GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF257 - Pyrococcus protein of unknown function DUF257
Pfam: PF03192 (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: 210
Sequences: 6174
Seq/Len: 29.4
HH_delta: 0.356 (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
41_P115_V0.839463.153
162_V165_K0.742982.790
8_I31_L0.683512.567
40_Y115_V0.670912.520
35_A116_I0.6542.456
14_V180_T0.649462.439
32_I118_I0.643922.418
15_L178_A0.640522.406
182_I193_F0.613342.304
10_P115_V0.60062.256
13_T144_S0.580182.179
14_V182_I0.569952.141
161_D164_E0.554762.084
32_I42_V0.540812.031
64_D70_N0.536462.015
9_K12_E0.510471.917
10_P151_R0.508141.908
5_L180_T0.500311.879
18_Y24_P0.445811.674
183_E196_K0.445521.673
1_I182_I0.443321.665
29_Y58_L0.441781.659
34_W37_E0.440591.655
104_E108_K0.433231.627
28_F157_F0.417341.567
102_Y106_L0.41431.556
28_F118_I0.414291.556
146_F150_E0.404681.520
184_I193_F0.399721.501
34_W38_K0.399441.500
73_V76_I0.393441.478
180_T198_S0.390451.466
31_L116_I0.389271.462
18_Y23_P0.385371.447
148_G179_T0.379511.425
16_V155_F0.379481.425
12_E180_T0.378621.422
18_Y184_I0.37131.394
1_I5_L0.36871.385
98_Y102_Y0.368191.383
43_L105_I0.365071.371
147_L154_A0.357641.343
137_I141_N0.3521.322
72_K112_K0.350471.316
12_E53_I0.349231.312
55_K59_E0.348111.307
103_E146_F0.340671.279
117_N152_R0.336961.266
10_P40_Y0.32831.233
41_P70_N0.324931.220
17_E183_E0.323631.215
102_Y105_I0.31681.190
99_L102_Y0.31161.170
113_E152_R0.309571.163
32_I44_I0.308551.159
23_P120_L0.304511.144
97_V101_E0.304321.143
41_P113_E0.303331.139
106_L117_N0.303331.139
116_I155_F0.302761.137
35_A40_Y0.299861.126
50_T53_I0.296631.114
146_F154_A0.296071.112
175_E181_V0.294341.105
21_S200_N0.293841.104
40_Y116_I0.293231.101
51_L55_K0.293191.101
27_L184_I0.291221.094
145_R149_N0.29121.094
101_E105_I0.291171.094
46_D54_Y0.290511.091
16_V28_F0.28661.076
35_A42_V0.286281.075
99_L105_I0.285591.073
113_E150_E0.283761.066
18_Y25_E0.283541.065
12_E200_N0.280451.053
36_R71_I0.279741.051
102_Y117_N0.276791.040
146_F152_R0.275911.036
171_L181_V0.275121.033
44_I118_I0.273331.027
22_S191_L0.271521.020
118_I155_F0.271381.019
137_I173_L0.271051.018
28_F44_I0.270011.014
187_E190_K0.268691.009
6_D9_K0.265840.998
33_K37_E0.264910.995
1_I195_V0.260840.980
116_I153_I0.258420.971
96_S99_L0.257070.965
21_S24_P0.254060.954
158_I174_L0.253270.951
12_E179_T0.252150.947
104_E107_E0.250890.942
97_V102_Y0.250810.942
43_L114_K0.250680.941
19_S22_S0.250580.941
97_V100_K0.250310.940
24_P120_L0.24990.939
161_D165_K0.249570.937
103_E142_S0.249390.937
179_T199_P0.249020.935
95_P98_Y0.248370.933
21_S25_E0.248070.932
33_K63_I0.246770.927
147_L155_F0.246480.926
4_F195_V0.24360.915
132_S135_E0.242440.911
159_N171_L0.241920.909
25_E120_L0.241430.907
13_T140_F0.24120.906
13_T154_A0.241130.906
42_V116_I0.240240.902
31_L35_A0.239560.900
136_L140_F0.239080.898
2_F7_S0.238840.897
126_F145_R0.238050.894
97_V105_I0.237820.893
145_R148_G0.237780.893
117_N154_A0.237180.891
99_L104_E0.236890.890
8_I155_F0.23650.888
17_E196_K0.231250.869
18_Y22_S0.231030.868
19_S183_E0.22840.858
172_P175_E0.227290.854
15_L174_L0.227270.854
