GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AIG2 - AIG2-like family
Pfam: PF06094 (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: CL0278
Length: 102
Sequences: 2230
Seq/Len: 21.86
HH_delta: 0.151 (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
2_F56_G1.138384.929
70_D81_R0.795933.446
70_D99_Y0.63332.742
66_L81_R0.632692.739
83_R95_E0.48472.099
85_P95_E0.482482.089
48_G51_S0.454121.966
13_N72_Y0.438941.900
84_V98_V0.429781.861
81_R97_W0.415521.799
58_L96_A0.387581.678
62_D65_E0.375411.625
85_P93_E0.370521.604
45_L54_V0.352511.526
45_L98_V0.341911.480
3_V6_T0.334681.449
34_R40_G0.332681.440
8_M57_E0.330951.433
17_L60_E0.327961.420
13_N17_L0.31651.370
58_L88_L0.312881.355
88_L92_E0.310721.345
1_L7_L0.308281.335
73_E79_Y0.304731.319
7_L43_P0.303531.314
28_P31_L0.301671.306
1_L69_L0.297151.287
86_V96_A0.2891.251
58_L86_V0.283681.228
33_G36_L0.278471.206
9_D57_E0.27461.189
70_D79_Y0.270051.169
34_R37_Y0.267441.158
3_V7_L0.264551.145
88_L91_G0.261151.131
26_G29_A0.257811.116
79_Y99_Y0.25531.105
33_G37_Y0.254371.101
28_P32_G0.254261.101
4_Y7_L0.242831.051
1_L13_N0.242691.051
26_G59_Y0.242411.050
14_H57_E0.242031.048
7_L72_Y0.241221.044
88_L93_E0.240251.040
67_A71_E0.238061.031
83_R97_W0.228720.990
15_S18_G0.228020.987
29_A53_R0.226660.981
23_K60_E0.218130.944
87_E91_G0.217640.942
81_R99_Y0.214490.929
87_E93_E0.212050.918
10_G57_E0.210910.913
38_G42_Y0.210510.911
40_G44_A0.20620.893
6_T72_Y0.196010.849
21_G62_D0.195620.847
41_G44_A0.194650.843
28_P86_V0.192490.833
30_T78_L0.192230.832
6_T69_L0.191240.828
53_R87_E0.190630.825
38_G41_G0.190430.824
25_I87_E0.190180.823
3_V13_N0.189840.822
12_V43_P0.189730.821
16_V72_Y0.188840.818
23_K87_E0.188690.817
9_D24_F0.188630.817
50_G63_D0.185630.804
37_Y40_G0.185290.802
68_R71_E0.184750.800
2_F5_G0.18260.791
10_G68_R0.180140.780
14_H17_L0.179290.776
64_E67_A0.179010.775
18_G21_G0.178970.775
89_G93_E0.178580.773
27_E55_E0.178430.773
17_L69_L0.178110.771
12_V68_R0.176130.763
73_E76_G0.175970.762
6_T79_Y0.175730.761
82_V100_V0.175710.761
3_V57_E0.175070.758
55_E89_G0.173880.753
32_G50_G0.173180.750
26_G31_L0.172560.747
75_E80_R0.172420.747
25_I60_E0.172040.745
63_D87_E0.171840.744
9_D27_E0.171640.743
25_I28_P0.171430.742
25_I57_E0.170660.739
33_G38_G0.167890.727
90_D93_E0.167780.726
27_E31_L0.167690.726
29_A55_E0.165850.718
4_Y69_L0.165580.717
10_G14_H0.165230.715
37_Y46_V0.164940.714
82_V85_P0.163190.707
1_L72_Y0.163160.706
37_Y41_G0.162030.702
7_L13_N0.160640.696
2_F29_A0.160260.694
22_A28_P0.160070.693
30_T45_L0.159410.690
13_N69_L0.15940.690
24_F27_E0.157920.684
1_L43_P0.157880.684
84_V96_A0.153770.666
7_L44_A0.153450.664
10_G13_N0.152890.662
90_D95_E0.152250.659
18_G65_E0.151950.658
96_A100_V0.151060.654
49_E63_D0.150320.651
36_L39_G0.14890.645
34_R39_G0.14870.644
46_V50_G0.148510.643
7_L73_E0.148440.643
80_R85_P0.147960.641
6_T73_E0.14780.640
61_V78_L0.147630.639
71_E90_D0.14740.638
24_F29_A0.147310.638
29_A56_G0.147190.637
45_L84_V0.147020.637
12_V16_V0.146970.636
65_E69_L0.146740.635
3_V17_L0.14550.630
76_G84_V0.145160.628
46_V71_E0.145150.628
22_A58_L0.144920.627
4_Y79_Y0.144350.625
34_R41_G0.144330.625
39_G44_A0.14420.624
10_G60_E0.144160.624
47_P100_V0.142980.619
53_R71_E0.142780.618
38_G43_P0.142750.618
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
3cryA0.990299.70.151
2g0qA0.941299.70.163
2qikA0.931499.70.169
3judA199.70.171
2jqvA0.941299.70.172
1xhsA0.90299.70.172
2qikA0.960899.60.173
1vkbA0.990299.60.176
1v30A0.882499.60.21
tr|CX0.960898.20.578

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