GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4434 - Domain of unknown function (DUF4434)
Pfam: PF14488 (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: CL0058
Length: 166
Sequences: 3981
Seq/Len: 23.98
HH_delta: 0.303 (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
27_R77_Y1.297084.375
68_E114_R1.069073.606
68_E115_Y0.811222.736
26_F74_A0.808722.728
23_R73_A0.74792.523
23_R76_K0.716052.415
75_D118_H0.696962.351
26_F77_Y0.684572.309
23_R77_Y0.652082.199
74_A81_V0.641212.163
73_A76_K0.636532.147
29_M34_I0.593142.001
30_K77_Y0.568891.919
72_D76_K0.563511.901
105_K143_L0.553241.866
73_A77_Y0.543471.833
27_R31_A0.525921.774
109_D113_Q0.5211.757
82_F123_G0.515811.740
71_L81_V0.508481.715
101_A143_L0.508421.715
142_A146_K0.503471.698
152_S155_K0.497871.679
146_K150_Q0.472041.592
41_W44_Y0.449151.515
106_Q109_D0.447311.509
28_A31_A0.440381.485
69_M73_A0.425491.435
74_A79_M0.420871.420
124_W152_S0.410931.386
137_A140_R0.398221.343
143_L146_K0.394131.329
102_E106_Q0.387551.307
38_I128_Y0.385341.300
110_E113_Q0.382811.291
80_K122_Y0.378011.275
71_L121_F0.377881.275
36_T80_K0.361561.219
147_Y150_Q0.353581.193
127_P130_I0.348511.175
68_E72_D0.34621.168
90_D93_D0.343831.160
148_L157_V0.34221.154
144_L148_L0.34031.148
26_F73_A0.339351.145
36_T122_Y0.33871.142
113_Q116_G0.337621.139
72_D75_D0.33661.135
102_E105_K0.33621.134
72_D118_H0.330341.114
37_L79_M0.325011.096
145_G157_V0.324471.094
42_T45_G0.322741.089
105_K109_D0.317691.072
23_R69_M0.316251.067
108_A124_W0.315711.065
147_Y151_I0.307971.039
75_D120_S0.304831.028
121_F124_W0.304711.028
24_E28_A0.303611.024
36_T82_F0.299791.011
124_W155_K0.299361.010
145_G149_K0.297981.005
143_L147_Y0.296160.999
24_E27_R0.295710.997
41_W45_G0.294280.993
88_D127_P0.292240.986
109_D147_Y0.280580.946
26_F79_M0.275690.930
26_F70_I0.273580.923
65_D68_E0.271990.917
71_L115_Y0.268170.904
38_I129_E0.265480.895
103_R107_V0.264020.890
84_G125_Y0.262850.887
30_K79_M0.262390.885
95_G98_D0.261020.880
40_Q84_G0.259620.876
21_Q25_E0.258770.873
112_W151_I0.25450.858
39_L84_G0.250530.845
65_D114_R0.247240.834
75_D119_P0.24710.833
40_Q86_Y0.246850.833
105_K147_Y0.245060.827
80_K123_G0.244870.826
112_W147_Y0.242820.819
106_Q110_E0.242660.818
30_K78_G0.241090.813
35_D79_M0.240920.813
149_K152_S0.235450.794
35_D80_K0.234280.790
108_A149_K0.233220.787
31_A77_Y0.232470.784
28_A32_I0.229040.773
101_A104_N0.227040.766
108_A112_W0.226150.763
38_I84_G0.224280.756
114_R118_H0.22350.754
37_L74_A0.223410.754
66_L69_M0.221990.749
105_K108_A0.217080.732
139_E143_L0.21670.731
26_F37_L0.216650.731
25_E29_M0.216440.730
75_D78_G0.215310.726
23_R27_R0.21520.726
26_F30_K0.215080.725
100_E104_N0.214550.724
127_P131_D0.212990.718
137_A141_F0.209730.707
116_G152_S0.20930.706
71_L118_H0.206620.697
86_Y125_Y0.206290.696
38_I130_I0.205060.692
113_Q151_I0.205020.691
92_W125_Y0.203050.685
126_I141_F0.202380.683
38_I125_Y0.201780.681
21_Q24_E0.200540.676
67_L83_V0.199880.674
25_E28_A0.199110.672
149_K157_V0.19820.668
127_P141_F0.197560.666
107_V127_P0.197220.665
37_L70_I0.194950.658
83_V115_Y0.194820.657
135_W138_P0.194530.656
65_D69_M0.192160.648
113_Q147_Y0.191570.646
22_W70_I0.190730.643
69_M72_D0.189770.640
131_D134_N0.189510.639
131_D140_R0.188680.636
29_M32_I0.188080.634
89_P98_D0.187690.633
39_L81_V0.187170.631
96_D99_W0.186990.631
39_L83_V0.186760.630
81_V120_S0.186520.629
133_Y136_N0.18580.627
100_E103_R0.185370.625
116_G151_I0.185210.625
108_A155_K0.185150.624
27_R30_K0.184680.623
52_S136_N0.183080.617
125_Y130_I0.180790.610
37_L92_W0.180750.610
40_Q83_V0.180570.609
35_D132_D0.179570.606
141_F145_G0.179460.605
102_E146_K0.179010.604
23_R26_F0.178250.601
109_D112_W0.17740.598
38_I82_F0.176640.596
144_L147_Y0.176280.595
29_M79_M0.17540.592
127_P144_L0.175060.590
85_L144_L0.175050.590
109_D151_I0.174010.587
144_L157_V0.173530.585
134_N137_A0.172920.583
149_K153_P0.172590.582
109_D150_Q0.172410.582
140_R144_L0.169770.573
33_G79_M0.169430.571
103_R106_Q0.168150.567
85_L108_A0.167820.566
111_L114_R0.166970.563
54_L97_L0.166120.560
71_L75_D0.163870.553
39_L74_A0.163780.552
92_W127_P0.16370.552
39_L67_L0.163480.551
110_E116_G0.162790.549
87_F104_N0.162450.548
28_A67_L0.162010.546
132_D150_Q0.161350.544
142_A145_G0.160720.542
126_I157_V0.160030.540
93_D96_D0.159290.537
121_F125_Y0.159090.537
71_L83_V0.159050.536
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
4h41A199.90.303
3pzgA0.957899.80.352
2osxA0.957899.80.355
3aofA0.963999.80.357
1ceoA0.957899.80.361
3ncoA0.963999.80.364
1bqcA0.915799.80.366
1rh9A0.969999.80.369
1uuqA0.963999.80.37
1vjzA0.951899.80.372

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