Mercurial > repos > tduigou > selenzy

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selenzy.xml	Wed Dec 15 13:59:04 2021 +0000
@@ -0,0 +1,98 @@
+<tool id="selenzy-wrapper" name="Selenzyme" version="0.1.0">
+    <description>Performs enzyme selection from a reaction query</description>
+	<requirements>
+        <requirement type="package" version="0.1.0">selenzy_wrapper</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+	    python -m selenzy_wrapper '$pathway' '$uniprot_ids'
+        --nb_targets '$adv.nb_targets'
+        --d '$adv.direction'
+        #if str($adv.NoMSA) == "false":
+            --NoMSA
+        #end if
+        --taxonIDs '$adv.taxonIDs'
+        --nb_ids '$adv.nb_ids'
+        --to_csv '$uniprot_ids_csv'
+    ]]></command>
+    <inputs>
+		<param name="pathway" type="data" format="xml" label="Pathway (SBML)" />
+        <section name="adv" title="Advanced Options" expanded="false">
+		    <param name="nb_ids"        type="integer" value="-1"       label="Number of uniprot IDs with top score to keep" />
+		    <param name="nb_targets"        type="integer" value="500"       label="Number of targets to display in results" />
+            <param name="direction"        type="float" value="0"       label="Use similiarity values for preferred reaction direction only" />
+            <param name="NoMSA"     type="boolean" label="Do not compute MSA/conservation scores ?"       checked="true"   display="checkboxes" />
+            <param name="taxonIDs" type="text" label="Comma separated taxon ids (first considered as the host)" value="83333" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="uniprot_ids" format="xml" label="Uniprot IDs" />
+        <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="pathway" value="pathway.xml" />
+            <output name="uniprot_ids" file="uniprod_ids_out.xml" ftype="xml" compare="diff" sort="true"/>
+            <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Selenzyme
+================
+
+Performs enzyme selection from a reaction query.
+
+Input
+-----
+
+* **pathway_file**\ : (string) path to pathway file
+* **nb_targets**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 20]
+* **nb_ids**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]
+* **direction**\ : (float) Use similiarity values for preferred reaction direction only [default=0 (OFF)]
+* **NoMSA**\ : (boolean) Do not compute MSA/conservation scores
+* **taxonIDs**\ : (string) Comma separated taxon ids [default: 83333 (E. coli K12)]. The first taxon ID is the one of the chassis, following ones are taxon IDs of output enzyme sequences
+
+Output
+------
+
+* **outfile**\ : (string) Path to output file
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
+
+Version
+----------
+
+0.1.0
+
+Authors
+-------
+* **Joan Hérisson**
+
+License
+-------
+
+* `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@article{10.1093/bioinformatics/bty065,
+  title={Selenzyme: enzyme selection tool for pathway design},
+  author={Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano, Nicholas J Turner, Nigel S Scrutton, Douglas B Kell, Rainer Breitling, Jean-Loup Faulon},
+  volume={34},
+  pages={2153–2154},
+  year={2018},
+  doi = {10.1093/bioinformatics/bty065},
+  url = {https://doi.org/10.1093/bioinformatics/bty065},
+}
+        </citation>
+    </citations>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathway.xml	Wed Dec 15 13:59:04 2021 +0000
@@ -0,0 +1,626 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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">
+  <model metaid="ab7a7ab71c6ccfe1bb89180d9a6fb504a8ea4784c1ace396ce99cb6892d1b81e" id="RP_model_003_0261" name="003_0261" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
+    <listOfCompartments>
+      <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
+                  <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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+                  <brsynth:units value="kilojoule / mole"/>
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+                  <brsynth:units value="kilojoule / mole"/>
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+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
+                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
+                <brsynth:fba_biomass_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_biomass_shadow_price>
+                <brsynth:fba_fraction_shadow_price>
+                  <brsynth:value value="None"/>
+                </brsynth:fba_fraction_shadow_price>
+                <brsynth:thermo_standard_dg_formation>
+                  <brsynth:value value="-1966.8036657706114"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_standard_dg_formation>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.92"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.85"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.84"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.31"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.81"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.88"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.-"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.68"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.10"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <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"/>
+                <brsynth:rp2_transfo_id value="TRS_0_2_742"/>
+                <brsynth:rule_ids>
+                  <brsynth:RR-02-07adee9ac9c42c7d-14-F/>
+                  <brsynth:RR-02-1494429c7e6e0694-14-F/>
+                  <brsynth:RR-02-1d50852f3f343682-14-F/>
+                  <brsynth:RR-02-3bf131230c6b2bf2-14-F/>
+                  <brsynth:RR-02-58d0f0d25e47b74a-14-F/>
+                  <brsynth:RR-02-b3db29f084fc7a81-14-F/>
+                  <brsynth:RR-02-f9759fe03c57b29f-14-F/>
+                </brsynth:rule_ids>
+                <brsynth:tmpl_rxn_ids>
+                  <brsynth:MNXR100137/>
+                  <brsynth:MNXR112247/>
+                  <brsynth:MNXR116653/>
+                  <brsynth:MNXR100621/>
+                  <brsynth:MNXR99634/>
+                  <brsynth:MNXR112069/>
+                  <brsynth:MNXR99650/>
+                  <brsynth:MNXR109677/>
+                  <brsynth:MNXR113141/>
+                  <brsynth:MNXR105052/>
+                  <brsynth:MNXR109713/>
+                  <brsynth:MNXR110950/>
+                  <brsynth:MNXR110952/>
+                  <brsynth:MNXR112246/>
+                  <brsynth:MNXR112250/>
+                  <brsynth:MNXR112251/>
+                  <brsynth:MNXR112252/>
+                  <brsynth:MNXR116656/>
+                  <brsynth:MNXR117266/>
+                  <brsynth:MNXR139515/>
+                  <brsynth:MNXR139637/>
+                  <brsynth:MNXR112249/>
+                  <brsynth:MNXR116655/>
+                  <brsynth:MNXR103150/>
+                  <brsynth:MNXR112248/>
+                  <brsynth:MNXR116654/>
+                </brsynth:tmpl_rxn_ids>
+                <brsynth:rule_score value="0.7358363677022237"/>
+                <brsynth:idx_in_path value="1"/>
+                <brsynth:selenzy/>
