GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_Tnp_IS240 - DDE domain
Pfam: PF13610 (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: CL0219
Length: 140
Sequences: 12457
Seq/Len: 88.98
HH_delta: 0.152 (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
22_R103_H1.617943.183
89_H95_L1.490442.932
34_Y50_R1.353462.662
101_R104_R1.183372.328
9_T107_K1.037542.041
40_D43_A1.019662.006
26_A98_R1.00151.970
101_R105_T1.001281.970
77_L81_G0.983721.935
116_F125_T0.968241.905
104_R108_R0.938021.845
118_S121_S0.890311.751
41_T45_K0.878771.729
39_R69_A0.868711.709
99_I103_H0.858281.688
88_E96_N0.851091.674
64_T85_D0.842361.657
49_K77_L0.842071.656
119_F123_Q0.820731.614
117_K121_S0.817421.608
23_A47_F0.815241.604
6_V64_T0.810241.594
38_R43_A0.795241.564
78_N83_L0.794141.562
66_K87_V0.782861.540
61_V86_K0.780341.535
96_N99_I0.768661.512
22_R99_I0.751241.478
123_Q127_S0.746671.469
106_I126_L0.708271.393
6_V62_I0.699551.376
92_R95_L0.699391.376
34_Y46_R0.688691.355
21_W70_Y0.673581.325
66_K90_R0.67311.324
10_Y17_W0.670831.320
89_H92_R0.66781.314
6_V23_A0.657071.292
74_I78_N0.632851.245
88_E95_L0.622561.225
10_Y19_Y0.622141.224
45_K49_K0.621361.222
36_S46_R0.612031.204
68_P71_P0.611811.203
114_N125_T0.599351.179
30_I102_D0.596111.173
78_N85_D0.593261.167
122_A126_L0.587641.156
125_T128_G0.584521.150
25_D28_G0.583031.147
94_Y97_N0.565331.112
64_T70_Y0.55671.095
110_T125_T0.556471.095
24_I98_R0.556031.094
36_S43_A0.553261.088
76_E80_E0.54891.080
37_K119_F0.542941.068
32_D50_R0.53871.060
19_Y39_R0.538691.060
78_N81_G0.529091.041
63_V86_K0.518421.020
96_N100_E0.510051.003
21_W44_A0.505390.994
75_K85_D0.503670.991
45_K77_L0.503010.989
24_I99_I0.501130.986
67_L70_Y0.498630.981
109_R129_F0.496230.976
23_A51_A0.495810.975
13_I16_K0.494290.972
29_N98_R0.489070.962
48_L64_T0.482760.950
121_S125_T0.482240.949
101_R108_R0.475730.936
63_V88_E0.473640.932
21_W47_F0.472950.930
41_T72_A0.468180.921
24_I102_D0.467140.919
71_P87_V0.466240.917
8_E69_A0.463680.912
20_L106_I0.460990.907
100_E103_H0.460870.907
105_T108_R0.460090.905
42_A46_R0.458090.901
24_I29_N0.453650.892
76_E79_P0.44920.884
103_H106_I0.44580.877
18_H119_F0.444150.874
93_K97_N0.439770.865
73_A76_E0.439660.865
6_V70_Y0.429630.845
9_T103_H0.428650.843
22_R102_D0.425660.837
90_R93_K0.422270.831
49_K53_K0.41680.820
75_K79_P0.415950.818
61_V84_H0.413090.813
77_L80_E0.411570.810
42_A45_K0.410990.808
63_V96_N0.410840.808
64_T87_V0.408780.804
110_T116_F0.407910.802
65_D100_E0.407710.802
126_L130_E0.405620.798
9_T20_L0.404730.796
120_R123_Q0.402870.792
66_K71_P0.401230.789
88_E92_R0.39980.786
6_V21_W0.392470.772
31_L51_A0.389560.766
122_A129_F0.38840.764
25_D29_N0.385570.758
32_D47_F0.385440.758
43_A46_R0.384130.756
39_R44_A0.382140.752
58_E81_G0.381180.750
105_T109_R0.37990.747
30_I33_F0.379790.747
12_K17_W0.379660.747
68_P72_A0.378270.744
62_I74_I0.377160.742
33_F130_E0.376830.741
74_I77_L0.37640.740
125_T129_F0.376130.740
21_W43_A0.373550.735
103_H107_K0.371360.730
127_S130_E0.37090.730
51_A55_H0.370350.728
102_D106_I0.367350.723
118_S122_A0.364450.717
32_D54_R0.3620.712
30_I130_E0.360330.709
59_P84_H0.359410.707
46_R50_R0.359190.707
39_R43_A0.357550.703
67_L71_P0.356130.701
52_L83_L0.355740.700
49_K81_G0.355330.699
35_L123_Q0.351340.691
120_R127_S0.350620.690
120_R124_R0.350020.688
108_R112_P0.347030.683
93_K103_H0.346740.682
24_I103_H0.34440.677
88_E91_Q0.343790.676
36_S47_F0.343750.676
93_K96_N0.341180.671
97_N100_E0.338410.666
48_L62_I0.336690.662
52_L57_G0.333830.657
62_I83_L0.33380.657
72_A75_K0.333150.655
124_R127_S0.332490.654
121_S124_R0.331990.653
63_V95_L0.329990.649
33_F127_S0.329610.648
33_F36_S0.329070.647
8_E39_R0.328720.647
66_K91_Q0.326170.642
23_A48_L0.324730.639
74_I85_D0.323130.636
48_L52_L0.322940.635
47_F50_R0.322390.634
124_R128_G0.321280.632
11_I15_G0.320340.630
95_L98_R0.319560.629
44_A70_Y0.31790.625
26_A29_N0.313560.617
30_I35_L0.312460.615
34_Y47_F0.310310.610
85_D88_E0.310310.610
36_S40_D0.309680.609
35_L126_L0.309670.609
107_K111_R0.309460.609
52_L59_P0.305340.601
112_P115_G0.303350.597
14_K117_K0.302470.595
50_R54_R0.302230.594
34_Y43_A0.301010.592
113_M116_F0.30090.592
6_V9_T0.300130.590
87_V93_K0.299550.589
110_T126_L0.298580.587
47_F51_A0.298360.587
60_R83_L0.297660.586
43_A47_F0.297440.585
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
1c0mA0.985799.80.152
1bcoA0.978699.80.18
4fw1A0.992999.80.187
3kksA0.928699.80.189
4fw2A0.992999.80.202
1cxqA0.985799.80.212
1ex4A0.935799.70.232
3f9kA0.942999.70.234
1c6vA0.935799.70.235
2x78A0.971499.70.237

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