142_S145_R0.226230.850
4_F198_S0.225310.846
27_L31_L0.224960.845
13_T156_Y0.222040.834
161_D172_P0.221740.833
13_T178_A0.22160.832
165_K170_V0.220940.830
5_L182_I0.220730.829
10_P153_I0.219760.825
69_D72_K0.219580.825
173_L181_V0.218810.822
187_E192_K0.217530.817
9_K180_T0.217210.816
133_P173_L0.216840.814
101_E108_K0.213590.802
30_E34_W0.211910.796
51_L54_Y0.211020.793
155_F180_T0.210350.790
8_I116_I0.210260.790
30_E33_K0.210180.789
11_G151_R0.209660.787
36_R42_V0.20880.784
41_P72_K0.208770.784
184_I191_L0.208740.784
41_P114_K0.208630.784
99_L107_E0.208480.783
8_I154_A0.207660.780
18_Y21_S0.20560.772
96_S100_K0.205110.770
28_F155_F0.204740.769
17_E175_E0.203640.765
12_E198_S0.202180.759
100_K105_I0.201860.758
9_K198_S0.200870.754
101_E104_E0.200580.753
169_E178_A0.200040.751
141_N145_R0.199280.748
131_N135_E0.199070.748
140_F177_I0.199020.747
64_D69_D0.198790.747
105_I108_K0.198730.746
178_A181_V0.198690.746
48_L53_I0.198060.744
5_L9_K0.197420.741
13_T143_I0.196590.738
24_P48_L0.196530.738
18_Y120_L0.195990.736
33_K61_M0.194280.730
164_E169_E0.192680.724
108_K112_K0.192540.723
25_E29_Y0.192460.723
58_L62_G0.190850.717
59_E63_I0.190620.716
27_L193_F0.190490.715
45_D117_N0.188740.709
144_S177_I0.188460.708
117_N120_L0.1870.702
98_Y106_L0.185160.695
8_I14_V0.185160.695
16_V182_I0.185130.695
45_D102_Y0.18460.693
53_I57_H0.183050.687
21_S120_L0.182280.685
31_L34_W0.182170.684
149_N153_I0.181820.683
122_I174_L0.181490.682
5_L195_V0.180840.679
182_I195_V0.17950.674
51_L65_T0.179220.673
32_I116_I0.179160.673
120_L199_P0.179050.672
19_S185_E0.178860.672
25_E54_Y0.178810.672
3_E38_K0.178460.670
185_E192_K0.177390.666
20_S157_F0.176150.662
21_S198_S0.176030.661
54_Y57_H0.175750.660
39_G113_E0.172920.649
98_Y101_E0.171330.643
100_K104_E0.171290.643
69_D76_I0.171090.643
112_K189_K0.170740.641
48_L57_H0.170550.641
164_E170_V0.170530.640
76_I136_L0.170520.640
48_L159_N0.170290.640
173_L177_I0.170130.639
43_L117_N0.170040.639
59_E64_D0.169710.637
98_Y125_L0.169610.637
8_I35_A0.169440.636
3_E70_N0.168730.634
96_S107_E0.168710.634
102_Y125_L0.16790.631
41_P112_K0.167090.628
165_K188_G0.166760.626
37_E188_G0.16640.625
100_K103_E0.166250.624
146_F149_N0.166110.624
46_D49_D0.166090.624
102_Y146_F0.166060.624
1_I193_F0.166010.623
19_S196_K0.165550.622
96_S102_Y0.165090.620
147_L153_I0.164780.619
115_V152_R0.164450.618
144_S156_Y0.163360.614
72_K75_K0.163280.613
140_F156_Y0.163120.613
14_V153_I0.162470.610
159_N169_E0.161790.608
39_G70_N0.160650.603
108_K128_F0.160220.602
34_W112_K0.16020.602
189_K194_R0.160180.602
37_E113_E0.160050.601
193_F197_K0.160040.601
30_E61_M0.159960.601
163_L172_P0.159670.600
97_V106_L0.159140.598
107_E150_E0.159130.598
72_K128_F0.158830.597
185_E194_R0.158420.595
121_G176_E0.158110.594
47_I58_L0.158070.594
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
3bs4A0.966799.90.356
2ztsA0.98199.90.359
3cmwA0.885799.90.366
3cmuA0.885799.90.372
3cmuA0.885799.90.381
3cmwA0.885799.90.387
1q57A0.985799.90.389
3bgwA0.985799.90.389
3bh0A0.985799.90.39
2z43A0.928699.90.394

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