GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF302 - Domain of unknown function DUF302
Pfam: PF03625 (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: 65
Sequences: 795
Seq/Len: 12.23
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
17_P38_P0.551242.531
18_P52_E0.491492.257
19_Y41_G0.486692.235
3_D6_E0.469662.157
25_C46_C0.435942.002
5_S18_P0.429781.974
31_Y35_K0.414291.902
4_H21_I0.396421.820
6_E10_E0.378551.738
41_G49_L0.362391.664
51_Y59_W0.336721.546
51_Y61_S0.327691.505
33_L40_I0.305861.404
7_E10_E0.289151.328
17_P52_E0.288511.325
43_F63_M0.267221.227
8_L16_L0.258471.187
33_L44_L0.244961.125
19_Y49_L0.236611.086
4_H34_L0.23131.062
54_E59_W0.231111.061
25_C30_A0.227431.044
21_I47_R0.227421.044
54_E57_K0.227361.044
2_I23_E0.226711.041
38_P51_Y0.224151.029
4_H25_C0.223871.028
2_I44_L0.223361.026
52_E58_V0.220371.012
20_R59_W0.220021.010
37_D61_S0.217040.997
55_D60_V0.213940.982
8_L31_Y0.209970.964
3_D20_R0.209330.961
2_I10_E0.209070.960
14_E55_D0.209040.960
14_E57_K0.208230.956
20_R50_V0.207180.951
24_F34_L0.206970.950
52_E59_W0.202150.928
23_E30_A0.200370.920
24_F64_N0.197920.909
4_H7_E0.194030.891
11_K30_A0.192990.886
39_E63_M0.190660.875
50_V60_V0.190630.875
48_V62_Y0.188310.865
7_E11_K0.18690.858
39_E61_S0.184830.849
19_Y43_F0.181370.833
11_K46_C0.181130.832
27_P44_L0.180690.830
49_L61_S0.178590.820
17_P51_Y0.177820.817
52_E57_K0.176830.812
19_Y38_P0.176710.811
52_E56_G0.175440.806
32_Q36_A0.17390.799
29_I32_Q0.172230.791
23_E49_L0.169030.776
5_S14_E0.168360.773
25_C42_L0.168030.772
47_R63_M0.167040.767
16_L35_K0.166790.766
14_E35_K0.163570.751
29_I36_A0.161260.740
32_Q48_V0.160210.736
39_E55_D0.159810.734
55_D59_W0.159690.733
39_E49_L0.158280.727
29_I33_L0.157610.724
28_K35_K0.153710.706
50_V54_E0.152290.699
22_L46_C0.151680.697
24_F43_F0.15150.696
26_N45_P0.150180.690
22_L41_G0.148910.684
47_R62_Y0.146950.675
27_P48_V0.146420.672
21_I25_C0.144780.665
39_E59_W0.144470.663
11_K25_C0.142410.654
32_Q40_I0.141440.649
4_H46_C0.141420.649
14_E31_Y0.141340.649
16_L19_Y0.140990.647
29_I61_S0.13960.641
37_D49_L0.139240.639
27_P50_V0.13820.635
5_S64_N0.137680.632
17_P54_E0.137310.631
35_K56_G0.136040.625
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
1q9uA0.969299.60.084
1j3mA0.984699.60.096
4ifdG0.953812.30.866
1cb8A0.938512.20.866
3lduA0.89239.50.872
3n6xA0.90779.20.873
3ldgA19.10.873
3k0bA18.20.876
2nn6G0.95388.20.876
1hn0A0.92317.90.877

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