X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=examples%2FexampleFeatures.txt;h=99af214e177ba4b5364d62c0598eb114185eaa40;hp=210aab22347f42130d72bb75a897ed364f6a8e03;hb=5104921c5c24afc2066ad6dc127f2dcb9e07daa5;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt index 210aab2..99af214 100755 --- a/examples/exampleFeatures.txt +++ b/examples/exampleFeatures.txt @@ -1,30 +1,12 @@ -#------------------------------------------------------------------------------- -# Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) -# Copyright (C) 2014 The Jalview Authors -# -# This file is part of Jalview. -# -# Jalview is free software: you can redistribute it and/or -# modify it under the terms of the GNU General Public License -# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -# -# Jalview is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty -# of MERCHANTABILITY or FITNESS FOR A PARTICULAR -# PURPOSE. See the GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License along with Jalview. If not, see . -# The Jalview Authors are detailed in the 'AUTHORS' file. -#------------------------------------------------------------------------------- -ST-TURN-IIL 705b23 -GAMMA-TURN-CLASSIC 788763 +ST-TURN-IIL blue +GAMMA-TURN-CLASSIC lightgray BETA-TURN-IR 9a6a94 BETA-TURN-IL d6a6ca BETA-BULGE 1dc451 Pfam dc206a PHOSPHORYLATION (S) b974a5 PHOSPHORYLATION (Y) 7d3881 -Cath 93b1d2 +Cath 93b1d1 ASX-TURN-IR 4ccc6e BETA-BULGE-LOOP-5 4066da CATMAT-4 4dc465 @@ -42,75 +24,82 @@ BETA-TURN-IIR c79792 PHOSPHORYLATION (T) c88395 BETA-TURN-IIL 8b5b50 ST-MOTIF ac25a1 +kdHydrophobicity ccffcc|333300|-3.9|4.5|above|-2.0 + +STARTFILTERS +GAMMA-TURN-INVERSE Label Contains PDB +kdHydrophobicity (Score LT 1.5) OR (Score GE 2.8) +ENDFILTERS STARTGROUP uniprot -Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL -Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL -Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL -Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL -Fer2 Status: True Positive Pfam 8_8 FER_CAPAA -1 8 83 Pfam +Pfam family FER_CAPAA -1 0 0 Pfam +Iron-sulfur (2Fe-2S) FER_CAPAA -1 39 39 METAL +Iron-sulfur (2Fe-2S) FER_CAPAA -1 44 44 METAL +Iron-sulfur (2Fe-2S) FER_CAPAA -1 47 47 METAL +Iron-sulfur (2Fe-2S) FER_CAPAA -1 77 77 METAL +Fer2 Status: True Positive Pfam 8_8 FER_CAPAA -1 8 83 Pfam Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath -Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL -Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL -Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL -Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL -Fer2 Status: True Positive Pfam 55_13 FER_CAPAN -1 55 130 Pfam +Iron-sulfur (2Fe-2S) FER_CAPAN -1 86 86 METAL +Iron-sulfur (2Fe-2S) FER_CAPAN -1 91 91 METAL +Iron-sulfur (2Fe-2S) FER_CAPAN -1 94 94 METAL +Iron-sulfur (2Fe-2S) FER_CAPAN -1 124 124 METAL +Fer2 Status: True Positive Pfam 55_13 FER_CAPAN -1 55 130 Pfam Ferredoxin_fold Status: True Positive FER_CAPAN -1 45 140 Cath -Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL -Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL -Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL -Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL -Fer2 Status: True Positive Pfam 55_13 FER1_SOLLC -1 55 130 Pfam +Iron-sulfur (2Fe-2S) FER1_SOLLC -1 86 86 METAL +Iron-sulfur (2Fe-2S) FER1_SOLLC -1 91 91 METAL +Iron-sulfur (2Fe-2S) FER1_SOLLC -1 94 94 METAL +Iron-sulfur (2Fe-2S) FER1_SOLLC -1 124 124 METAL +Fer2 Status: True Positive Pfam 55_13 FER1_SOLLC -1 55 130 Pfam Ferredoxin_fold Status: True Positive FER1_SOLLC -1 45 140 Cath -Fer2 Status: True Positive Pfam 55_13 Q93XJ9_SOLTU -1 55 130 Pfam +Fer2 Status: True Positive Pfam 55_13 Q93XJ9_SOLTU -1 55 130 Pfam Ferredoxin_fold Status: True Positive Q93XJ9_SOLTU -1 45 140 Cath -Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL -Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL -Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL -Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL -Fer2 Status: True Positive Pfam 60_13 FER1_PEA -1 60 135 Pfam +Iron-sulfur (2Fe-2S) FER1_PEA -1 91 91 METAL +Iron-sulfur (2Fe-2S) FER1_PEA -1 96 96 METAL +Iron-sulfur (2Fe-2S) FER1_PEA -1 99 99 METAL +Iron-sulfur (2Fe-2S) FER1_PEA -1 129 129 METAL +Fer2 Status: True Positive Pfam 60_13 FER1_PEA -1 60 135 Pfam Ferredoxin_fold Status: True Positive FER1_PEA -1 50 145 Cath -Fer2 Status: True Positive Pfam 63_13 Q7XA98_TRIPR -1 63 138 Pfam +Fer2 Status: True Positive Pfam 63_13 Q7XA98_TRIPR -1 63 138 Pfam Ferredoxin_fold Status: True Positive Q7XA98_TRIPR -1 53 148 Cath -Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL -Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL -Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL -Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL -Fer2 Status: True Positive Pfam 59_13 FER1_MESCR -1 59 134 Pfam +Iron-sulfur (2Fe-2S) FER1_MESCR -1 90 90 METAL +Iron-sulfur (2Fe-2S) FER1_MESCR -1 95 95 METAL +Iron-sulfur (2Fe-2S) FER1_MESCR -1 98 98 METAL +Iron-sulfur (2Fe-2S) FER1_MESCR -1 128 128 METAL +Fer2 Status: True Positive Pfam 59_13 FER1_MESCR -1 59 134 Pfam Ferredoxin_fold Status: True Positive FER1_MESCR -1 49 144 Cath -Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL -Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL -Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL -Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL -Fer2 Status: True Positive Pfam 58_13 FER1_SPIOL -1 58 133 Pfam +Iron-sulfur (2Fe-2S) FER1_SPIOL -1 89 89 METAL +Iron-sulfur (2Fe-2S) FER1_SPIOL -1 94 94 METAL +Iron-sulfur (2Fe-2S) FER1_SPIOL -1 97 97 METAL +Iron-sulfur (2Fe-2S) FER1_SPIOL -1 127 127 METAL +Fer2 Status: True Positive Pfam 58_13 FER1_SPIOL -1 58 133 Pfam Ferredoxin_fold Status: True Positive FER1_SPIOL -1 48 143 Cath -Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL -Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL -Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL -Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL -Fer2 Status: True Positive Pfam 8_8 FER3_RAPSA -1 8 83 Pfam +Iron-sulfur (2Fe-2S) FER3_RAPSA -1 39 39 METAL +Iron-sulfur (2Fe-2S) FER3_RAPSA -1 44 44 METAL +Iron-sulfur (2Fe-2S) FER3_RAPSA -1 47 47 METAL +Iron-sulfur (2Fe-2S) FER3_RAPSA -1 77 77 METAL +Fer2 Status: True Positive Pfam 8_8 FER3_RAPSA -1 8 83 Pfam Ferredoxin_fold