Change test 2 expected results

tests/fixtures/test_elm.json

@@ -1125,7 +1125,7 @@
         "ELME000333",
         "SUMO interaction site",
         "Non-covalent binding to SUMO proteins is mediated via the SUMO-interacting motif (SIM). SUMO-interacting proteins predominantly function in the nucleus. The SIM is essential for a variety of cellular processes including transcriptional regulation, sub-nuclear localization, nuclear body assembly, and anti-viral response. Viral proteins are also known to utilize such processes via their SIMs upon host cell invasion.",
-        "This SUMO interacting motif variant is for SIMs bound as a beta-augmented strand in the parallel orientation. The SIM peptide inserts into a groove on the SUMO surface so that the motif has a hydrophobic core of four residues (preference V, I or L), the 3rd position being more variable. At the variable 3rd position, in addition to hydrophobic residues, acidic residues (D or E) and the phosphorylatable residue serine are allowed. A stretch of 1 to 5 acidic or phosphorylatable residues is considered necessary C-terminally from the hydrophobic core. Another negative stretch N-terminal to the core appears more optional, though both are usually present. These acidic stretches complement positively-charged residues on the SUMO surface. The length of the acidic stretch may be involved in determining the orientation of binding. When the longer acidic stretch is C-terminal, the beta strand seems usually to be parallel. The two crystal structures of PIAS2 (2ASQ, Song,2005, O75928) and Daxx (1Z5S, Chang,2011, O75928) support this theory: They both bind in parallel orientation and have a C-terminal acidic stretch. The crystal structure of RanBP2 (1Z5S, Reverter,2005, P49792) can be contrasted: It binds as an anti-parallel beta strand and has an N-terminal acidic patch. Because of the high similarity of the motif patterns for the parallel and antiparallel orientations, many SIMs will be detected by both of the motifs in ELM. Quite possibly, some SIM peptides may be able to bind to SUMO in both orientations.",
+        "This SUMO interacting motif variant is for SIMs bound as a beta-augmented strand in the parallel orientation. The SIM peptide inserts into a groove on the SUMO surface so that the motif has a hydrophobic core of four residues (preference V, I or L), the 3rd position being more variable. At the variable 3rd position, in addition to hydrophobic residues, acidic residues (D or E) and the phosphorylatable residue serine are allowed. A stretch of 1 to 5 acidic or phosphorylatable residues is considered necessary C-terminally from the hydrophobic core. Another negative stretch N-terminal to the core appears more optional, though both are usually present. These acidic stretches complement positively-charged residues on the SUMO surface. The length of the acidic stretch may be involved in determining the orientation of binding. When the longer acidic stretch is C-terminal, the beta strand seems usually to be parallel. The two crystal structures of PIAS2 (2ASQ, Song,2005, O75928) and Daxx (2KQS, Chang,2011, O75928) support this theory: They both bind in parallel orientation and have a C-terminal acidic stretch. The crystal structure of RanBP2 (1Z5S, Reverter,2005, P49792) can be contrasted: It binds as an anti-parallel beta strand and has an N-terminal acidic patch. Because of the high similarity of the motif patterns for the parallel and antiparallel orientations, many SIMs will be detected by both of the motifs in ELM. Quite possibly, some SIM peptides may be able to bind to SUMO in both orientations.",
         "LIG_SUMO_SIM_anti_2   LIG_SUMO_SIM_par_1",
         "[DEST]{0,5}.[VILPTM][VIL][DESTVILMA][VIL].{0,1}[DEST]{1,10}",
         "0.0045452",
@@ -1419,7 +1419,7 @@
         "ELME000335",
         "SUMO interaction site",
         "Non-covalent binding to SUMO proteins is mediated via the SUMO-interacting motif (SIM). SUMO-interacting proteins predominantly function in the nucleus. The SIM is essential for a variety of cellular processes including transcriptional regulation, sub-nuclear localization, nuclear body assembly, and anti-viral response. Viral proteins are also known to utilize such processes via their SIMs upon host cell invasion.",
