:member groups:idRef="TARGET_0000000001"/>
370 <groups:member groups:idRef="MNXM34"/>
371 <groups:member groups:idRef="CMPD_0000000001"/>
372 </groups:listOfMembers>
373 </groups:group>
374 <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
375 <annotation>
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377 <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
378 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
379 </rdf:BRSynth>
380 </rdf:RDF>
381 </annotation>
382 <groups:listOfMembers>
383 <groups:member groups:idRef="MNXM36"/>
384 <groups:member groups:idRef="MNXM8975"/>
385 <groups:member groups:idRef="MNXM11"/>
386 </groups:listOfMembers>
387 </groups:group>
388 <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
389 <annotation>
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391 <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
392 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
393 </rdf:BRSynth>
394 </rdf:RDF>
395 </annotation>
396 <groups:listOfMembers>
397 <groups:member groups:idRef="MNXM34"/>
398 <groups:member groups:idRef="MNXM11"/>
399 <groups:member groups:idRef="MNXM83"/>
400 </groups:listOfMembers>
401 </groups:group>
402 </groups:listOfGroups>
403 </model>
404 </sbml>