GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DALR_2 - DALR domain
Pfam: PF09190 (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: CL0258
Length: 63
Sequences: 2198
Seq/Len: 34.89
HH_delta: 0.127 (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
1_E18_A0.687892.149
49_L55_L0.684882.140
2_F6_M0.612971.915
11_N14_E0.584711.827
3_I7_D0.558121.744
14_E17_A0.540711.689
2_F15_A0.531011.659
5_A14_E0.522341.632
1_E4_E0.500321.563
18_A21_E0.474521.483
44_A47_K0.463641.449
23_V45_L0.433641.355
42_A46_R0.414931.296
13_P17_A0.414871.296
12_T16_L0.411491.286
1_E21_E0.410561.283
6_M12_T0.402731.258
46_R55_L0.387121.209
39_E43_A0.374421.170
5_A15_A0.371021.159
34_D37_D0.363961.137
25_E28_R0.358561.120
41_L44_A0.353741.105
35_K39_E0.352681.102
19_L48_L0.347641.086
26_I41_L0.33771.055
37_D41_L0.334471.045
15_A18_A0.328811.027
36_E39_E0.327281.023
25_E29_A0.323411.010
7_D51_V0.317560.992
17_A20_F0.317470.992
43_A47_K0.31640.989
6_M27_N0.31550.986
2_F48_L0.314210.982
2_F20_F0.298350.932
29_A37_D0.294570.920
49_L53_G0.284340.888
5_A18_A0.284310.888
2_F18_A0.280470.876
45_L55_L0.279650.874
11_N17_A0.278450.870
13_P20_F0.276430.864
32_S35_K0.273310.854
37_D40_A0.270810.846
28_R31_E0.266280.832
43_A46_R0.264110.825
8_D51_V0.253480.792
45_L49_L0.251810.787
20_F24_K0.249010.778
44_A48_L0.24830.776
37_D44_A0.247680.774
16_L54_L0.245660.768
23_V27_N0.244820.765
19_L23_V0.243970.762
8_D12_T0.243040.759
20_F45_L0.239940.750
42_A45_L0.237820.743
39_E42_A0.2350.734
12_T15_A0.234090.731
30_L45_L0.232260.726
9_D44_A0.230910.721
21_E25_E0.230120.719
31_E39_E0.229630.717
24_K27_N0.228760.715
6_M15_A0.226430.707
17_A21_E0.226340.707
46_R49_L0.224020.700
20_F23_V0.223650.699
14_E18_A0.222510.695
12_T22_L0.220260.688
38_L42_A0.218750.683
25_E31_E0.21850.683
50_D55_L0.213890.668
32_S41_L0.213040.666
40_A44_A0.212590.664
26_I29_A0.209440.654
19_L49_L0.207640.649
31_E36_E0.207560.648
9_D34_D0.206770.646
44_A55_L0.205310.641
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
3tqoA199.10.127
3sp1A0.87398.50.294
1li5A0.984198.50.298
3c8zA0.825497.70.459
2d5bA0.984193.50.647
2csxA0.984193.10.652
2x1lA0.968392.50.659
1iq0A0.936592.40.66
1rqgA0.984190.70.675
4arcA0.984189.30.684

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