JAL-3992 fix path
[jalview.git] / examples / exampleFeatures.txt
index 689cd43..99af214 100755 (executable)
@@ -1,5 +1,5 @@
-ST-TURN-IIL    blue|255,0,255|absolute|20.0|95.0|below|66.0
-GAMMA-TURN-CLASSIC     red|0,255,255|20.0|95.0|below|66.0
+ST-TURN-IIL    blue
+GAMMA-TURN-CLASSIC     lightgray
 BETA-TURN-IR   9a6a94
 BETA-TURN-IL   d6a6ca
 BETA-BULGE     1dc451
@@ -24,13 +24,19 @@ 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
+<html><a href="http://pfam.xfam.org/family/PF00111">Pfam family</a></html>     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
-<html><a href="http://pfam.xfam.org/family/PF00111">Pfam family</a></html>     FER_CAPAA       -1      0       0       Pfam
 <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html>     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
@@ -79,12 +85,12 @@ Iron-sulfur (2Fe-2S)        FER_BRANA       -1      47      47      METAL
 Iron-sulfur (2Fe-2S)   FER_BRANA       -1      77      77      METAL
 <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html>     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
-<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html>   FER2_ARATH      -1      60      135     Pfam
-Ferredoxin_fold Status: True Positive  FER2_ARATH      -1      50      145     Cath
+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
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html>   FER1_ARATH      -1      60      135     Pfam
+Ferredoxin_fold Status: True Positive  FER1_ARATH      -1      50      145     Cath
 <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_11</a></html>   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
@@ -127,13 +133,13 @@ STARTGROUP        netphos
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 112_11</a></html>     FER1_SPIOL      -1      112     112     PHOSPHORYLATION (S)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 139_13</a></html>     FER1_SPIOL      -1      139     139     PHOSPHORYLATION (T)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 73_7</a></html>       FER1_SPIOL      -1      73      73      PHOSPHORYLATION (Y)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html>   FER1_ARATH      -1      19      19      PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html>   FER1_ARATH      -1      24      24      PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html>   FER1_ARATH      -1      90      90      PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_ARATH      -1      107     107     PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_ARATH      -1      114     114     PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_ARATH      -1      141     141     PHOSPHORYLATION (T)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html>   FER1_ARATH      -1      75      75      PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html>   FER2_ARATH      -1      19      19      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html>   FER2_ARATH      -1      24      24      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html>   FER2_ARATH      -1      90      90      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER2_ARATH      -1      107     107     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER2_ARATH      -1      114     114     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER2_ARATH      -1      141     141     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html>   FER2_ARATH      -1      75      75      PHOSPHORYLATION (Y)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html>       FER_BRANA       -1      38      38      PHOSPHORYLATION (S)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 62_6</a></html>       FER_BRANA       -1      62      62      PHOSPHORYLATION (S)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html>       FER_BRANA       -1      89      89      PHOSPHORYLATION (T)
@@ -310,3 +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