-        "This SUMO interacting motif variant is for SIMs bound as a beta-augmented strand in the antiparallel orientation. The SIM peptide inserts into a groove on the SUMO surface so that the motif has a hydrophobic core of four residues (preference V, I or L), the 2nd position being more variable. At the variable 2nd position, in addition to hydrophobic residues, acidic residues (D or E) and the phosphorylatable residue serine are allowed. A short stretch of 1 to 5 acidic or phosphorylatable residues is considered necessary C-terminally from the hydrophobic core. Another negative stretch N-terminal to the core appears more optional, though both are usually present. These acidic stretches complement positively-charged residues on the SUMO surface. The length of the acidic stretch may be involved in determining the orientation of binding. When the longer acidic stretch is C-terminal, the beta strand seems usually to be parallel. The two crystal structures of PIAS2 (2ASQ, Song,2005, O75928) and Daxx (1Z5S, Chang,2011, O75928) support this theory: They both bind in parallel orientation and have a C-terminal acidic stretch. The crystal structure of RanBP2 (1Z5S, Reverter,2005, P49792) can be contrasted: It binds as an anti-parallel beta strand and has an N-terminal acidic patch. Because of the high similarity of the motif patterns for the parallel and antiparallel orientations, many SIMs will be detected by both of the motifs in ELM. Quite possibly, some SIM peptides may be able to bind to SUMO in both orientations.",
+        "This SUMO interacting motif variant is for SIMs bound as a beta-augmented strand in the antiparallel orientation. The SIM peptide inserts into a groove on the SUMO surface so that the motif has a hydrophobic core of four residues (preference V, I or L), the 2nd position being more variable. At the variable 2nd position, in addition to hydrophobic residues, acidic residues (D or E) and the phosphorylatable residue serine are allowed. A short stretch of 1 to 5 acidic or phosphorylatable residues is considered necessary C-terminally from the hydrophobic core. Another negative stretch N-terminal to the core appears more optional, though both are usually present. These acidic stretches complement positively-charged residues on the SUMO surface. The length of the acidic stretch may be involved in determining the orientation of binding. When the longer acidic stretch is C-terminal, the beta strand seems usually to be parallel. The two crystal structures of PIAS2 (2ASQ, Song,2005, O75928) and Daxx (2KQS, Chang,2011, O75928) support this theory: They both bind in parallel orientation and have a C-terminal acidic stretch. The crystal structure of RanBP2 (1Z5S, Reverter,2005, P49792) can be contrasted: It binds as an anti-parallel beta strand and has an N-terminal acidic patch. Because of the high similarity of the motif patterns for the parallel and antiparallel orientations, many SIMs will be detected by both of the motifs in ELM. Quite possibly, some SIM peptides may be able to bind to SUMO in both orientations.",
         "LIG_SUMO_SIM_anti_2   LIG_SUMO_SIM_par_1",
         "[DEST]{1,10}.{0,1}[VIL][DESTVILMA][VIL][VILM].[DEST]{0,5}",
         "0.0023495",
@@ -1440,7 +1440,7 @@
         "ELME000335",
         "SUMO interaction site",
         "Non-covalent binding to SUMO proteins is mediated via the SUMO-interacting motif (SIM). SUMO-interacting proteins predominantly function in the nucleus. The SIM is essential for a variety of cellular processes including transcriptional regulation, sub-nuclear localization, nuclear body assembly, and anti-viral response. Viral proteins are also known to utilize such processes via their SIMs upon host cell invasion.",
-        "This SUMO interacting motif variant is for SIMs bound as a beta-augmented strand in the antiparallel orientation. The SIM peptide inserts into a groove on the SUMO surface so that the motif has a hydrophobic core of four residues (preference V, I or L), the 2nd position being more variable. At the variable 2nd position, in addition to hydrophobic residues, acidic residues (D or E) and the phosphorylatable residue serine are allowed. A short stretch of 1 to 5 acidic or phosphorylatable residues is considered necessary C-terminally from the hydrophobic core. Another negative stretch N-terminal to the core appears more optional, though both are usually present. These acidic stretches complement positively-charged residues on the SUMO surface. The length of the acidic stretch may be involved in determining the orientation of binding. When the longer acidic stretch is C-terminal, the beta strand seems usually to be parallel. The two crystal structures of PIAS2 (2ASQ, Song,2005, O75928) and Daxx (1Z5S, Chang,2011, O75928) support this theory: They both bind in parallel orientation and have a C-terminal acidic stretch. The crystal structure of RanBP2 (1Z5S, Reverter,2005, P49792) can be contrasted: It binds as an anti-parallel beta strand and has an N-terminal acidic patch. Because of the high similarity of the motif patterns for the parallel and antiparallel orientations, many SIMs will be detected by both of the motifs in ELM. Quite possibly, some SIM peptides may be able to bind to SUMO in both orientations.",
