GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GAF - GAF domain
Pfam: PF01590 (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: CL0161
Length: 154
Sequences: 16066
Seq/Len: 104.32
HH_delta: 0.036 (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
70_V140_L1.546232.808
10_L22_A1.398492.540
9_I150_L1.37212.492
61_Q65_S1.35462.460
14_A22_A1.231372.236
66_R115_I1.214842.206
20_D129_T1.18712.156
68_P144_E1.148032.085
21_R127_Y1.096651.991
73_D76_A1.030621.872
23_S125_S1.013681.841
72_S134_P0.999661.815
19_A126_L0.990181.798
136_T139_D0.942611.712
114_I151_A0.942391.711
111_C125_S0.90761.648
112_V147_A0.888111.613
14_A40_V0.88771.612
115_I120_L0.870711.581
8_R12_E0.861571.565
62_V111_C0.861571.565
57_S60_G0.848371.541
112_V143_L0.844821.534
128_R135_F0.822021.493
110_L143_L0.807871.467
66_R120_L0.796631.447
12_E15_E0.794471.443
137_E140_L0.791561.437
126_L143_L0.784361.424
128_R133_R0.76931.397
77_D80_F0.749811.362
7_Q11_R0.736541.338
135_F139_D0.735691.336
33_R51_R0.731121.328
68_P112_V0.72851.323
26_L121_I0.716931.302
137_E141_A0.700191.272
13_L146_F0.695861.264
116_S151_A0.694731.262
36_S39_G0.692891.258
28_D31_G0.680671.236
63_L120_L0.678451.232
106_V127_Y0.676171.228
20_D128_R0.664711.207
28_D35_Y0.650121.181
60_G64_Q0.649031.179
19_A128_R0.643881.169
17_L139_D0.634381.152
11_R40_V0.630411.145
29_P32_N0.624661.134
25_F36_S0.62161.129
19_A135_F0.613841.115
116_S119_R0.611051.110
114_I122_G0.609441.107
25_F125_S0.606691.102
67_E144_E0.600391.090
70_V110_L0.599821.089
145_S149_Q0.597761.086
68_P140_L0.59491.080
73_D107_R0.584421.061
24_I114_I0.584241.061
140_L144_E0.581861.057
59_C123_V0.579131.052
61_Q79_R0.573221.041
4_E8_R0.561121.019
22_A126_L0.559661.016
75_A107_R0.557121.012
6_L24_I0.555711.009
12_E16_L0.55521.008
11_R15_E0.552711.004
13_L150_L0.549580.998
141_A144_E0.543530.987
53_S56_E0.541750.984
149_Q152_I0.534520.971
138_E141_A0.534080.970
63_L123_V0.532440.967
10_L24_I0.531910.966
59_C125_S0.531360.965
110_L135_F0.529650.962
3_D7_Q0.52740.958
28_D32_N0.518970.942
107_R131_P0.518060.941
147_A151_A0.512410.931
108_S135_F0.510910.928
23_S127_Y0.507430.921
110_L140_L0.507330.921
4_E7_Q0.507180.921
133_R139_D0.506910.921
113_P120_L0.506680.920
5_L153_A0.504770.917
42_L45_P0.496460.902
55_D60_G0.494670.898
14_A19_A0.494370.898
3_D37_V0.493950.897
62_V123_V0.493240.896
41_G44_D0.489610.889
128_R134_P0.48880.888
8_R11_R0.487480.885
145_S148_Q0.484550.880
148_Q151_A0.47870.869
115_I151_A0.478270.869
144_E148_Q0.474630.862
109_Y125_S0.470710.855
61_Q69_I0.46780.850
111_C123_V0.465270.845
124_L147_A0.464920.844
27_L32_N0.459690.835
61_Q64_Q0.452770.822
105_G129_T0.451760.820
141_A145_S0.450830.819
65_S69_I0.448220.814
109_Y127_Y0.444050.806
13_L124_L0.442280.803
17_L126_L0.441020.801
27_L31_G0.440260.800
28_D33_R0.437870.795
17_L142_L0.43760.795
13_L16_L0.436450.793
13_L126_L0.435680.791
115_I119_R0.434870.790
10_L36_S0.433080.786
149_Q153_A0.420690.764
128_R131_P0.418540.760
27_L30_D0.416810.757
13_L19_A0.41620.756
63_L66_R0.413950.752
71_I74_V0.413780.751
55_D58_I0.411640.748
108_S128_R0.41060.746
74_V77_D0.409720.744
62_V69_I0.406040.737
62_V65_S0.405730.737
29_P119_R0.405590.737
146_F150_L0.404720.735
5_L9_I0.403250.732
27_L63_L0.401810.730
114_I121_I0.401720.730
25_F123_V0.398040.723
39_G42_L0.396220.720
27_L54_M0.395510.718
72_S133_R0.395270.718
116_S121_I0.392340.712
59_C111_C0.390990.710
12_E146_F0.386590.702
42_L46_P0.38460.698
13_L22_A0.381850.693
59_C109_Y0.380060.690
147_A150_L0.379550.689
128_R139_D0.377340.685
142_L149_Q0.376310.683
54_M57_S0.373190.678
5_L152_I0.372170.676
25_F59_C0.366190.665
51_R54_M0.363860.661
74_V109_Y0.362920.659
17_L143_L0.361170.656
114_I147_A0.360510.655
66_R113_P0.359380.653
71_I77_D0.358240.651
18_G130_R0.358160.650
50_R53_S0.357980.650
27_L122_G0.357140.649
19_A22_A0.355970.646
146_F149_Q0.354330.643
114_I150_L0.353080.641
24_I147_A0.352930.641
9_I13_L0.351720.639
21_R25_F0.349430.635
78_P81_A0.345070.627
62_V67_E0.344530.626
108_S131_P0.344420.625
13_L17_L0.343440.624
61_Q80_F0.343390.624
111_C127_Y0.340250.618
38_A41_G0.339750.617
112_V144_E0.334270.607
115_I121_I0.333990.607
32_N36_S0.333150.605
35_Y38_A0.333080.605
72_S76_A0.331420.602
26_L37_V0.328470.596
21_R40_V0.32750.595
58_I62_V0.322580.586
20_D130_R0.322310.585
31_G51_R0.321460.584
47_P50_R0.319060.579
148_Q152_I0.31830.578
115_I118_G0.317810.577
10_L14_A0.315740.573
56_E60_G0.315460.573
112_V126_L0.315290.573
21_R129_T0.311930.566
71_I75_A0.30810.560
23_S59_C0.307950.559
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
4glqA0.909199.60.036
2zmfA0.909199.60.08
3dbaA0.909199.60.083
3trcA0.896199.50.086
2e4sA0.909199.50.097
3ibjA0.896199.50.102
3hcyA0.876699.50.106
3e0yA0.883199.50.108
3oovA0.928699.50.113
3vv4A0.909199.50.113

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