Commit d175914c authored by Marek Ostaszewski's avatar Marek Ostaszewski
Browse files

harmonised files

parent a5b5f698
Pipeline #36423 passed with stages
in 58 seconds
This source diff could not be displayed because it is too large. You can view the blob instead.
...@@ -6,8 +6,11 @@ ...@@ -6,8 +6,11 @@
<head> <head>
<title/> <title/>
</head> </head>
<body>Author(s): <body>
Author:
Muhammed Naveez, Riga Technical University, Latvia
Description: Description:
Interactions of the SARS-CoV-2 Orf3a with human proteins, especially in the context of the HOPS Complex.
</body> </body>
</html> </html>
</notes> </notes>
......
...@@ -225,7 +225,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -225,7 +225,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:speciesIdentity> </celldesigner:speciesIdentity>
</celldesigner:annotation> </celldesigner:annotation>
</celldesigner:species> </celldesigner:species>
<celldesigner:species id="s3576" name="ACE2"> <celldesigner:species id="s3579" name="ACE2">
<celldesigner:notes> <celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml"> <html xmlns="http://www.w3.org/1999/xhtml">
<head> <head>
...@@ -235,7 +235,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -235,7 +235,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</html> </html>
</celldesigner:notes> </celldesigner:notes>
<celldesigner:annotation> <celldesigner:annotation>
<celldesigner:complexSpecies>s3575</celldesigner:complexSpecies> <celldesigner:complexSpecies>s3578</celldesigner:complexSpecies>
<celldesigner:speciesIdentity> <celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr2</celldesigner:proteinReference> <celldesigner:proteinReference>pr2</celldesigner:proteinReference>
...@@ -248,7 +248,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -248,7 +248,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:speciesIdentity> </celldesigner:speciesIdentity>
</celldesigner:annotation> </celldesigner:annotation>
</celldesigner:species> </celldesigner:species>
<celldesigner:species id="s3577" name="S"> <celldesigner:species id="s3580" name="S">
<celldesigner:notes> <celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml"> <html xmlns="http://www.w3.org/1999/xhtml">
<head> <head>
...@@ -258,7 +258,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -258,7 +258,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</html> </html>
</celldesigner:notes> </celldesigner:notes>
<celldesigner:annotation> <celldesigner:annotation>
<celldesigner:complexSpecies>s3575</celldesigner:complexSpecies> <celldesigner:complexSpecies>s3578</celldesigner:complexSpecies>
<celldesigner:speciesIdentity> <celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class> <celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr34</celldesigner:proteinReference> <celldesigner:proteinReference>pr34</celldesigner:proteinReference>
...@@ -271,6 +271,47 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -271,6 +271,47 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:speciesIdentity> </celldesigner:speciesIdentity>
</celldesigner:annotation> </celldesigner:annotation>
</celldesigner:species> </celldesigner:species>
<celldesigner:species id="s3588" name="NRP1">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body/>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s3586</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr68</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s3589" name="S1">
<celldesigner:notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>
http://www.ebi.ac.uk/interpro/entry/InterPro/IPR002551/
</body>
</html>
</celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s3586</celldesigner:complexSpecies>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr16</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfStructuralStates>
<celldesigner:structuralState structuralState="CendR"/>
</celldesigner:listOfStructuralStates>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
</celldesigner:listOfIncludedSpecies> </celldesigner:listOfIncludedSpecies>
<celldesigner:listOfCompartmentAliases> <celldesigner:listOfCompartmentAliases>
<celldesigner:compartmentAlias id="ca189" compartment="c182"> <celldesigner:compartmentAlias id="ca189" compartment="c182">
...@@ -427,7 +468,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -427,7 +468,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:compartmentAlias> </celldesigner:compartmentAlias>
</celldesigner:listOfCompartmentAliases> </celldesigner:listOfCompartmentAliases>
<celldesigner:listOfComplexSpeciesAliases> <celldesigner:listOfComplexSpeciesAliases>
<celldesigner:complexSpeciesAlias id="csa430" species="s3575" compartmentAlias="ca189"> <celldesigner:complexSpeciesAlias id="csa430" species="s3578" compartmentAlias="ca189">
<celldesigner:activity>inactive</celldesigner:activity> <celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="533.5" y="350.5" w="192.0" h="168.0"/> <celldesigner:bounds x="533.5" y="350.5" w="192.0" h="168.0"/>
