GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CARD - Caspase recruitment domain
Pfam: PF00619 (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: CL0041
Length: 85
Sequences: 856
Seq/Len: 10.07
HH_delta: 0.031 (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
35_E59_K0.5043.368
60_G63_A0.411292.748
8_R54_D0.293211.959
12_V50_R0.291451.948
64_F68_C0.283181.892
42_E51_K0.265841.776
39_I44_T0.241391.613
25_L30_V0.227141.518
28_R66_I0.224291.499
26_L33_E0.21691.449
15_L49_A0.215791.442
23_D50_R0.203871.362
56_L67_F0.201591.347
45_R48_K0.196981.316
67_F71_L0.196651.314
11_L15_L0.193131.291
15_L21_I0.184621.234
38_E51_K0.183141.224
76_P80_D0.181891.215
66_I70_A0.177611.187
12_V23_D0.175741.174
28_R69_Q0.17551.173
51_K54_D0.17341.159
36_Y40_R0.171241.144
3_L64_F0.169051.130
38_E45_R0.167451.119
24_H70_A0.166391.112
39_I42_E0.16491.102
44_T48_K0.163731.094
25_L52_L0.163421.092
25_L58_R0.162611.087
11_L82_L0.161771.081
72_R80_D0.161051.076
69_Q72_R0.159511.066
5_R29_G0.158851.061
31_L52_L0.156881.048
10_E78_L0.154821.035
15_L67_F0.151811.014
5_R57_K0.151451.012
52_L67_F0.151091.010
22_L40_R0.148270.991
33_E76_P0.146950.982
29_G33_E0.145880.975
53_L57_K0.144840.968
15_L18_L0.144640.967
61_P65_D0.14440.965
31_L55_I0.142140.950
14_D81_D0.14120.944
14_D77_H0.140780.941
10_E34_E0.140120.936
59_K63_A0.137360.918
49_A54_D0.13690.915
72_R76_P0.136620.913
68_C79_A0.134690.900
3_L15_L0.134520.899
22_L26_L0.134450.898
36_Y54_D0.134340.898
4_L64_F0.134340.898
25_L31_L0.134210.897
37_E58_R0.13350.892
6_K62_E0.13330.891
24_H27_S0.133220.890
3_L7_N0.131310.877
30_V70_A0.131220.877
50_R54_D0.130740.874
35_E55_I0.130110.869
42_E47_D0.129020.862
28_R43_P0.128040.856
77_H80_D0.126650.846
19_D40_R0.125630.839
18_L22_L0.125140.836
8_R60_G0.124720.833
42_E61_P0.124490.832
79_A82_L0.123960.828
44_T47_D0.123860.828
34_E50_R0.122520.819
30_V73_E0.122360.818
19_D48_K0.122250.817
75_Q78_L0.121540.812
9_Q80_D0.119140.796
16_D75_Q0.118930.795
10_E37_E0.117740.787
50_R68_C0.117310.784
9_Q37_E0.117210.783
10_E13_E0.116420.778
30_V63_A0.115740.773
37_E48_K0.115380.771
8_R23_D0.115320.771
48_K55_I0.115240.770
15_L74_N0.1150.768
14_D72_R0.114730.767
77_H81_D0.114560.766
32_T46_Q0.114380.764
6_K9_Q0.114250.763
33_E45_R0.113690.760
13_E28_R0.113490.758
12_V51_K0.113270.757
29_G32_T0.112960.755
3_L16_D0.112320.751
5_R26_L0.110850.741
6_K13_E0.110490.738
59_K64_F0.110190.736
20_D32_T0.110020.735
23_D27_S0.10990.734
4_L35_E0.108640.726
39_I56_L0.108320.724
26_L36_Y0.107310.717
30_V82_L0.107310.717
29_G46_Q0.10690.714
39_I55_I0.106650.713
31_L36_Y0.106550.712
12_V42_E0.105950.708
61_P70_A0.105850.707
8_R79_A0.105730.707
24_H80_D0.10570.706
24_H74_N0.105360.704
5_R41_S0.104930.701
4_L79_A0.104890.701
39_I48_K0.104880.701
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
4i16A0.988299.60.031
3ygsP0.988299.60.038
3crdA0.976599.60.061
2p1hA0.988299.60.072
3katA0.988299.50.121
2kn6A0.988299.50.123
4ikmA199.30.224
1z6tA0.988299.20.25
2nz7A0.964799.20.259
1vt4I0.964799.10.301

Page generated in 0.037 seconds.