Status: True Positive FER3_RAPSA -1 3 93 Cath -Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL -Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL -Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL -Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL -Fer2 Status: True Positive Pfam 8_8 FER_BRANA -1 8 83 Pfam +Iron-sulfur (2Fe-2S) FER_BRANA -1 39 39 METAL +Iron-sulfur (2Fe-2S) FER_BRANA -1 44 44 METAL +Iron-sulfur (2Fe-2S) FER_BRANA -1 47 47 METAL +Iron-sulfur (2Fe-2S) FER_BRANA -1 77 77 METAL +Fer2 Status: True Positive Pfam 8_8 FER_BRANA -1 8 83 Pfam Ferredoxin_fold Status: True Positive FER_BRANA -1 2 96 Cath -Iron-sulfur (2Fe-2S) FER2_ARATH -1 91 91 METAL -Iron-sulfur (2Fe-2S) FER2_ARATH -1 96 96 METAL -Iron-sulfur (2Fe-2S) FER2_ARATH -1 99 99 METAL -Iron-sulfur (2Fe-2S) FER2_ARATH -1 129 129 METAL -Fer2 Status: True Positive Pfam 60_13 FER2_ARATH -1 60 135 Pfam -Ferredoxin_fold Status: True Positive FER2_ARATH -1 50 145 Cath -Fer2 Status: True Positive Pfam 60_11 Q93Z60_ARATH -1 60 118 Pfam +Iron-sulfur (2Fe-2S) FER1_ARATH -1 91 91 METAL +Iron-sulfur (2Fe-2S) FER1_ARATH -1 96 96 METAL +Iron-sulfur (2Fe-2S) FER1_ARATH -1 99 99 METAL +Iron-sulfur (2Fe-2S) FER1_ARATH -1 129 129 METAL +Fer2 Status: True Positive Pfam 60_13 FER1_ARATH -1 60 135 Pfam +Ferredoxin_fold Status: True Positive FER1_ARATH -1 50 145 Cath +Fer2 Status: True Positive Pfam 60_11 Q93Z60_ARATH -1 60 118 Pfam Ferredoxin_fold Status: True Positive Q93Z60_ARATH -1 52 118 Cath -Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL -Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL -Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL -Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL -Fer2 Status: True Positive Pfam 60_13 FER1_MAIZE -1 60 135 Pfam +Iron-sulfur (2Fe-2S) FER1_MAIZE -1 91 91 METAL +Iron-sulfur (2Fe-2S) FER1_MAIZE -1 96 96 METAL +Iron-sulfur (2Fe-2S) FER1_MAIZE -1 99 99 METAL +Iron-sulfur (2Fe-2S) FER1_MAIZE -1 129 129 METAL +Fer2 Status: True Positive Pfam 60_13 FER1_MAIZE -1 60 135 Pfam Ferredoxin_fold Status: True Positive FER1_MAIZE -1 50 145 Cath -Fer2 Status: True Positive Pfam 52_12 O80429_MAIZE -1 52 127 Pfam +Fer2 Status: True Positive Pfam 52_12 O80429_MAIZE -1 52 127 Pfam Ferredoxin_fold Status: True Positive O80429_MAIZE -1 42 137 Cath ENDGROUP uniprot @@ -144,13 +133,13 @@ STARTGROUP netphos High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 112_11 FER1_SPIOL -1 112 112 PHOSPHORYLATION (S) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 139_13 FER1_SPIOL -1 139 139 PHOSPHORYLATION (T) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 73_7 FER1_SPIOL -1 73 73 PHOSPHORYLATION (Y) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER1_ARATH -1 19 19 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 FER1_ARATH -1 24 24 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER1_ARATH -1 90 90 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER1_ARATH -1 107 107 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER1_ARATH -1 114 114 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER1_ARATH -1 141 141 PHOSPHORYLATION (T) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 