<celldesigner:font size="12"/> <celldesigner:font size="12"/>
...@@ -574,7 +615,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -574,7 +615,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:briefView> </celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/> <celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:complexSpeciesAlias> </celldesigner:complexSpeciesAlias>
<celldesigner:complexSpeciesAlias id="csa368" species="s3575" compartmentAlias="ca189"> <celldesigner:complexSpeciesAlias id="csa368" species="s3578" compartmentAlias="ca189">
<celldesigner:activity>inactive</celldesigner:activity> <celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="3444.3461538461524" y="378.41346153846143" w="192.0" h="168.0"/> <celldesigner:bounds x="3444.3461538461524" y="378.41346153846143" w="192.0" h="168.0"/>
<celldesigner:font size="12"/> <celldesigner:font size="12"/>
...@@ -973,6 +1014,27 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -973,6 +1014,27 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:briefView> </celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/> <celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:complexSpeciesAlias> </celldesigner:complexSpeciesAlias>
<celldesigner:complexSpeciesAlias id="csa441" species="s3586" compartmentAlias="ca189">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="1806.0" y="343.0" w="115.0" h="135.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:backupSize w="0.0" h="0.0"/>
<celldesigner:backupView state="none"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="1782.0" y="-110.0"/>
<celldesigner:boxSize width="115.0" height="135.0"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:complexSpeciesAlias>
</celldesigner:listOfComplexSpeciesAliases> </celldesigner:listOfComplexSpeciesAliases>
<celldesigner:listOfSpeciesAliases> <celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa1420" species="s3567" complexSpeciesAlias="csa352"> <celldesigner:speciesAlias id="sa1420" species="s3567" complexSpeciesAlias="csa352">
...@@ -1152,6 +1214,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -1152,6 +1214,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
<celldesigner:bounds x="3063.0" y="255.0" w="80.0" h="40.0"/> <celldesigner:bounds x="3063.0" y="255.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/> <celldesigner:font size="12"/>
<celldesigner:view state="usual"/> <celldesigner:view state="usual"/>
<celldesigner:structuralState angle="1.5707963267948966"/>
<celldesigner:usualView> <celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/> <celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/> <celldesigner:boxSize width="80.0" height="40.0"/>
...@@ -1224,7 +1287,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -1224,7 +1287,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:briefView> </celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/> <celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias> </celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa1550" species="s3577" complexSpeciesAlias="csa368"> <celldesigner:speciesAlias id="sa1550" species="s3580" complexSpeciesAlias="csa368">
<celldesigner:activity>inactive</celldesigner:activity> <celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="3542.53882959146" y="399.1371457489877" w="86.0" h="46.0"/> <celldesigner:bounds x="3542.53882959146" y="399.1371457489877" w="86.0" h="46.0"/>
<celldesigner:font size="12"/> <celldesigner:font size="12"/>
...@@ -1244,7 +1307,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -1244,7 +1307,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:briefView> </celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/> <celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias> </celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa1551" species="s3576" complexSpeciesAlias="csa368"> <celldesigner:speciesAlias id="sa1551" species="s3579" complexSpeciesAlias="csa368">
<celldesigner:activity>inactive</celldesigner:activity> <celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="3501.5" y="459.5" w="86.0" h="56.0"/> <celldesigner:bounds x="3501.5" y="459.5" w="86.0" h="56.0"/>
<celldesigner:font size="12"/> <celldesigner:font size="12"/>
...@@ -3207,7 +3270,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -3207,7 +3270,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:briefView> </celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/> <celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias> </celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2174" species="s3577" complexSpeciesAlias="csa368"> <celldesigner:speciesAlias id="sa2174" species="s3580" complexSpeciesAlias="csa368">
<celldesigner:activity>inactive</celldesigner:activity> <celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="3451.03882959146" y="399.75" w="86.0" h="46.0"/> <celldesigner:bounds x="3451.03882959146" y="399.75" w="86.0" h="46.0"/>
