GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Globin - Globin
Pfam: PF00042 (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: CL0090
Length: 110
Sequences: 2187
Seq/Len: 19.88
HH_delta: 0.041 (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
98_T101_H0.568152.608
13_K72_D0.537572.468
15_D18_E0.528932.428
3_K7_Q0.492042.259
9_W68_D0.451662.073
22_E25_Q0.440152.020
27_L104_L0.425531.953
90_R94_R0.407451.870
6_R75_D0.393881.808
4_L8_S0.375881.725
21_S25_Q0.365231.676
22_E26_R0.358841.647
30_E108_A0.351081.612
59_H63_V0.343551.577
17_D61_Q0.34171.568
20_G64_M0.322831.482
19_F22_E0.311051.428
9_W71_V0.308511.416
2_K75_D0.307621.412
68_D71_V0.290691.334
30_E107_E0.287121.318
26_R108_A0.286461.315
24_F59_H0.285651.311
61_Q65_E0.280231.286
70_A80_L0.27051.242
31_Y34_Y0.263831.211
23_F109_L0.262821.206
37_L101_H0.261381.200
68_D72_D0.255511.173
38_F91_H0.254751.169
75_D80_L0.252151.157
73_N76_D0.251951.156
26_R30_E0.248431.140
21_S60_A0.24731.135
97_V102_F0.246941.133
28_F32_P0.244041.120
56_F60_A0.243731.119
5_V71_V0.241911.110
24_F63_V0.240481.104
27_L105_F0.238081.093
27_L108_A0.234951.078
106_G109_L0.227561.045
23_F105_F0.224011.028
90_R93_K0.223781.027
11_K14_P0.218781.004
100_E103_E0.218281.002
106_G110_L0.217941.000
7_Q11_K0.215030.987
41_F63_V0.213990.982
98_T103_E0.213620.981
37_L97_V0.213270.979
70_A74_L0.212960.978
54_P58_A0.210680.967
54_P63_V0.210490.966
15_D19_F0.209110.960
87_L102_F0.206340.947
58_A62_R0.205610.944
86_K90_R0.20550.943
77_P80_L0.201750.926
14_P18_E0.20130.924
104_L108_A0.201080.923
25_Q29_E0.200240.919
65_E68_D0.199270.915
15_D64_M0.197010.904
66_A69_E0.196480.902
25_Q56_F0.19580.899
3_K6_R0.194910.895
89_R93_K0.191170.877
8_S23_F0.190320.874
4_L7_Q0.189590.870
20_G60_A0.189430.870
73_N83_M0.187220.859
18_E21_S0.186930.858
95_G98_T0.185140.850
31_Y104_L0.184980.849
34_Y101_H0.18480.848
24_F38_F0.183960.844
15_D21_S0.182660.838
66_A83_M0.181190.832
40_K55_E0.1810.831
31_Y108_A0.180140.827
9_W12_V0.17770.816
28_F90_R0.177170.813
102_F105_F0.175790.807
71_V74_L0.175760.807
83_M92_K0.175570.806
77_P81_E0.175070.804
2_K6_R0.174570.801
33_D84_L0.172670.793
35_K40_K0.171820.789
76_D82_A0.171410.787
10_A72_D0.170440.782
77_P84_L0.169640.779
69_E72_D0.169290.777
58_A63_V0.168170.772
91_H97_V0.168010.771
57_K82_A0.167270.768
10_A14_P0.166860.766
12_V71_V0.164170.754
11_K15_D0.163850.752
34_Y37_L0.163010.748
38_F63_V0.162230.745
60_A95_G0.161090.739
13_K68_D0.160660.737
19_F68_D0.158320.727
70_A92_K0.157060.721
33_D57_K0.155760.715
64_M68_D0.154770.710
24_F102_F0.154090.707
21_S55_E0.153660.705
73_N81_E0.153590.705
23_F59_H0.153520.705
7_Q12_V0.153040.702
65_E107_E0.152890.702
13_K65_E0.152730.701
103_E107_E0.15220.699
63_V105_F0.151480.695
87_L104_L0.151240.694
86_K89_R0.150440.691
9_W20_G0.148930.684
99_P106_G0.148520.682
17_D21_S0.147950.679
10_A16_K0.14790.679
9_W13_K0.147230.676
35_K41_F0.146960.675
58_A65_E0.146390.672
36_K107_E0.144850.665
103_E106_G0.144720.664
35_K81_E0.144620.664
70_A88_G0.143510.659
85_R89_R0.143090.657
88_G92_K0.142190.653
9_W72_D0.1420.652
31_Y107_E0.141940.652
59_H69_E0.141860.651
69_E86_K0.140480.645
38_F59_H0.140110.643
10_A13_K0.138920.638
57_K89_R0.138660.636
85_R88_G0.13820.634
64_M109_L0.138060.634
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
4hrrA0.963699.80.041
1mbaA0.981899.80.051
1x3kA0.981899.80.053
4b4yA0.990999.80.054
3pt8B0.981899.80.055
3pt8A0.981899.80.056
1b0bA0.981899.80.057
2c0kA0.981899.80.059
2dc3A0.990999.80.061
2lhbA0.990999.80.061

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