GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Crystall_3 - BetaGamma crystallin
Pfam: PF08964 (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: CL0333
Length: 86
Sequences: 979
Seq/Len: 11.38
HH_delta: 0.198 (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
6_I19_C0.387012.146
53_E60_K0.378692.100
10_E39_S0.372692.066
52_Y61_Y0.306041.697
49_V63_Y0.303361.682
7_F20_Y0.29621.642
7_F38_F0.295851.640
35_N54_H0.288471.599
10_E14_Q0.288371.599
54_H60_K0.287521.594
73_L76_I0.281271.560
67_G70_Q0.269791.496
39_S77_G0.26871.490
25_T28_N0.264861.469
6_I44_G0.263061.459
49_V52_Y0.260621.445
42_K69_D0.248971.380
49_V65_E0.239811.330
6_I43_V0.235231.304
51_I64_L0.229081.270
41_V51_I0.22771.263
35_N51_I0.22381.241
45_P66_W0.220431.222
54_H58_N0.215411.194
4_K19_C0.213741.185
38_F41_V0.213511.184
27_Y57_F0.209341.161
29_L33_K0.207241.149
53_E59_G0.207241.149
43_V46_G0.199861.108
12_N27_Y0.196231.088
71_P75_S0.195191.082
51_I65_E0.194841.080
52_Y57_F0.193031.070
20_Y34_L0.192461.067
48_K61_Y0.191541.062
9_T37_K0.188161.043
11_K72_D0.186951.037
55_N58_N0.186821.036
49_V57_F0.185961.031
16_E22_E0.184591.023
36_D54_H0.1831.015
16_E37_K0.182771.013
17_S26_V0.174440.967
20_Y38_F0.174340.967
26_V29_L0.171910.953
73_L77_G0.171330.950
5_V51_I0.164860.914
47_S63_Y0.159370.884
26_V33_K0.159150.882
57_F61_Y0.157510.873
69_D76_I0.156310.867
10_E36_D0.155370.861
18_F36_D0.154840.859
70_Q76_I0.153040.849
43_V64_L0.153010.848
6_I17_S0.15260.846
18_F32_D0.150840.836
12_N37_K0.150460.834
9_T39_S0.150440.834
22_E35_N0.148860.825
18_F26_V0.147720.819
12_N66_W0.146660.813
48_K64_L0.145120.805
4_K29_L0.145020.804
12_N44_G0.144740.803
5_V43_V0.140830.781
49_V61_Y0.139850.775
9_T77_G0.138730.769
11_K14_Q0.138630.769
41_V62_I0.138290.767
51_I57_F0.137030.760
16_E45_P0.136830.759
6_I36_D0.136530.757
13_Y75_S0.136270.756
20_Y33_K0.135390.751
51_I62_I0.134590.746
25_T29_L0.134450.745
13_Y69_D0.132810.736
15_G40_S0.132280.733
69_D73_L0.132090.732
46_G52_Y0.130340.723
71_P74_S0.129250.717
66_W70_Q0.128820.714
13_Y47_S0.127930.709
48_K63_Y0.127340.706
10_E34_L0.127150.705
75_S78_G0.125390.695
55_N74_S0.123650.686
28_N55_N0.123590.685
70_Q73_L0.123390.684
15_G46_G0.121860.676
24_D42_K0.121390.673
17_S25_T0.121020.671
54_H61_Y0.120790.670
9_T59_G0.120390.668
13_Y71_P0.11940.662
26_V55_N0.119210.661
59_G67_G0.11880.659
69_D72_D0.118650.658
10_E77_G0.118570.657
65_E78_G0.118470.657
17_S33_K0.11840.656
7_F34_L0.118270.656
9_T13_Y0.117370.651
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
1bd7A0.953599.70.198
1h4aX0.90799.60.209
1hdfA0.988499.60.212
1ytqA0.965199.60.214
1zwmA0.930299.60.22
3qk3A0.941999.60.225
2bv2A0.918699.60.226
3snyA0.976799.60.228
1ytqA0.941999.60.233
3lwkA0.941999.60.233

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