+                <brsynth:fba_biomass>
+                  <brsynth:value value="0.0"/>
+                  <brsynth:units value="gDW / gDW / hour"/>
+                </brsynth:fba_biomass>
+                <brsynth:fba_fraction>
+                  <brsynth:value value="0.4741875610167627"/>
+                  <brsynth:units value="milimole / gDW / hour"/>
+                </brsynth:fba_fraction>
+                <brsynth:thermo_dG0_prime>
+                  <brsynth:value value="-71.55654770059041"/>
+                  <brsynth:error value="2.9407032504945367"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG0_prime>
+                <brsynth:thermo_dGm_prime>
+                  <brsynth:value value="-71.55654770059041"/>
+                  <brsynth:error value="2.9407032504945367"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dGm_prime>
+                <brsynth:thermo_dG_prime>
+                  <brsynth:value value="-71.55654770059041"/>
+                  <brsynth:error value="2.9407032504945367"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG_prime>
+                <brsynth:thermo_dG>
+                  <brsynth:value value="-26.40520582450108"/>
+                  <brsynth:error value="2.9407032504945367"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="MNXM34" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM83" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM11" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.32"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.99"/>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.96"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <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])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])([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].O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:rp2_transfo_id value="TRS_0_1_9"/>
+                <brsynth:rule_ids>
+                  <brsynth:RR-02-bedda4e2f5001e0c-14-F/>
+                </brsynth:rule_ids>
+                <brsynth:tmpl_rxn_ids>
+                  <brsynth:MNXR111250/>
+                  <brsynth:MNXR111499/>
+                  <brsynth:MNXR113543/>
+                  <brsynth:MNXR118024/>
+                  <brsynth:MNXR139549/>
+                </brsynth:tmpl_rxn_ids>
+                <brsynth:rule_score value="0.5518755963407151"/>
+                <brsynth:idx_in_path value="2"/>
+                <brsynth:selenzy/>
+                <brsynth:fba_biomass>
+                  <brsynth:value value="0.0"/>
+                  <brsynth:units value="gDW / gDW / hour"/>
+                </brsynth:fba_biomass>
+                <brsynth:fba_fraction>
+                  <brsynth:value value="0.4741875610167627"/>
+                  <brsynth:units value="milimole / gDW / hour"/>
+                </brsynth:fba_fraction>
+                <brsynth:thermo_dG0_prime>
+                  <brsynth:value value="-119.13360567395966"/>
+                  <brsynth:error value="11.000567449695138"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG0_prime>
+                <brsynth:thermo_dGm_prime>
+                  <brsynth:value value="-153.36328074340173"/>
+                  <brsynth:error value="11.000567449695138"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dGm_prime>
+                <brsynth:thermo_dG_prime>
+                  <brsynth:value value="-119.13360567395966"/>
+                  <brsynth:error value="11.000567449695138"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG_prime>
+                <brsynth:thermo_dG>
+                  <brsynth:value value="-1501.0650763644926"/>
+                  <brsynth:error value="11.000567449695138"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.31"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <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]"/>
+                <brsynth:rp2_transfo_id value="TRS_0_0_1"/>
+                <brsynth:rule_ids>
+                  <brsynth:RR-02-ae41ec5771136ea5-14-F/>
+                </brsynth:rule_ids>
+                <brsynth:tmpl_rxn_ids>
+                  <brsynth:MNXR125832/>
+                </brsynth:tmpl_rxn_ids>
+                <brsynth:rule_score value="0.7358363677022237"/>
+                <brsynth:idx_in_path value="3"/>
+                <brsynth:selenzy/>
+                <brsynth:fba_biomass>
+                  <brsynth:value value="0.0"/>
+                  <brsynth:units value="gDW / gDW / hour"/>
+                </brsynth:fba_biomass>
+                <brsynth:fba_fraction>
+                  <brsynth:value value="0.4741875610167627"/>
+                  <brsynth:units value="milimole / gDW / hour"/>
+                </brsynth:fba_fraction>
+                <brsynth:thermo_dG0_prime>
+                  <brsynth:value value="162.18254376952495"/>
+                  <brsynth:error value="12.808033567928218"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG0_prime>
+                <brsynth:thermo_dGm_prime>
+                  <brsynth:value value="162.18254376952495"/>
+                  <brsynth:error value="12.808033567928218"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dGm_prime>
+                <brsynth:thermo_dG_prime>
+                  <brsynth:value value="162.18254376952495"/>
+                  <brsynth:error value="12.808033567928218"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG_prime>
+                <brsynth:thermo_dG>
+                  <brsynth:value value="-27.202610383152432"/>
+                  <brsynth:error value="12.808033567928218"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM35" stoichiometry="4" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="MNXM24" stoichiometry="4" constant="true"/>
+          <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+    </listOfReactions>
+    <groups:listOfGroups>
+      <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:fba_biomass>
+                  <brsynth:value value="0.8769972144269784"/>
+                  <brsynth:units value="gDW / gDW / hour"/>
+                </brsynth:fba_biomass>
+                <brsynth:fba_fraction>
+                  <brsynth:value value="0.4741875610167627"/>
+                  <brsynth:units value="milimole / gDW / hour"/>
+                </brsynth:fba_fraction>
+                <brsynth:thermo_dG0_prime>
+                  <brsynth:value value="-28.507609605022708"/>
+                  <brsynth:error value="19.469504383090346"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG0_prime>
+                <brsynth:thermo_dGm_prime>
+                  <brsynth:value value="-62.737284674464775"/>
+                  <brsynth:error value="19.469504383090346"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dGm_prime>
+                <brsynth:thermo_dG_prime>
+                  <brsynth:value value="-28.507609605022708"/>
+                  <brsynth:error value="19.469504383090346"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG_prime>
+                <brsynth:thermo_dG>
+                  <brsynth:value value="-1554.6728925721447"/>
+                  <brsynth:error value="19.469504383090346"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG>
