GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GGDEF - GGDEF domain
Pfam: PF00990 (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: CL0276
Length: 161
Sequences: 25826
Seq/Len: 160.41
HH_delta: -0.093 (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
10_P14_Y2.536612.723
42_N159_R2.496052.679
71_R74_D2.413282.590
34_A131_V2.35932.532
15_F85_A2.227172.391
19_L140_A2.177982.338
15_F77_A1.842921.978
9_L63_A1.83651.971
36_V127_I1.810071.943
41_D126_S1.802061.934
145_K149_Q1.755441.884
57_E60_R1.684271.808
14_Y18_K1.682191.806
137_G146_K1.675821.799
9_L76_L1.668491.791
79_L85_A1.605271.723
18_K77_A1.591681.708
126_S154_A1.571821.687
18_K21_S1.563271.678
40_I62_I1.545481.659
153_E157_Q1.536771.650
36_V100_A1.511971.623
22_L25_R1.497671.608
104_E108_D1.484181.593
53_E145_K1.457471.564
58_I123_L1.449641.556
139_D142_E1.429571.534
38_I127_I1.416271.520
54_V57_E1.411131.515
61_Q65_R1.387361.489
2_F14_Y1.386211.488
38_I125_L1.3571.457
66_L76_L1.324781.422
36_V88_L1.315371.412
61_Q64_K1.309471.406
31_E90_D1.304491.400
18_K22_L1.291631.386
47_N55_G1.281171.375
37_L144_L1.250461.342
33_F132_Y1.250241.342
101_E104_E1.218671.308
70_L76_L1.214691.304
37_L79_L1.213551.303
18_K75_I1.197921.286
5_P13_R1.194431.282
64_K67_K1.187131.274
2_F10_P1.172811.259
79_L144_L1.157461.242
42_N45_E1.148011.232
146_K150_A1.142821.227
108_D160_N1.139081.223
12_R16_E1.131561.215
2_F17_E1.123491.206
154_A158_G1.114781.197
33_F87_L1.103961.185
22_L89_P1.098531.179
4_D78_R1.094051.174
14_Y17_E1.085171.165
3_I10_P1.074181.153
36_V103_L1.072881.152
69_Q106_L1.068661.147
33_F143_L1.068521.147
70_L86_I1.055731.133
44_D48_E1.051421.129
57_E61_Q1.036181.112
25_R89_P1.035591.112
65_R110_L1.021771.097
124_T160_N1.020081.095
132_Y143_L1.015611.090
45_E49_K1.013381.088
60_R64_K1.011881.086
153_E156_E1.005861.080
20_E140_A1.003981.078
99_L103_L0.986891.059
37_L151_L0.985281.058
14_Y77_A0.981251.053
10_P75_I0.97781.050
130_A147_A0.975691.047
142_E146_K0.974561.046
7_T59_L0.963991.035
34_A129_I0.953141.023
148_D152_Q0.951061.021
101_E105_R0.943631.013
103_L106_L0.937531.006
5_P16_E0.933891.002
63_A76_L0.928610.997
17_E21_S0.92510.993
99_L102_R0.923810.992
132_Y137_G0.92350.991
39_D155_K0.920750.988
138_Q146_K0.920370.988
38_I66_L0.918190.986
46_L121_V0.916440.984
36_V129_I0.907140.974
46_L58_I0.906580.973
38_I86_I0.904850.971
20_E24_E0.904780.971
16_E141_D0.903120.969
61_Q114_I0.893750.959
10_P77_A0.887180.952
69_Q102_R0.883880.949
130_A143_L0.865130.929
12_R56_D0.864090.927
37_L85_A0.863590.927
138_Q142_E0.851640.914
88_L99_L0.847890.910
130_A146_K0.847080.909
102_R105_R0.846350.908
39_D82_D0.845460.908
140_A144_L0.843230.905
62_I66_L0.842870.905
100_A104_E0.842820.905
70_L74_D0.832130.893
128_G147_A0.827580.888
102_R106_L0.827170.888
93_S131_V0.825590.886
