GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cys_rich_CWC - Cysteine-rich CWC
Pfam: PF14375 (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. )
Length: 50
Sequences: 239
Seq/Len: 4.78
HH_delta: 0.827 (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_G27_P0.228551.916
3_R24_V0.210631.766
8_F40_D0.206711.733
5_G31_L0.19731.654
20_W44_P0.187391.571
29_A34_L0.187151.569
17_S45_A0.183621.540
3_R8_F0.169351.420
17_S36_E0.155551.304
9_E45_A0.151781.273
26_L38_Y0.149841.256
32_E36_E0.149291.252
31_L34_L0.144261.210
3_R49_E0.142741.197
7_P36_E0.142341.194
24_V38_Y0.140341.177
22_F47_L0.140191.175
8_F47_L0.137491.153
27_P42_L0.132081.107
11_G16_I0.130291.092
6_A45_A0.129321.084
32_E37_E0.127671.071
24_V42_L0.127131.066
18_Q22_F0.125541.053
16_I48_Q0.124311.042
26_L42_L0.123881.039
10_C21_C0.123021.032
10_C19_C0.119461.002
33_Y44_P0.117310.984
7_P18_Q0.115540.969
11_G22_F0.115290.967
45_A49_E0.113790.954
7_P29_A0.112670.945
3_R6_A0.112080.940
2_P40_D0.112080.940
24_V49_E0.111760.937
11_G26_L0.110920.930
11_G20_W0.110170.924
9_E16_I0.109270.916
44_P48_Q0.10710.898
9_E40_D0.107050.898
8_F26_L0.106580.894
9_E14_G0.103670.869
17_S40_D0.103570.868
7_P22_F0.100780.845
23_S40_D0.099680.836
5_G39_K0.096950.813
7_P32_E0.095080.797
33_Y45_A0.094330.791
28_P32_E0.093820.787
3_R42_L0.093290.782
9_E23_S0.091320.766
18_Q23_S0.091230.765
6_A42_L0.090870.762
8_F38_Y0.089390.750
23_S36_E0.089150.748
14_G42_L0.088930.746
2_P37_E0.088890.745
23_S32_E0.08870.744
26_L48_Q0.087720.736
3_R38_Y0.087680.735
30_L39_K0.087660.735
5_G44_P0.087360.733
3_R47_L0.086930.729
15_G25_P0.08650.725
2_P9_E0.086370.724
6_A24_V0.084050.705
23_S44_P0.082910.695
33_Y42_L0.081930.687
17_S32_E0.080520.675
28_P34_L0.079450.666
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
3u6pA0.5214.30.827
2wnfA0.5213.40.83
1k82A0.5212.60.832
1k3xA0.5212.30.832
1ee8A0.5811.80.834
3u5eg0.911.70.834
2xzfA0.5411.50.834
3j39g0.910.30.837
3j3bg0.910.20.838
2y69F0.349.60.839
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