+                <brsynth:global_score value="0.9863117098808288"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="rxn_1"/>
+          <groups:member groups:idRef="rxn_2"/>
+          <groups:member groups:idRef="rxn_3"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="CMPD_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+          <groups:member groups:idRef="CMPD_0000000001"/>
+          <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="MNXM83"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM35"/>
+          <groups:member groups:idRef="MNXM24"/>
+          <groups:member groups:idRef="MNXM11"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
+          <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="MNXM11"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM35"/>
+          <groups:member groups:idRef="MNXM24"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM35"/>
+          <groups:member groups:idRef="MNXM24"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+        </groups:listOfMembers>
+      </groups:group>
+    </groups:listOfGroups>
+  </model>
+</sbml>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/uniprod_ids_out.csv	Wed Dec 15 13:59:04 2021 +0000
@@ -0,0 +1,1486 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/uniprod_ids_out.xml	Wed Dec 15 13:59:04 2021 +0000
@@ -0,0 +1,7968 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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">
+  <model metaid="ab7a7ab71c6ccfe1bb89180d9a6fb504a8ea4784c1ace396ce99cb6892d1b81e" id="RP_model_003_0261" name="003_0261" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
+                  <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
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+    </listOfSpecies>
+    <listOfParameters>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q298G6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9VHS7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q66JT7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q96H96"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q499N4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q2KIQ4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q16QL3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q5R6U3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P53798"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P37268"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q02769"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q32KR6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B2C4D4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9SSU8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/I6RAQ6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/I6QPS5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/I6QSN0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q6ZJL3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D5KXD2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B2C4D5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B2C4D0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8SA63"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q5GJ60"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q2NM15"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9FQ26"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q70EZ7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q70EZ6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/C7E5V8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/C7E5V7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4U3F6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8S3A6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8S3A5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q1PDD2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/F8UL80"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9FQ27"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8LSC3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8LSC2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4U3F7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B0FGA9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O64961"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/K4LMW2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q7XB13"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q0DAK7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q7XB14"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P49085"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P37273"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P08196"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q49SP3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q5SBP6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q49SP6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q49SP4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9FXY7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q84ZW8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/C7E5W0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/C7E5V9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P59287"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/E2E2N7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q49SP5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q7XYS8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P0C565"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q84LB2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B9RXW0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q66PX8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q93YP7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P0CV96"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P0CV95"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P0CV94"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q84UU4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P37272"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4KSH9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q38833"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O48935"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9LX33"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q38920"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O80642"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9T0K1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9T0J9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B4YYR2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/J7LMP2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q0WUA3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q66PX9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P0CJ43"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A4FVP2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q1ACB3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B2KSJ6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P49293"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P37271"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D0VMR8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D0VMR7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D0VMR6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q6Q3