3_I14_Y0.823890.884
2_F13_R0.815820.876
14_Y75_I0.814340.874
16_E20_E0.810.869
104_E107_I0.804790.864
150_A154_A0.797850.856
47_N56_D0.793090.851
41_D159_R0.788370.846
36_V86_I0.783620.841
23_L132_Y0.775810.833
65_R114_I0.766940.823
93_S97_E0.760980.817
107_I125_L0.760930.817
22_L33_F0.760190.816
26_A33_F0.75790.814
61_Q110_L0.749260.804
142_E145_K0.747080.802
53_E57_E0.743340.798
115_D120_E0.743180.798
141_D145_K0.741780.796
19_L87_L0.741510.796
94_E97_E0.738870.793
19_L23_L0.732690.786
132_Y136_D0.731890.786
60_R63_A0.729850.783
35_L144_L0.72470.778
116_I119_I0.720360.773
47_N81_D0.71950.772
97_E101_E0.715330.768
54_V121_V0.706230.758
35_L143_L0.701790.753
62_I125_L0.694260.745
6_L59_L0.693940.745
54_V116_I0.69340.744
116_I121_V0.690780.741
44_D152_Q0.686280.737
100_A106_L0.685090.735
16_E140_A0.685070.735
83_E148_D0.684380.735
66_L86_I0.684080.734
42_N82_D0.682730.733
65_R69_Q0.680030.730
130_A150_A0.67890.729
149_Q153_E0.675870.725
37_L147_A0.673290.723
105_R108_D0.671550.721
28_R73_S0.667520.717
43_L59_L0.667180.716
40_I125_L0.662010.711
136_D146_K0.656990.705
67_K76_L0.656580.705
111_N122_H0.656230.704
109_E112_E0.65310.701
74_D102_R0.643460.691
105_R109_E0.640330.687
110_L114_I0.637780.685
53_E141_D0.637340.684
43_L82_D0.636830.684
52_Y148_D0.636150.683
15_F19_L0.633620.680
92_D98_E0.631160.677
16_E77_A0.627260.673
32_P131_V0.627180.673
4_D7_T0.626310.672
41_D124_T0.623890.670
57_E117_D0.62120.667
46_L54_V0.620470.666
16_E19_L0.618630.664
48_E152_Q0.616580.662
64_K68_K0.61120.656
51_G55_G0.609580.654
71_R102_R0.606350.651
88_L91_T0.606340.651
50_Y54_V0.604950.649
85_A144_L0.604370.649
35_L85_A0.604250.649
15_F87_L0.604120.648
18_K87_L0.60410.648
6_L60_R0.59670.640
65_R106_L0.593890.637
13_R16_E0.592230.636
21_S25_R0.592160.636
146_K149_Q0.588840.632
76_L86_I0.582180.625
62_I110_L0.582050.625
80_G83_E0.576740.619
50_Y119_I0.574790.617
52_Y152_Q0.573920.616
98_E101_E0.572610.615
8_G60_R0.569250.611
66_L70_L0.564350.606
26_A132_Y0.561870.603
107_I110_L0.561290.602
31_E89_P0.560940.602
62_I123_L0.56070.602
46_L55_G0.55880.600
26_A30_G0.558050.599
70_L103_L0.555590.596
22_L26_A0.555010.596
128_G150_A0.553450.594
45_E82_D0.553030.594
88_L102_R0.551350.592
3_I8_G0.5490.589
43_L55_G0.548650.589
39_D47_N0.545720.586
39_D152_Q0.545660.586
83_E152_Q0.541320.581
69_Q105_R0.539890.580
50_Y121_V0.538650.578
111_N160_N0.536670.576
26_A31_E0.535020.574
23_L140_A0.533810.573
81_D152_Q0.533730.573
58_I82_D0.529530.568
151_L154_A0.528010.567
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
3tvkA0.956599.9-0.093
1w25A0.975299.9-0.068
3hvbA0.975299.9-0.027
3ignA0.975299.9-0.026
3hvaA0.975299.9-0.021
3iclA0.968999.9-0.009
3ezuA0.956599.9-0.003
3i5cA199.9-0
4h54A0.956599.90.004
3mtkA0.944199.90.008

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