GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_C14 - Caspase domain
Pfam: PF00656 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0093
Length: 248
Sequences: 2533
Seq/Len: 10.21
HH_delta: 0.258 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
75_H127_C0.618323.711
5_I24_A0.595093.571
176_A183_S0.563753.383
48_R52_L0.526573.160
26_A199_L0.508933.054
3_A31_L0.463742.783
47_T50_N0.396212.378
217_L220_E0.356762.141
33_K203_K0.355322.132
43_I46_A0.354152.125
36_F67_S0.354062.125
174_L194_F0.350462.103
6_I70_F0.346912.082
26_A191_G0.346722.081
11_Y74_G0.329231.976
9_N20_A0.325451.953
123_I198_L0.312571.876
30_A199_L0.306691.840
69_V123_I0.29631.778
201_A224_E0.294971.770
185_E192_G0.290651.744
181_Q234_T0.290321.742
9_N21_V0.29031.742
31_L69_V0.288191.729
54_A57_E0.2871.722
4_L58_L0.278381.671
17_L185_E0.276351.658
27_M71_Y0.275681.654
10_Y16_P0.271211.628
200_E228_K0.265831.595
49_A53_K0.259591.558
6_I51_I0.259171.555
69_V121_L0.259161.555
8_V46_A0.247991.488
216_E224_E0.247731.487
191_G196_Y0.237371.424
217_L221_L0.236031.416
8_V51_I0.235791.415
10_Y45_N0.231551.390
219_E223_T0.230451.383
103_L111_L0.230161.381
128_R175_S0.229661.378
23_D192_G0.229471.377
29_E32_E0.229161.375
58_L68_V0.226561.360
37_D40_N0.225071.351
29_E203_K0.223281.340
218_L221_L0.222571.336
195_T199_L0.221171.327
177_S181_Q0.220271.322
76_G127_C0.220031.320
5_I27_M0.219041.314
216_E221_L0.217931.308
94_L98_D0.215161.291
201_A221_L0.213151.279
204_G224_E0.20911.255
201_A204_G0.208391.251
103_L106_E0.205181.231
221_L229_V0.204871.229
200_E204_G0.203451.221
19_G185_E0.202511.215
71_Y195_T0.198871.193
22_N25_E0.198461.191
222_L226_N0.198031.188
50_N53_K0.197231.184
77_I93_Y0.196151.177
2_R61_R0.194961.170
27_M69_V0.192781.157
96_P99_A0.192681.156
198_L202_L0.191881.151
217_L222_L0.190691.144
93_Y98_D0.186991.122
8_V45_N0.186731.121
28_A32_E0.186381.118
17_L125_D0.184981.110
107_L111_L0.181521.089
8_V11_Y0.180491.083
225_V229_V0.179521.077
46_A51_I0.178621.072
26_A29_E0.175361.052
191_G199_L0.174971.050
7_G24_A0.173341.040
30_A203_K0.17251.035
73_S195_T0.171931.032
128_R177_S0.171071.027
177_S183_S0.170981.026
74_G125_D0.170891.026
17_L20_A0.17041.023
123_I221_L0.170141.021
196_Y200_E0.168921.014
7_G17_L0.166591.000
120_K170_G0.165190.991
127_C183_S0.164610.988
50_N54_A0.162840.977
46_A50_N0.16130.968
92_G104_D0.160390.963
78_Q128_R0.160240.962
124_L132_F0.158980.954
4_L54_A0.156780.941
192_G195_T0.15630.938
77_I95_L0.156040.936
57_E61_R0.155840.935
26_A190_S0.155770.935
21_V25_E0.154980.930
27_M195_T0.154490.927
185_E191_G0.153830.923
94_L124_L0.153810.923
193_L197_A0.15320.919
215_D219_E0.152880.917
178_R236_Q0.152750.917
30_A34_L0.152570.916
123_I218_L0.152490.915
7_G73_S0.15160.910
185_E193_L0.151550.909
109_D116_P0.150940.906
36_F69_V0.150620.904
22_N191_G0.148930.894
75_H183_S0.148310.890
73_S192_G0.148020.888
46_A97_L0.146070.877
56_R110_L0.145880.875
117_K120_K0.145860.875
226_N229_V0.144490.867
123_I174_L0.143690.862
10_Y44_D0.1430.858
19_G191_G0.142910.858
93_Y99_A0.142710.856
106_E111_L0.142460.855
197_A200_E0.142410.855
75_H233_Q0.142250.854
217_L229_V0.142240.854
43_I54_A0.142220.853
62_A68_V0.142020.852
51_I96_P0.141620.850
199_L203_K0.141290.848
52_L105_D0.140930.846
26_A203_K0.140320.842
186_D193_L0.139850.839
26_A196_Y0.139770.839
28_A38_V0.139080.835
30_A202_L0.13810.829
95_L98_D0.137960.828
46_A54_A0.137890.827
175_S180_G0.137440.825