H3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/J9RLZ7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/E5GAG1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q94JS8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4JHG3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q308N0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q6USK1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/E4ZUB5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q52QW5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q93YV0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B1B1U3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D2YZP9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q0VHD6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P53800"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q0V6M5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B2WAQ3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P53797"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/C9K2Q3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O48666"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P53799"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8I7J4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/E3Q717"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D1Z4K7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B2ATB0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8X0Z1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P37295"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A2PZA5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q2U4X9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/E4UPP6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D4D802"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A2QM49"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q84KL5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O23118"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O64404"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O64405"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q675L6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4QSN4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P85964"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O81086"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A0A097ZPE3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q675K8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P32378"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q675L0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A8NE23"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8GUE4"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9C448"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q10252"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q7S4Z6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4P0S6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/E6ZZ11"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D8SAZ5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/G1DGI7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D8RLD3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9UUQ6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q7Z859"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q67GH9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9HGZ6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P11491"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/D8RNZ9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9P854"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O34707"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9Y753"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q752X9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P78589"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P39582"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P29704"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q92459"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O74165"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9X839"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P9WIP2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P65651"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P36596"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P9WIP3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A1JHN0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9ACU1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q99R75"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8NUQ5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q7A3E1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q6G6B2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q5HCY8"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q2FDU5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O07854"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q55500"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q2FV59"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9K498"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O07134"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/W0LV34"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q54U71"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4L976"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q2YWE7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/O07333"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P37294"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q2L6E3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P55350"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A9JQL9"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9SDW9"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P54975"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/G0Y286"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q54DR1"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/P44739"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q971A3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q4J8K2"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A8A9J7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A4YI21"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A2BIU7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A1S066"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9UWY6"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9V2P5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9HRP0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8TZM7"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8TWS9"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8TS44"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8PV96"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q6LWN2"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q57727"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q46BD9"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q9YEF5"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/Q8ZTX5"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/C4KIS5"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/C3NFV6"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/C3MRH0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/B1YAF0"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A4YJ26"/>