FER1_ARATH -1 75 75 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER2_ARATH -1 19 19 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 FER2_ARATH -1 24 24 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER2_ARATH -1 90 90 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER2_ARATH -1 107 107 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER2_ARATH -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER2_ARATH -1 141 141 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 FER2_ARATH -1 75 75 PHOSPHORYLATION (Y) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 38_3 FER_BRANA -1 38 38 PHOSPHORYLATION (S) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 62_6 FER_BRANA -1 62 62 PHOSPHORYLATION (S) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8 FER_BRANA -1 89 89 PHOSPHORYLATION (T) @@ -327,3 +316,54 @@ NEST-RL FER1_MAIZE -1 124 126 NEST-RL NEST-RL FER1_MAIZE -1 241 243 NEST-RL NEST-RL FER1_MAIZE -1 292 294 NEST-RL ENDGROUP s3dm + +STARTGROUP kd +A Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8 +A Q93XJ9_SOLTU -1 49 49 kdHydrophobicity -0.8 +A Q93XJ9_SOLTU -1 50 50 kdHydrophobicity -1.3 +A Q93XJ9_SOLTU -1 51 51 kdHydrophobicity -3.9 +A Q93XJ9_SOLTU -1 52 52 kdHydrophobicity 4.2 +A Q93XJ9_SOLTU -1 53 53 kdHydrophobicity -3.9 +A Q93XJ9_SOLTU -1 54 54 kdHydrophobicity 3.8 +A Q93XJ9_SOLTU -1 55 55 kdHydrophobicity 4.5 +A Q93XJ9_SOLTU -1 56 56 kdHydrophobicity -0.7 +A Q93XJ9_SOLTU -1 57 57 kdHydrophobicity -1.6 +A Q93XJ9_SOLTU -1 58 58 kdHydrophobicity -3.5 +A Q93XJ9_SOLTU -1 59 59 kdHydrophobicity -0.4 +A Q93XJ9_SOLTU -1 60 60 kdHydrophobicity -1.6 +A Q93XJ9_SOLTU -1 61 61 kdHydrophobicity 4.5 +A Q93XJ9_SOLTU -1 62 62 kdHydrophobicity -3.5 +A Q93XJ9_SOLTU -1 63 63 kdHydrophobicity 2.8 +A FER1_SPIOL -1 51 51 kdHydrophobicity 1.8 +A FER1_SPIOL -1 52 52 kdHydrophobicity 1.8 +A FER1_SPIOL -1 53 53 kdHydrophobicity -1.3 +A FER1_SPIOL -1 54 54 kdHydrophobicity -3.9 +A FER1_SPIOL -1 55 55 kdHydrophobicity 4.2 +A FER1_SPIOL -1 56 56 kdHydrophobicity -0.7 +A FER1_SPIOL -1 57 57 kdHydrophobicity 3.8 +A FER1_SPIOL -1 58 58 kdHydrophobicity 4.2 +A FER1_SPIOL -1 59 59 kdHydrophobicity -0.7 +A FER1_SPIOL -1 60 60 kdHydrophobicity -1.6 +A FER1_SPIOL -1 61 61 kdHydrophobicity -0.7 +A FER1_SPIOL -1 62 62 kdHydrophobicity -0.4 +A FER1_SPIOL -1 63 63 kdHydrophobicity -3.5 +A FER1_SPIOL -1 64 64 kdHydrophobicity 4.2 +A FER1_SPIOL -1 65 65 kdHydrophobicity -3.5 +A FER1_SPIOL -1 66 66 kdHydrophobicity 2.8 +C FER1_MAIZE -1 53 53 kdHydrophobicity 1.8 +C FER1_MAIZE -1 54 54 kdHydrophobicity -0.7 +C FER1_MAIZE -1 55 55 kdHydrophobicity -1.3 +C FER1_MAIZE -1 56 56 kdHydrophobicity -3.5 +C FER1_MAIZE -1 57 57 kdHydrophobicity 4.2 +C FER1_MAIZE -1 58 58 kdHydrophobicity -3.9 +C FER1_MAIZE -1 59 59 kdHydrophobicity 3.8 +C FER1_MAIZE -1 60 60 kdHydrophobicity 4.5 +C FER1_MAIZE -1 61 61 kdHydrophobicity -0.7 +C FER1_MAIZE -1 62 62 kdHydrophobicity -1.6 +C FER1_MAIZE -1 63 63 kdHydrophobicity -3.5 +C FER1_MAIZE -1 64 64 kdHydrophobicity -0.4 +C FER1_MAIZE -1 65 65 kdHydrophobicity -3.5 +C FER1_MAIZE -1 66 66 kdHydrophobicity 4.2 +C FER1_MAIZE -1 67 67 kdHydrophobicity -3.5 +C FER1_MAIZE -1 68 68 kdHydrophobicity 3.8 +ENDGROUP kd