GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF87 - Domain of unknown function DUF87
Pfam: PF01935 (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: CL0023
Length: 229
Sequences: 1627
Seq/Len: 7.1
HH_delta: 0.552 (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
25_H32_T0.265322.779
62_G209_D0.238222.495
56_I208_I0.21742.277
28_I40_V0.213422.235
70_P74_D0.205972.157
69_D73_K0.183511.922
71_D74_D0.179451.879
17_D20_K0.178341.868
30_G34_S0.177661.861
128_E179_R0.1661.739
46_E50_K0.161771.694
128_E132_K0.157861.653
18_L51_K0.154061.614
126_A148_I0.151061.582
44_L57_I0.147911.549
42_V46_E0.147721.547
69_D72_Y0.147581.546
134_E137_N0.146271.532
57_I60_P0.141591.483
40_V64_Y0.140151.468
123_L170_L0.140111.467
134_E151_E0.138631.452
35_G59_D0.138411.450
78_V81_I0.137891.444
23_N32_T0.137341.438
25_H61_H0.136411.429
70_P73_K0.13591.423
41_K64_Y0.135621.420
24_R32_T0.132831.391
147_F151_E0.130861.371
166_T169_A0.129671.358
48_L205_I0.127861.339
37_S41_K0.127541.336
51_K134_E0.122331.281
57_I64_Y0.118691.243
125_E129_K0.118641.243
14_V148_I0.118121.237
76_V188_P0.117161.227
122_I166_T0.116151.216
103_A123_L0.115431.209
166_T172_R0.114371.198
173_R176_R0.113331.187
30_G68_F0.11321.186
74_D78_V0.113171.185
30_G35_G0.112481.178
11_D15_Y0.11191.172
137_N150_E0.111441.167
20_K81_I0.110351.156
161_S169_A0.110081.153
131_K139_I0.109871.151
37_S61_H0.108941.141
93_P96_D0.108931.141
27_A37_S0.108331.135
41_K63_E0.108011.131
134_E139_I0.107651.127
25_H119_Q0.107631.127
76_V79_F0.107181.123
17_D37_S0.107121.122
30_G33_G0.106971.120
92_I96_D0.10671.117
21_L24_R0.106581.116
160_N168_R0.105941.110
88_R191_I0.105811.108
40_V63_E0.104671.096
12_V50_K0.104091.090
177_L182_S0.104031.090
55_V205_I0.103811.087
149_L167_I0.103781.087
135_L139_I0.103361.083
47_L53_A0.102281.071
68_F124_K0.101711.065
62_G211_S0.101461.063
13_P73_K0.100931.057
61_H101_D0.100761.055
39_T183_F0.100491.052
121_P175_E0.100471.052
30_G64_Y0.100431.052
72_Y76_V0.100251.050
77_K80_T0.099921.046
57_I164_S0.099491.042
98_N101_D0.099231.039
120_R124_K0.098841.035
38_N45_E0.097751.024
25_H46_E0.097521.021
37_S64_Y0.096591.012
54_K206_V0.096241.008
31_T34_S0.09621.008
30_G38_N0.096031.006
169_A172_R0.095931.005
185_S193_K0.095340.999
38_N64_Y0.095160.997
37_S206_V0.095050.995
31_T41_K0.095030.995
22_F47_L0.0950.995
45_E67_L0.094490.990
147_F152_L0.093780.982
60_P213_V0.093170.976
187_T190_D0.093140.975
30_G67_L0.093060.975
32_T62_G0.09260.970
37_S87_D0.09240.968
122_I162_S0.092030.964
52_G187_T0.091810.962
132_K159_L0.091760.961
40_V44_L0.091560.959
32_T38_N0.091360.957
21_L204_K0.091250.956
13_P43_L0.091160.955
60_P180_R0.090840.951
20_K137_N0.090180.944
96_D188_P0.09010.944
105_L173_R0.090070.943
189_E194_L0.089660.939
38_N41_K0.08960.938
37_S57_I0.089590.938
53_A177_L0.089560.938
76_V80_T0.089520.938
145_I171_L0.088640.928
29_F67_L0.08860.928
25_H33_G0.08850.927
23_N38_N0.088140.923
189_E193_K0.088090.923
129_K158_K0.088080.922
59_D119_Q0.087840.920
16_L184_F0.087730.919
65_A76_V0.087340.915
23_N61_H0.087060.912
159_L170_L0.086880.910
47_L65_A0.086810.909
42_V70_P0.086610.907
38_N207_I0.086530.906
13_P17_D0.086310.904
48_L55_V0.086260.903
12_V15_Y0.086250.903
24_R61_H0.086050.901
16_L117_E0.085930.900
192_I195_L0.08590.900
117_E172_R0.085750.898