+        "This SUMO interacting motif variant is for SIMs bound as a beta-augmented strand in the antiparallel orientation. The SIM peptide inserts into a groove on the SUMO surface so that the motif has a hydrophobic core of four residues (preference V, I or L), the 2nd position being more variable. At the variable 2nd position, in addition to hydrophobic residues, acidic residues (D or E) and the phosphorylatable residue serine are allowed. A short stretch of 1 to 5 acidic or phosphorylatable residues is considered necessary C-terminally from the hydrophobic core. Another negative stretch N-terminal to the core appears more optional, though both are usually present. These acidic stretches complement positively-charged residues on the SUMO surface. The length of the acidic stretch may be involved in determining the orientation of binding. When the longer acidic stretch is C-terminal, the beta strand seems usually to be parallel. The two crystal structures of PIAS2 (2ASQ, Song,2005, O75928) and Daxx (2KQS, Chang,2011, O75928) support this theory: They both bind in parallel orientation and have a C-terminal acidic stretch. The crystal structure of RanBP2 (1Z5S, Reverter,2005, P49792) can be contrasted: It binds as an anti-parallel beta strand and has an N-terminal acidic patch. Because of the high similarity of the motif patterns for the parallel and antiparallel orientations, many SIMs will be detected by both of the motifs in ELM. Quite possibly, some SIM peptides may be able to bind to SUMO in both orientations.",
         "LIG_SUMO_SIM_anti_2   LIG_SUMO_SIM_par_1",
         "[DEST]{1,10}.{0,1}[VIL][DESTVILMA][VIL][VILM].[DEST]{0,5}",
         "0.0023495",
@@ -1461,7 +1461,7 @@
         "ELME000335",
         "SUMO interaction site",
         "Non-covalent binding to SUMO proteins is mediated via the SUMO-interacting motif (SIM). SUMO-interacting proteins predominantly function in the nucleus. The SIM is essential for a variety of cellular processes including transcriptional regulation, sub-nuclear localization, nuclear body assembly, and anti-viral response. Viral proteins are also known to utilize such processes via their SIMs upon host cell invasion.",
-        "This SUMO interacting motif variant is for SIMs bound as a beta-augmented strand in the antiparallel orientation. The SIM peptide inserts into a groove on the SUMO surface so that the motif has a hydrophobic core of four residues (preference V, I or L), the 2nd position being more variable. At the variable 2nd position, in addition to hydrophobic residues, acidic residues (D or E) and the phosphorylatable residue serine are allowed. A short stretch of 1 to 5 acidic or phosphorylatable residues is considered necessary C-terminally from the hydrophobic core. Another negative stretch N-terminal to the core appears more optional, though both are usually present. These acidic stretches complement positively-charged residues on the SUMO surface. The length of the acidic stretch may be involved in determining the orientation of binding. When the longer acidic stretch is C-terminal, the beta strand seems usually to be parallel. The two crystal structures of PIAS2 (2ASQ, Song,2005, O75928) and Daxx (1Z5S, Chang,2011, O75928) support this theory: They both bind in parallel orientation and have a C-terminal acidic stretch. The crystal structure of RanBP2 (1Z5S, Reverter,2005, P49792) can be contrasted: It binds as an anti-parallel beta strand and has an N-terminal acidic patch. Because of the high similarity of the motif patterns for the parallel and antiparallel orientations, many SIMs will be detected by both of the motifs in ELM. Quite possibly, some SIM peptides may be able to bind to SUMO in both orientations.",
+        "This SUMO interacting motif variant is for SIMs bound as a beta-augmented strand in the antiparallel orientation. The SIM peptide inserts into a groove on the SUMO surface so that the motif has a hydrophobic core of four residues (preference V, I or L), the 2nd position being more variable. At the variable 2nd position, in addition to hydrophobic residues, acidic residues (D or E) and the phosphorylatable residue serine are allowed. A short stretch of 1 to 5 acidic or phosphorylatable residues is considered necessary C-terminally from the hydrophobic core. Another negative stretch N-terminal to the core appears more optional, though both are usually present. These acidic stretches complement positively-charged residues on the SUMO surface. The length of the acidic stretch may be involved in determining the orientation of binding. When the longer acidic stretch is C-terminal, the beta strand seems usually to be parallel. The two crystal structures of PIAS2 (2ASQ, Song,2005, O75928) and Daxx (2KQS, Chang,2011, O75928) support this theory: They both bind in parallel orientation and have a C-terminal acidic stretch. The crystal structure of RanBP2 (1Z5S, Reverter,2005, P49792) can be contrasted: It binds as an anti-parallel beta strand and has an N-terminal acidic patch. Because of the high similarity of the motif patterns for the parallel and antiparallel orientations, many SIMs will be detected by both of the motifs in ELM. Quite possibly, some SIM peptides may be able to bind to SUMO in both orientations.",
         "LIG_SUMO_SIM_anti_2   LIG_SUMO_SIM_par_1",
         "[DEST]{1,10}.{0,1}[VIL][DESTVILMA][VIL][VILM].[DEST]{0,5}",
         "0.0023495",