<celldesigner:font size="12"/> <celldesigner:font size="12"/>
...@@ -3227,7 +3290,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -3227,7 +3290,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:briefView> </celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/> <celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias> </celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2175" species="s3576" complexSpeciesAlias="csa430"> <celldesigner:speciesAlias id="sa2175" species="s3579" complexSpeciesAlias="csa430">
<celldesigner:activity>inactive</celldesigner:activity> <celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="590.6538461538476" y="431.58653846153857" w="86.0" h="56.0"/> <celldesigner:bounds x="590.6538461538476" y="431.58653846153857" w="86.0" h="56.0"/>
<celldesigner:font size="12"/> <celldesigner:font size="12"/>
...@@ -3247,7 +3310,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -3247,7 +3310,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:briefView> </celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/> <celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias> </celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2176" species="s3577" complexSpeciesAlias="csa430"> <celldesigner:speciesAlias id="sa2176" species="s3580" complexSpeciesAlias="csa430">
<celldesigner:activity>inactive</celldesigner:activity> <celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="540.1926757453075" y="371.83653846153857" w="86.0" h="46.0"/> <celldesigner:bounds x="540.1926757453075" y="371.83653846153857" w="86.0" h="46.0"/>
<celldesigner:font size="12"/> <celldesigner:font size="12"/>
...@@ -3267,7 +3330,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -3267,7 +3330,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:briefView> </celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/> <celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias> </celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2177" species="s3577" complexSpeciesAlias="csa430"> <celldesigner:speciesAlias id="sa2177" species="s3580" complexSpeciesAlias="csa430">
<celldesigner:activity>inactive</celldesigner:activity> <celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="631.6926757453075" y="371.22368421052624" w="86.0" h="46.0"/> <celldesigner:bounds x="631.6926757453075" y="371.22368421052624" w="86.0" h="46.0"/>
<celldesigner:font size="12"/> <celldesigner:font size="12"/>
...@@ -5313,6 +5376,121 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -5313,6 +5376,121 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:briefView> </celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/> <celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias> </celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2369" species="s3581" compartmentAlias="ca189">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="357.0" y="444.5" w="113.0" h="42.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="333.0" y="-8.5"/>
<celldesigner:boxSize width="113.0" height="42.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccff66" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2370" species="s3581" compartmentAlias="ca189">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="3678.5" y="446.0" w="113.0" h="42.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="3654.5" y="-7.0"/>
<celldesigner:boxSize width="113.0" height="42.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccff66" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2371" species="s3582" compartmentAlias="ca189">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="2665.0" y="441.0" w="80.0" h="50.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="2641.0" y="-12.0"/>
<celldesigner:boxSize width="80.0" height="50.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2372" species="s3583" compartmentAlias="ca189">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="1985.0" y="447.5" w="83.0" h="36.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="1961.0" y="-5.5"/>
<celldesigner:boxSize width="83.0" height="36.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccff66" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2374" species="s3588" complexSpeciesAlias="csa441">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="1822.5" y="403.0" w="80.0" h="50.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="16.5" y="60.0"/>
<celldesigner:boxSize width="80.0" height="50.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2376" species="s3589" complexSpeciesAlias="csa441">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="1824.0" y="359.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:structuralState angle="1.5707963267948966"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="18.0" y="16.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffcccc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases> </celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/> <celldesigner:listOfGroups/>