24_R66_S0.08550.895
14_V176_R0.085440.895
20_K92_I0.085360.894
34_S61_H0.085320.894
150_E193_K0.08520.892
17_D21_L0.084740.888
22_F31_T0.084620.886
44_L152_L0.084530.885
186_S191_I0.084450.884
165_S168_R0.083770.877
11_D14_V0.083430.874
26_I29_F0.083240.872
185_S188_P0.08320.871
39_T42_V0.08260.865
137_N202_P0.082510.864
44_L205_I0.08250.864
40_V91_K0.082390.863
74_D191_I0.082030.859
102_L213_V0.081960.858
123_L126_A0.081390.852
52_G75_R0.081240.851
82_D209_D0.08120.850
128_E171_L0.080920.847
90_L173_R0.080560.844
30_G36_K0.080120.839
143_D203_G0.080030.838
15_Y18_L0.079990.838
25_H205_I0.079980.838
27_A46_E0.079950.837
142_D191_I0.079920.837
116_A119_Q0.079910.837
28_I50_K0.079830.836
28_I98_N0.079820.836
23_N37_S0.079770.835
118_V124_K0.079760.835
61_H108_I0.079580.833
79_F191_I0.079490.833
167_I171_L0.079460.832
28_I143_D0.079190.829
124_K176_R0.079150.829
40_V172_R0.07910.828
23_N91_K0.079060.828
61_H64_Y0.079060.828
20_K139_I0.078970.827
79_F190_D0.07870.824
78_V134_E0.078690.824
106_L123_L0.078580.823
90_L208_I0.078370.821
59_D120_R0.078250.820
146_E179_R0.078180.819
144_P174_L0.078050.817
148_I162_S0.07790.816
134_E148_I0.077650.813
104_S168_R0.077590.813
51_K208_I0.077430.811
29_F61_H0.07720.809
102_L145_I0.077160.808
58_F90_L0.077080.807
187_T193_K0.076980.806
13_P195_L0.07690.805
138_K143_D0.076750.804
91_K193_K0.076690.803
41_K177_L0.076650.803
96_D146_E0.076490.801
69_D191_I0.076020.796
95_W140_S0.075940.795
17_D194_L0.075770.794
30_G42_V0.075760.793
11_D46_E0.07570.793
52_G58_F0.075670.793
125_E179_R0.075590.792
17_D192_I0.07550.791
38_N63_E0.07540.790
75_R79_F0.075340.789
18_L144_P0.07530.789
51_K190_D0.07520.788
29_F41_K0.075140.787
46_E194_L0.075140.787
162_S182_S0.07510.787
42_V105_L0.075050.786
171_L174_L0.075040.786
125_E158_K0.075010.786
31_T81_I0.074980.785
24_R206_V0.074820.784
37_S63_E0.07480.783
44_L64_Y0.074720.783
12_V78_V0.074580.781
142_D146_E0.074560.781
120_R176_R0.074550.781
68_F128_E0.07450.780
122_I126_A0.074480.780
75_R187_T0.074430.780
65_A207_I0.074280.778
27_A61_H0.074220.777
29_F37_S0.074140.776
128_E169_A0.074060.776
142_D178_F0.074060.776
103_A128_E0.074050.776
90_L209_D0.074030.775
47_L106_L0.07380.773
29_F188_P0.073770.773
171_L213_V0.073710.772
20_K134_E0.073180.766
152_L158_K0.073150.766
125_E162_S0.073060.765
78_V82_D0.073020.765
149_L152_L0.072960.764
80_T153_K0.072930.764
79_F92_I0.072890.763
125_E190_D0.072750.762
144_P152_L0.072650.761
40_V43_L0.072640.761
17_D82_D0.072580.760
55_V123_L0.072580.760
32_T61_H0.072570.760
184_F207_I0.072550.760
39_T43_L0.072410.758
78_V173_R0.072290.757
193_K202_P0.072230.756
163_A174_L0.072070.755
153_K167_I0.072070.755
79_F195_L0.071990.754
93_P98_N0.071950.754
29_F59_D0.071690.751
37_S172_R0.071630.750
41_K61_H0.071630.750
190_D194_L0.071520.749
14_V147_F0.071420.748
11_D134_E0.071380.748
81_I183_F0.071370.747
29_F92_I0.071220.746
15_Y213_V0.071130.745
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
4ag6A0.877799.70.552
1e9rA0.886599.50.641
2iutA0.890898.70.754
2iusA0.781798.20.79
4f4cA0.812297.10.843
2gzaA0.834196.70.852
2oap10.908396.70.852
2pt7A0.777396.70.852
3fb4A0.790496.70.853
4ihqA0.803596.60.855
If you are interested in a protein containing this domain,
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