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+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A3MUU3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A3DN81"/>
+                  <rdf:li rdf:resource="http://identifiers.org/uniprot/A2BIS8"/>
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+                  <brsynth:units value="kilojoule / mole"/>
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+                  <brsynth:units value="kilojoule / mole"/>
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+        </annotation>
+        <listOfReactants>
+          <speciesReference species="MNXM34" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM83" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
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+          <speciesReference species="MNXM11" stoichiometry="1" constant="true"/>
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+      </reaction>
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+        </annotation>
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+          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
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+                <brsynth:selenzy_P11712>
+                  <brsynth:score value="-8.823"/>
+                  <brsynth:target_ID value="9606"/>
+                </brsynth:selenzy_P11712>
+                <brsynth:selenzy_P33261>
+                  <brsynth:score value="-8.823"/>
+                  <brsynth:target_ID value="9606"/>
+                </brsynth:selenzy_P33261>
+                <brsynth:selenzy_O70276>
+                  <brsynth:score value="-8.926"/>
+                  <brsynth:target_ID value="10116"/>
+                </brsynth:selenzy_O70276>
+                <brsynth:selenzy_P23141>
+                  <brsynth:score value="-9.826"/>
+                  <brsynth:target_ID value="9606"/>
+                </brsynth:selenzy_P23141>
+                <brsynth:selenzy_Q16518>
+                  <brsynth:score value="-9.826"/>
+                  <brsynth:target_ID value="9606"/>
+                </brsynth:selenzy_Q16518>
+                <brsynth:selenzy_Q91ZQ5>
+                  <brsynth:score value="-9.826"/>
+                  <brsynth:target_ID value="10090"/>
+                </brsynth:selenzy_Q91ZQ5>
+                <brsynth:selenzy_Q9XT71>
+                  <brsynth:score value="-9.926"/>
+                  <brsynth:target_ID value="9534"/>
+                </brsynth:selenzy_Q9XT71>
+                <brsynth:selenzy_Q9I993>
+                  <brsynth:score value="-10.135"/>
+                  <brsynth:target_ID value="9031"/>
+                </brsynth:selenzy_Q9I993>
+                <brsynth:selenzy_O93344>
+                  <brsynth:score value="-10.138"/>
+                  <brsynth:target_ID value="9031"/>
+                </brsynth:selenzy_O93344>
+                <brsynth:selenzy_P27463>
+                  <brsynth:score value="-10.138"/>
+                  <brsynth:target_ID value="9031"/>
+                </brsynth:selenzy_P27463>
+                <brsynth:fba_biomass>
+                  <brsynth:value value="0.0"/>
+                  <brsynth:units value="gDW / gDW / hour"/>
+                </brsynth:fba_biomass>
+                <brsynth:fba_fraction>
+                  <brsynth:value value="0.4741875610167627"/>
+                  <brsynth:units value="milimole / gDW / hour"/>
+                </brsynth:fba_fraction>
+                <brsynth:thermo_dG0_prime>
+                  <brsynth:value value="162.18254376952495"/>
+                  <brsynth:error value="12.808033567928218"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG0_prime>
+                <brsynth:thermo_dGm_prime>
+                  <brsynth:value value="162.18254376952495"/>
+                  <brsynth:error value="12.808033567928218"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dGm_prime>
+                <brsynth:thermo_dG_prime>
+                  <brsynth:value value="162.18254376952495"/>
+                  <brsynth:error value="12.808033567928218"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG_prime>
+                <brsynth:thermo_dG>
+                  <brsynth:value value="-27.202610383152432"/>
+                  <brsynth:error value="12.808033567928218"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM35" stoichiometry="4" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="MNXM24" stoichiometry="4" constant="true"/>
+          <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+    </listOfReactions>
+    <groups:listOfGroups>
+      <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:fba_biomass>
+                  <brsynth:value value="0.8769972144269784"/>
+                  <brsynth:units value="gDW / gDW / hour"/>
+                </brsynth:fba_biomass>
+                <brsynth:fba_fraction>
+                  <brsynth:value value="0.4741875610167627"/>
+                  <brsynth:units value="milimole / gDW / hour"/>
+                </brsynth:fba_fraction>
+                <brsynth:thermo_dG0_prime>
+                  <brsynth:value value="-28.507609605022708"/>
+                  <brsynth:error value="19.469504383090346"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG0_prime>
+                <brsynth:thermo_dGm_prime>
+                  <brsynth:value value="-62.737284674464775"/>
+                  <brsynth:error value="19.469504383090346"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dGm_prime>
+                <brsynth:thermo_dG_prime>
+                  <brsynth:value value="-28.507609605022708"/>
+                  <brsynth:error value="19.469504383090346"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG_prime>
+                <brsynth:thermo_dG>
+                  <brsynth:value value="-1554.6728925721447"/>
+                  <brsynth:error value="19.469504383090346"/>
+                  <brsynth:units value="kilojoule / mole"/>
+                </brsynth:thermo_dG>
+                <brsynth:global_score value="0.9863117098808288"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="rxn_1"/>
+          <groups:member groups:idRef="rxn_2"/>
+          <groups:member groups:idRef="rxn_3"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="CMPD_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="CMPD_0000000001"/>
+          <groups:member groups:idRef="MNXM83"/>
+          <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM35"/>
+          <groups:member groups:idRef="MNXM11"/>
+          <groups:member groups:idRef="MNXM24"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
+          <groups:member groups:idRef="MNXM11"/>
+          <groups:member groups:idRef="MNXM34"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM35"/>
+          <groups:member groups:idRef="MNXM24"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:BRSynth rdf:about="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM35"/>
+          <groups:member groups:idRef="MNXM24"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+        </groups:listOfMembers>
+      </groups:group>
+    </groups:listOfGroups>
+  </model>
+</sbml>