<celldesigner:listOfProteins> <celldesigner:listOfProteins>
...@@ -5361,6 +5539,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -5361,6 +5539,7 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</celldesigner:protein> </celldesigner:protein>
<celldesigner:protein id="pr50" name="Nsp1" type="GENERIC"/> <celldesigner:protein id="pr50" name="Nsp1" type="GENERIC"/>
<celldesigner:protein id="pr51" name="Nsp2" type="GENERIC"/> <celldesigner:protein id="pr51" name="Nsp2" type="GENERIC"/>
<celldesigner:protein id="pr68" name="NRP1" type="RECEPTOR"/>
</celldesigner:listOfProteins> </celldesigner:listOfProteins>
<celldesigner:listOfGenes/> <celldesigner:listOfGenes/>
<celldesigner:listOfRNAs> <celldesigner:listOfRNAs>
...@@ -5671,35 +5850,6 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en ...@@ -5671,35 +5850,6 @@ Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, en
</rdf:RDF> </rdf:RDF>
</annotation> </annotation>
</species> </species>
<species metaid="s2597" id="s2597" name="S1" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>http://www.ebi.ac.uk/interpro/entry/InterPro/IPR002551/
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr16</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s2597">
<bqbiol:isEncodedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:interpro:IPR002551"/>
</rdf:Bag>
</bqbiol:isEncodedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s2596" id="s2596" name="S2" compartment="c182" initialAmount="0"> <species metaid="s2596" id="s2596" name="S2" compartment="c182" initialAmount="0">
<notes> <notes>
<html xmlns="http://www.w3.org/1999/xhtml"> <html xmlns="http://www.w3.org/1999/xhtml">
...@@ -8148,20 +8298,6 @@ N: P0DTC9 ...@@ -8148,20 +8298,6 @@ N: P0DTC9
</rdf:RDF> </rdf:RDF>
</annotation> </annotation>
</species> </species>
<species metaid="s3575" id="s3575" name="ACE2:SPIKE complex" compartment="c182" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>ACE2:SPIKE complex</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re841"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3531" id="s3531" name="N (-)ss sgmRNA" compartment="c182" initialAmount="0"> <species metaid="s3531" id="s3531" name="N (-)ss sgmRNA" compartment="c182" initialAmount="0">
<annotation> <annotation>
<celldesigner:extension> <celldesigner:extension>
...@@ -8202,6 +8338,126 @@ N: P0DTC9 ...@@ -8202,6 +8338,126 @@ N: P0DTC9
</rdf:RDF> </rdf:RDF>
</annotation> </annotation>
</species> </species>
<species metaid="s3578" id="s3578" name="ACE2:SPIKE complex" compartment="c182" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>ACE2:SPIKE complex</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re841"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3581" id="s3581" name="Heparan sulfate" compartment="c182" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>Heparan sulfate</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re838"/>
<celldesigner:catalyzed reaction="re852"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s3581">
<bqbiol:isEncodedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A28815"/>
</rdf:Bag>
</bqbiol:isEncodedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s3582" id="s3582" name="NRP1" compartment="c182" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr68</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3583" id="s3583" name="cholesterol" compartment="c182" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
<celldesigner:name>cholesterol</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re855"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s3583">
<bqbiol:isEncodedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16113"/>
</rdf:Bag>
</bqbiol:isEncodedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s3586" id="s3586" name="S1:NRP1 complex" compartment="c182" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>S1:NRP1 complex</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re855"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s2597" id="s2597" name="S1" compartment="default" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>http://www.ebi.ac.uk/interpro/entry/InterPro/IPR002551/
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr16</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfStructuralStates>
<celldesigner:structuralState structuralState="CendR"/>
</celldesigner:listOfStructuralStates>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s2597">
<bqbiol:isEncodedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:interpro:IPR002551"/>
</rdf:Bag>
</bqbiol:isEncodedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies> </listOfSpecies>
<listOfReactions> <listOfReactions>
<reaction metaid="re838" id="re838" reversible="false"> <reaction metaid="re838" id="re838" reversible="false">
...@@ -8214,8 +8470,8 @@ N: P0DTC9 ...@@ -8214,8 +8470,8 @@ N: P0DTC9