20_A24_A0.137440.825
168_P171_F0.13660.820
19_G186_D0.135840.815
126_C129_S0.135650.814
120_K171_F0.135560.813
75_H129_S0.135390.812
112_C115_L0.134560.807
176_A184_Y0.134120.805
66_D118_K0.134020.804
46_A170_G0.133780.803
218_L222_L0.132790.797
2_R65_G0.13260.796
56_R221_L0.130870.785
166_P169_S0.130550.783
224_E228_K0.130440.783
18_P185_E0.130360.782
224_E227_Q0.12960.778
17_L73_S0.129120.775
174_L177_S0.12910.775
29_E33_K0.128990.774
190_S204_G0.128780.773
72_F95_L0.127370.764
53_K57_E0.12730.764
67_S122_F0.126770.761
104_D108_R0.126640.760
173_V176_A0.126340.758
55_L70_F0.126140.757
20_A73_S0.126040.756
179_P236_Q0.125640.754
22_N96_P0.125630.754
8_V97_L0.124620.748
7_G20_A0.124560.747
226_N234_T0.124390.746
191_G195_T0.123450.741
226_N230_A0.123280.740
32_E203_K0.123280.740
75_H126_C0.122870.737
17_L74_G0.122670.736
17_L192_G0.122650.736
19_G192_G0.122580.736
25_E200_E0.121940.732
9_N18_P0.121840.731
107_L110_L0.120980.726
27_M198_L0.120780.725
63_Q73_S0.120710.724
17_L23_D0.120320.722
115_L118_K0.119970.720
3_A69_V0.119880.719
59_L62_A0.119620.718
60_Q63_Q0.119460.717
216_E220_E0.119450.717
24_A71_Y0.119410.717
3_A70_F0.119140.715
31_L123_I0.11860.712
21_V44_D0.118490.711
139_S182_T0.118360.710
176_A194_F0.118050.708
34_L67_S0.116840.701
67_S121_L0.116660.700
3_A36_F0.116620.700
19_G126_C0.116290.698
7_G74_G0.115960.696
73_S185_E0.115610.694
169_S176_A0.115350.692
71_Y123_I0.11510.691
189_G196_Y0.11470.688
5_I28_A0.114660.688
13_N138_S0.114260.686
30_A33_K0.114240.686
116_P119_P0.113970.684
49_A52_L0.113640.682
9_N17_L0.113520.681
200_E205_N0.113070.679
2_R58_L0.112980.678
121_L172_I0.112950.678
70_F74_G0.112770.677
130_G175_S0.112750.677
109_D113_K0.112740.677
9_N185_E0.112670.676
5_I31_L0.112070.673
19_G193_L0.111970.672
172_I222_L0.111890.671
119_P177_S0.111530.669
108_R111_L0.111440.669
12_Q35_G0.111010.666
39_E54_A0.110830.665
91_D230_A0.11080.665
3_A71_Y0.110720.664
45_N97_L0.110610.664
173_V177_S0.110150.661
202_L221_L0.109450.657
70_F122_F0.109280.656
109_D118_K0.109070.655
73_S125_D0.10890.654
39_E61_R0.108650.652
178_R181_Q0.108380.650
31_L36_F0.10830.650
115_L170_G0.108280.650
181_Q195_T0.107350.644
52_L56_R0.10730.644
47_T98_D0.107250.644
78_Q92_G0.107120.643
7_G125_D0.106970.642
201_A216_E0.106940.642
32_E35_G0.106810.641
69_V115_L0.10680.641
23_D73_S0.106250.638
105_D131_G0.105720.634
219_E222_L0.105530.633
172_I185_E0.105510.633
161_N164_D0.105460.633
221_L228_K0.105440.633
25_E190_S0.105370.632
122_F133_I0.105340.632
67_S192_G0.105180.631
129_S133_I0.104970.630
73_S191_G0.104620.628
162_R165_V0.104580.628
94_L126_C0.10450.627
28_A40_N0.104310.626
6_I54_A0.104260.626
200_E224_E0.104130.625
11_Y76_G0.104070.625
22_N26_A0.104010.624
125_D192_G0.103950.624
119_P122_F0.103540.621
107_L124_L0.103190.619
166_P170_G0.102940.618
106_E109_D0.102790.617
91_D94_L0.102650.616
181_Q230_A0.102630.616
43_I68_V0.102610.616
205_N224_E0.10260.616
73_S183_S0.102540.615
30_A168_P0.102190.613
186_D197_A0.101840.611
34_L202_L0.101810.611
194_F198_L0.101690.610
35_G140_S0.101680.610
222_L229_V0.101530.609
218_L229_V0.101030.606
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3bijA0.95561000.258
4af8A0.94351000.266
3uoaB0.84681000.266
4f6oA0.96771000.292
4f6pA0.97181000.293
3e4cA0.91531000.315
1f1jA0.8711000.32
3sirA0.8751000.321
3od5A0.90731000.323
2nn3C0.86291000.323

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