GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GAF_2 - GAF domain
Pfam: PF13185 (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: 148
Sequences: 15912
Seq/Len: 107.51
HH_delta: 0.084 (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
11_I143_I1.578722.917
12_L24_G1.510252.791
77_G109_R1.501832.775
81_I133_L1.47312.722
79_P137_E1.309932.420
16_L24_G1.15672.137
3_D6_E1.103532.039
108_L144_A1.075141.987
109_R114_V1.070831.979
23_A121_Y1.05491.949
22_D123_K1.041111.924
25_A119_S0.986831.823
105_C119_S0.980121.811
21_A120_L0.938431.734
129_S132_D0.935211.728
83_N127_A0.878991.624
106_V136_L0.878771.624
122_S128_F0.876231.619
86_D89_F0.869721.607
28_L115_I0.866861.602
100_I121_Y0.835691.544
14_A17_E0.832891.539
10_Q14_A0.823891.522
9_Q13_D0.818651.513
26_I108_L0.799981.478
120_L136_L0.797241.473
77_G114_V0.785961.452
104_L136_L0.782621.446
106_V140_A0.769381.422
81_I104_L0.757191.399
27_Y119_S0.754491.394
79_P133_L0.753331.392
55_P58_P0.750051.386
128_F132_D0.745071.377
16_L41_S0.734311.357
130_E133_L0.733411.355
79_P106_V0.730981.351
4_L147_I0.70711.307
74_L114_V0.694521.283
110_S144_A0.670481.239
138_A142_Q0.661211.222
22_D122_S0.659211.218
122_S126_N0.652251.205
108_L116_G0.647071.196
7_L146_A0.627571.160
30_D36_L0.625581.156
5_E9_Q0.618921.144
101_R125_P0.618911.144
21_A128_F0.618111.142
130_E134_E0.61731.141
110_S113_E0.611411.130
54_L58_P0.600181.109
133_L137_E0.600031.109
21_A122_S0.598891.107
19_T132_D0.594641.099
13_D17_E0.582951.077
41_S44_P0.576891.066
24_G120_L0.571361.056
15_L139_L0.566631.047
104_L133_L0.562981.040
87_S90_P0.553661.023
30_D33_G0.550881.018
74_L117_V0.539610.997
102_S128_F0.537070.992
142_Q146_A0.535920.990
85_D89_F0.533380.986
6_E10_Q0.529420.978
27_Y37_P0.521940.964
8_L26_I0.520560.962
54_L57_P0.516960.955
14_A18_L0.512530.947
122_S127_A0.510940.944
35_L38_V0.510180.943
10_Q13_D0.51010.943
16_L21_A0.507810.938
134_E137_E0.507070.937
126_N132_D0.506950.937
29_Y74_L0.505020.933
13_D41_S0.504580.932
86_D90_P0.504410.932
35_L42_G0.501120.926
37_P40_A0.499480.923
104_L128_F0.498460.921
6_E9_Q0.498230.921
27_Y117_V0.497510.919
4_L8_L0.497410.919
93_E96_R0.494840.914
52_I55_P0.492760.911
95_A99_G0.4920.909
40_A43_D0.490430.906
78_E137_E0.487080.900
105_C117_V0.486870.900
29_Y33_G0.480840.888
131_E134_E0.47910.885
140_A144_A0.475670.879
88_S91_P0.475410.878
15_L143_I0.474310.876
19_T120_L0.471540.871
76_T80_I0.470760.870
108_L115_I0.463020.856
137_E141_D0.458560.847
103_I119_S0.458380.847
142_Q145_I0.456190.843
14_A139_L0.453680.838
77_G107_P0.453110.837
107_P114_V0.452830.837
86_D91_P0.452770.837
15_L24_G0.452630.836
15_L21_A0.451230.834
105_C121_Y0.445370.823
118_L140_A0.444740.822
12_L26_I0.444080.821
15_L118_L0.444020.820
138_A141_D0.440020.813
93_E97_H0.437530.808
109_R144_A0.435360.804
15_L120_L0.432940.800
92_W95_A0.430350.795
44_P47_F0.424240.784
42_G45_S0.4220.780
25_A121_Y0.421140.778
94_L98_P0.419460.775
49_K52_I0.419010.774
134_E138_A0.416040.769
36_L39_A0.415340.767
30_D34_Q0.412520.762
85_D88_S0.405050.748
103_I121_Y0.404990.748
109_R113_E0.403860.746
141_D144_A0.401520.742
110_S115_I0.400820.741
106_V137_E0.386560.714
15_L18_L0.38410.710
135_L142_Q0.382850.707
23_A27_Y0.382610.707
4_L7_L0.382310.706
46_E50_E0.381230.704
92_W96_R0.379840.702
116_G144_A0.377920.698
19_T135_L0.376860.696
139_L143_I0.376470.696
12_L16_L0.376270.695
74_L77_G0.371960.687
5_E39_A0.371040.686
7_L11_I0.370980.685
52_I57_P0.370730.685
21_A24_G0.370010.684
20_G132_D0.369370.683
131_E135_L0.365160.675
102_S122_S0.364310.673
83_N126_N0.359270.664
140_A143_I0.358080.662
94_L100_I0.355370.657
12_L38_V0.355070.656
108_L143_I0.353640.653
96_R99_G0.353450.653
47_F50_E0.353160.653
34_Q37_P0.351990.650
28_L147_I0.350370.647
80_I103_I0.350250.647
35_L39_A0.349720.646
122_S125_P0.349480.646
87_S91_P0.348590.644
28_L38_V0.344240.636
38_V41_S0.343230.634
94_L97_H0.342310.633
106_V120_L0.340680.630
122_S132_D0.339480.627
138_A145_I0.336870.622
19_T136_L0.335240.619
50_E53_P0.335240.619
108_L140_A0.334010.617
15_L19_T0.333090.615
119_S122_S0.330730.611
139_L142_Q0.330120.610
102_S125_P0.328660.607
28_L116_G0.327670.605
51_E54_L0.326760.604
45_S49_K0.323650.598
11_I15_L0.32340.598
109_R112_G0.323380.598
117_V121_Y0.322610.596
53_P56_P0.32080.593
79_P83_N0.320770.593
102_S127_A0.320010.591
29_Y116_G0.319330.590
22_D124_E0.318760.589
26_I140_A0.317520.587
20_G126_N0.31650.585
7_L145_I0.31560.583
93_E98_P0.315580.583
31_P113_E0.315080.582
23_A100_I0.314510.581
52_I56_P0.313210.579
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
4glqA0.952799.50.084
3o5yA0.932499.50.088
2zmfA0.986599.40.095
3k2nA0.952799.40.095
3hcyA0.912299.40.099
3trcA0.939299.40.101
2qybA0.939299.40.108
2e4sA0.979799.40.114
3oovA0.945999.40.116
2vjwA0.858199.40.117

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