GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Asp23 - Asp23 family
Pfam: PF03780 (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: 108
Sequences: 1426
Seq/Len: 13.2
HH_delta: 0.797 (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
63_D101_N0.674033.599
16_A62_V0.493782.637
65_H105_E0.423292.260
74_I104_V0.412882.205
86_K90_E0.401592.145
62_V89_V0.392352.095
65_H103_H0.374632.001
59_G96_E0.346731.852
64_L85_V0.344441.839
55_D59_G0.335471.791
15_I92_M0.334691.787
61_T98_S0.33051.765
66_V81_I0.319251.705
68_V77_V0.317391.695
90_E96_E0.314841.681
24_E80_E0.302651.616
67_V106_D0.298161.592
73_N76_E0.282191.507
88_A92_M0.276441.476
55_D61_T0.272991.458
61_T99_E0.272471.455
97_V100_V0.271921.452
68_V74_I0.27011.442
87_E91_E0.254741.360
59_G98_S0.253451.353
29_V49_G0.249121.330
10_R13_A0.24431.305
89_V97_V0.231271.235
55_D98_S0.229761.227
63_D103_H0.227181.213
72_V77_V0.225421.204
80_E83_E0.221681.184
20_A81_I0.221571.183
52_V62_V0.221351.182
8_S11_V0.218911.169
76_E79_E0.215661.152
22_E84_K0.214151.144
12_I93_T0.212891.137
19_A88_A0.211311.128
89_V93_T0.203091.085
6_T9_D0.196551.050
26_V81_I0.196171.048
81_I102_V0.19611.047
37_I42_G0.186450.996
83_E91_E0.186220.994
55_D58_G0.185530.991
16_A97_V0.185070.988
16_A89_V0.184910.987
20_A97_V0.181610.970
71_G74_I0.18130.968
86_K97_V0.181030.967
59_G95_I0.175490.937
13_A30_S0.175450.937
86_K100_V0.175310.936
82_Q92_M0.174540.932
82_Q86_K0.17450.932
80_E87_E0.172480.921
24_E69_E0.170820.912
76_E80_E0.169610.906
17_A46_P0.169510.905
14_K45_R0.168970.902
13_A52_V0.167730.896
84_K87_E0.167390.894
20_A83_E0.16610.887
2_L5_I0.165280.883
25_G69_E0.163490.873
28_G87_E0.163270.872
68_V107_V0.162850.870
3_G102_V0.162140.866
75_P79_E0.161210.861
12_I95_I0.160370.856
5_I82_Q0.160270.856
81_I85_V0.159950.854
12_I52_V0.156020.833
16_A52_V0.155730.832
79_E83_E0.155410.830
28_G67_V0.15520.829
39_D48_K0.15520.829
53_E72_V0.15470.826
80_E84_K0.153930.822
82_Q101_N0.153280.819
39_D43_R0.152580.815
12_I60_I0.15250.814
23_V81_I0.151850.811
20_A62_V0.150420.803
19_A81_I0.147710.789
22_E91_E0.14730.787
52_V60_I0.146840.784
20_A29_V0.146160.781
15_I93_T0.146150.780
78_A103_H0.146050.780
69_E96_E0.146030.780
2_L96_E0.14580.779
66_V105_E0.14540.776
2_L91_E0.144030.769
40_R46_P0.143850.768
59_G99_E0.142820.763
73_N78_A0.142560.761
78_A102_V0.142110.759
19_A85_V0.141950.758
42_G47_S0.141810.757
23_V28_G0.141770.757
22_E88_A0.141630.756
21_A28_G0.141180.754
27_V41_L0.140380.750
4_S8_S0.139190.743
40_R43_R0.139030.742
70_Y104_V0.138910.742
70_Y107_V0.138120.738
62_V97_V0.137110.732
23_V107_V0.1360.726
57_D94_G0.1360.726
23_V77_V0.135980.726
16_A19_A0.135590.724
78_A104_V0.134720.719
9_D13_A0.13470.719
11_V15_I0.13290.710
50_V74_I0.132760.709
5_I21_A0.131380.702
29_V77_V0.130680.698
23_V95_I0.130150.695
61_T101_N0.129650.692
20_A64_L0.129570.692
23_V82_Q0.129390.691
64_L81_I0.129110.689
38_S89_V0.128730.687
3_G74_I0.128610.687
7_I94_G0.128520.686
53_E98_S0.12780.682
44_K47_S0.127560.681
26_V51_K0.127430.680
46_P94_G0.127410.680
38_S64_L0.127340.680
18_K46_P0.12720.679
26_V64_L0.126860.677
7_I16_A0.126090.673
68_V81_I0.125880.672
14_K18_K0.125720.671
15_I19_A0.125430.670
58_G69_E0.125360.669
41_L48_K0.125280.669
7_I93_T0.125130.668
85_V102_V0.124980.667
15_I64_L0.124970.667
40_R44_K0.123830.661
9_D26_V0.123680.660
41_L83_E0.123280.658
28_G72_V0.122830.656
66_V104_V0.12270.655
37_I44_K0.122020.652
11_V31_G0.121970.651
80_E91_E0.121970.651
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
3j1zP0.78786.80.797
3h90A0.78784.60.804
2zztA0.777850.70.846
1wh9A0.768543.30.852
1mwwA0.916735.30.859
2aalA0.935233.80.86
1uizA0.879631.70.862
2os5A0.879631.30.863
1hfoA0.8796270.866
3bypA0.777825.80.868
If you are interested in a protein containing this domain,
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