GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAS - PAS fold
Pfam: PF00989 (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: CL0183
Length: 113
Sequences: 44240
Seq/Len: 391.5
HH_delta: -0.178 (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
12_D111_R3.34953.154
29_A32_E2.320322.185
15_F108_V2.319772.184
31_E38_R2.123171.999
7_L25_Y2.108221.985
18_D22_R2.098951.976
13_G110_F2.067681.947
26_V30_A2.062541.942
13_G33_L1.984421.868
90_E111_R1.800591.695
44_K48_D1.798941.694
22_R45_S1.794551.690
97_R103_I1.750651.648
91_V110_F1.748691.647
26_V31_E1.736051.635
28_Q32_E1.696831.598
81_L85_R1.654241.558
16_V105_G1.579051.487
16_V25_Y1.573241.481
24_L105_G1.566151.475
51_H54_D1.560791.470
38_R42_I1.558741.468
10_S14_I1.556421.465
15_F23_I1.518771.430
15_F30_A1.517991.429
26_V41_L1.488351.401
4_R8_E1.487251.400
17_I108_V1.484971.398
98_D102_Q1.464661.379
8_E28_Q1.45921.374
37_S40_E1.409491.327
28_Q31_E1.388551.307
36_Y40_E1.379141.299
78_R88_W1.377681.297
95_P103_I1.370321.290
16_V107_L1.368071.288
64_Q68_Q1.363521.284
18_D24_L1.363021.283
19_E103_I1.354071.275
63_R67_S1.342621.264
5_A9_N1.312671.236
89_V110_F1.306161.230
30_A34_L1.305641.229
31_E37_S1.297251.221
78_R81_L1.270721.196
80_R86_P1.231951.160
81_L87_R1.230181.158
45_S48_D1.221261.150
80_R83_D1.212611.142
92_R111_R1.210791.140
12_D109_I1.190561.121
87_R112_D1.180161.111
25_Y38_R1.180111.111
76_E79_F1.150881.084
16_V24_L1.137391.071
75_F78_R1.137121.071
93_A108_V1.124661.059
59_R63_R1.107451.043
15_F110_F1.101191.037
98_D101_G1.099161.035
74_S77_V1.067341.005
52_P55_R1.064711.003
28_Q38_R1.059390.997
69_G72_G1.057030.995
60_E64_Q1.056890.995
4_R25_Y1.042430.982
94_S107_L1.029390.969
78_R86_P0.961270.905
80_R85_R0.955960.900
96_V107_L0.949370.894
35_G83_D0.943520.888
51_H86_P0.941580.887
47_F55_R0.929930.876
13_G30_A0.929680.875
50_I55_R0.926490.872
17_I46_L0.926110.872
31_E41_L0.924740.871
19_E22_R0.913360.860
44_K49_L0.909830.857
17_I23_I0.900110.848
65_A68_Q0.897020.845
30_A41_L0.894930.843
74_S90_E0.889150.837
16_V96_V0.887370.836
93_A106_I0.88680.835
63_R66_L0.875750.825
50_I54_D0.872230.821
58_L61_R0.870890.820
34_L110_F0.865670.815
65_A69_G0.86110.811
50_I53_E0.855390.805
76_E81_L0.851480.802
5_A107_L0.834360.786
77_V80_R0.831720.783
29_A33_L0.830480.782
54_D58_L0.830070.782
51_H55_R0.806850.760
17_I106_I0.806390.759
61_R64_Q0.805570.759
47_F59_R0.794850.748
96_V105_G0.790910.745
72_G75_F0.789180.743
36_Y41_L0.78010.735
10_S109_I0.779380.734
7_L14_I0.773750.729
19_E102_Q0.772560.727
42_I45_S0.772340.727
27_N30_A0.768750.724
33_L89_V0.767760.723
13_G29_A0.760630.716
14_I109_I0.752720.709
65_A70_E0.748210.704
12_D29_A0.748060.704
97_R101_G0.739970.697
65_A72_G0.732130.689
33_L87_R0.724090.682
17_I93_A0.723320.681
26_V34_L0.713480.672
61_R65_A0.705630.664
88_W113_I0.702770.662
77_V91_V0.702540.661
26_V38_R0.697070.656
98_D105_G0.695190.655
6_I16_V0.693830.653
6_I10_S0.691750.651
76_E80_R0.691020.651
58_L65_A0.68380.644
59_R62_L0.681250.641
62_L66_L0.681070.641
73_E92_R0.677630.638
23_I26_V0.677140.638
40_E44_K0.677070.638
31_E34_L0.669550.630
31_E36_Y0.665490.627
14_I107_L0.663450.625
41_L44_K0.662380.624
17_I21_G0.658910.620
11_P29_A0.657310.619
9_N94_S0.65540.617
45_S49_L0.653510.615
46_L49_L0.648520.611
36_Y49_L0.647550.610
34_L89_V0.640940.603
90_E93_A0.63970.602
11_P92_R0.636140.599
14_I27_N0.63480.598
90_E113_I0.631520.595
64_Q67_S0.628120.591
47_F51_H0.617250.581
62_L67_S0.616730.581
97_R102_Q0.613090.577
36_Y81_L0.612560.577
76_E90_E0.611680.576
22_R42_I0.611160.575
73_E90_E0.606860.571
22_R43_G0.606820.571
8_E25_Y0.604670.569
34_L87_R0.59910.564
5_A8_E0.585620.551
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
3f1pB199.2-0.178
3p7nA0.991299.1-0.161
4hiaA0.991299.1-0.142
2gj3A0.991299.1-0.133
4gczA0.973599-0.12
4ehoA0.982399-0.115
4hh2A0.964699-0.107
3ewkA0.982399-0.097
2wkqA0.991299-0.094
3mxqA0.991299-0.093

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