GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
C2 - C2 domain
Pfam: PF00168 (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: CL0154
Length: 85
Sequences: 7628
Seq/Len: 89.74
HH_delta: -0.102 (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
39_K51_E1.60573.407
8_A49_W1.186632.518
7_S48_V1.174452.492
5_I38_T1.012082.147
70_W80_L0.998462.119
2_T54_E0.996182.114
41_K44_T0.992592.106
73_D79_E0.992572.106
4_T52_E0.978112.075
13_S17_N0.914721.941
2_T52_E0.862261.830
24_V38_T0.848111.800
66_S83_E0.833231.768
8_A11_L0.819261.738
24_V67_F0.81681.733
40_V72_K0.790981.678
80_L83_E0.776061.647
36_Y53_F0.775321.645
14_K81_I0.747621.586
5_I24_V0.734551.559
25_R68_E0.715211.518
68_E83_E0.681271.446
22_P71_D0.674811.432
20_P81_I0.672991.428
23_Y78_D0.657011.394
20_P45_S0.622561.321
27_S66_S0.618061.311
26_V67_F0.611521.298
5_I26_V0.587671.247
24_V69_V0.574141.218
27_S68_E0.569061.207
4_T50_N0.553771.175
59_D63_D0.548251.163
36_Y55_F0.548181.163
72_K78_D0.540961.148
60_P63_D0.540491.147
26_V53_F0.529021.123
13_S20_P0.489651.039
9_R48_V0.483791.027
44_T47_P0.483231.025
25_R37_K0.479161.017
11_L69_V0.469790.997
6_H50_N0.464630.986
13_S45_S0.454820.965
26_V65_L0.438310.930
42_K72_K0.433390.920
3_V26_V0.411030.872
41_K49_W0.404820.859
13_S19_K0.401640.852
27_S30_G0.399390.847
8_A69_V0.398410.845
15_D18_G0.397370.843
15_D20_P0.395640.839
19_K45_S0.39520.839
59_D62_L0.391370.830
70_W78_D0.384590.816
23_Y70_W0.384050.815
23_Y37_K0.379130.804
28_V55_F0.376340.799
68_E80_L0.3760.798
23_Y40_V0.375790.797
22_P40_V0.375590.797
22_P47_P0.375170.796
56_P59_D0.373550.793
27_S35_K0.372940.791
25_R70_W0.369850.785
18_G73_D0.36870.782
16_S19_K0.367850.781
5_I8_A0.366990.779
67_F70_W0.362620.769
61_D64_S0.35850.761
21_D79_E0.353740.751
8_A47_P0.349550.742
58_D63_D0.348340.739
29_N66_S0.346110.734
21_D40_V0.342410.727
24_V49_W0.337370.716
23_Y72_K0.330190.701
10_N45_S0.326730.693
9_R46_N0.323360.686
59_D64_S0.316350.671
58_D64_S0.313260.665
15_D73_D0.31280.664
17_N43_N0.312270.663
3_V55_F0.307910.653
25_R35_K0.307190.652
54_E58_D0.306070.649
11_L22_P0.305970.649
20_P44_T0.303890.645
71_D79_E0.302690.642
15_D21_D0.302110.641
54_E66_S0.300920.639
30_G61_D0.296390.629
58_D61_D0.292940.622
36_Y51_E0.289520.614
39_K50_N0.288750.613
12_P81_I0.287340.610
13_S18_G0.286790.609
52_E83_E0.286760.608
57_L60_P0.277630.589
26_V55_F0.276570.587
12_P84_V0.276140.586
73_D76_G0.269980.573
76_G79_E0.268190.569
71_D81_I0.262920.558
13_S43_N0.262810.558
27_S34_T0.262020.556
74_S77_K0.257680.547
4_T36_Y0.257020.545
10_N13_S0.256940.545
37_K72_K0.255690.543
29_N64_S0.249210.529
29_N52_E0.248450.527
73_D78_D0.247940.526
38_T49_W0.247380.525
38_T51_E0.243510.517
4_T9_R0.242760.515
30_G58_D0.240090.509
21_D43_N0.239830.509
50_N54_E0.23980.509
26_V51_E0.239030.507
30_G34_T0.237490.504
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
2z0uA199.3-0.102
1cjyA0.988299.3-0.093
3jzyA0.964799.3-0.091
3nsjA0.952999.3-0.089
1dqvA199.3-0.076
3f04A199.2-0.068
1rsyA199.2-0.068
2r83A199.2-0.065
1djxA199.2-0.057
1w15A199.2-0.054

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