GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF664 - Protein of unknown function (DUF664)
Pfam: PF04978 (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: CL0310
Length: 150
Sequences: 4222
Seq/Len: 28.15
HH_delta: 0.221 (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
21_S24_Q1.093724.082
14_L90_R0.867963.239
36_I141_A0.712392.659
104_L107_D0.684492.554
26_R37_G0.65952.461
81_T84_D0.635062.370
7_D97_R0.626832.339
10_R134_Y0.543222.027
25_L82_V0.522441.950
107_D110_G0.484851.809
24_Q27_R0.484771.809
94_A98_A0.479031.788
42_H137_H0.467551.745
44_A88_E0.462581.726
47_E93_R0.461911.724
48_R88_E0.452991.690
34_N38_G0.432961.616
83_A87_A0.420681.570
104_L108_A0.418281.561
17_V40_V0.41671.555
15_A18_E0.401261.497
87_A91_A0.391881.462
20_L36_I0.384711.436
97_R101_A0.366521.368
47_E96_T0.365851.365
132_E135_A0.360641.346
133_E137_H0.356681.331
18_E86_L0.351491.312
50_W129_H0.350291.307
90_R94_A0.349041.303
70_R73_E0.348981.302
100_L127_L0.347021.295
20_L24_Q0.344311.285
135_A139_G0.342131.277
87_A90_R0.337491.259
39_L140_H0.335231.251
14_L86_L0.324821.212
86_L90_R0.323281.206
13_V138_A0.317811.186
9_Q138_A0.315181.176
38_G41_K0.315031.176
91_A95_R0.314451.173
93_R97_R0.31381.171
22_D81_T0.312211.165
109_P124_R0.311611.163
6_L96_T0.310211.158
89_Y134_Y0.310211.158
43_L134_Y0.309791.156
22_D82_V0.30171.126
42_H133_E0.301341.125
35_S38_G0.301111.124
39_L141_A0.296671.107
34_N136_R0.295731.104
7_D101_A0.295671.103
28_R38_G0.294141.098
56_A59_D0.29151.088
49_Y53_R0.290481.084
22_D26_R0.289771.081
7_D11_D0.289661.081
25_L37_G0.285021.064
37_G41_K0.284971.063
28_R32_S0.28431.061
88_E91_A0.282221.053
111_A120_P0.279921.045
54_V126_V0.279721.044
43_L89_Y0.279711.044
55_F95_R0.27881.040
89_Y93_R0.273161.019
105_D108_A0.270371.009
122_T125_W0.266120.993
12_T15_A0.261990.978
72_A75_R0.258930.966
16_K138_A0.258030.963
95_R99_Y0.255310.953
10_R47_E0.250690.936
23_E27_R0.24970.932
34_N39_L0.246860.921
121_V125_W0.246020.918
98_A102_A0.245390.916
106_L109_P0.244470.912
37_G85_L0.243930.910
47_E134_Y0.243930.910
25_L40_V0.240740.898
41_K85_L0.238590.890
129_H132_E0.238170.889
11_D15_A0.237590.887
96_T130_V0.236350.882
103_A108_A0.235160.878
13_V134_Y0.234290.874
10_R93_R0.231750.865
13_V89_Y0.231660.865
46_V130_V0.230240.859
84_D87_A0.230.858
48_R92_A0.229880.858
54_V123_L0.229450.856
99_Y102_A0.228280.852
51_F92_A0.227160.848
91_A94_A0.227130.848
9_Q12_T0.226220.844
82_V86_L0.22590.843
41_K80_E0.223240.833
21_S25_L0.223130.833
23_E26_R0.222580.831
12_T138_A0.221810.828
85_L89_Y0.219630.820
51_F96_T0.219220.818
89_Y92_A0.218750.816
44_A85_L0.218670.816
9_Q13_V0.217430.811
46_V129_H0.216920.810
126_V129_H0.216380.807
93_R96_T0.215950.806
34_N139_G0.215750.805
13_V40_V0.214910.802
125_W132_E0.213950.798
41_K45_G0.21320.796
44_A92_A0.212720.794
48_R95_R0.212320.792
133_E140_H0.210420.785
10_R89_Y0.209770.783
7_D94_A0.20940.781
9_Q135_A0.209110.780
109_P122_T0.206610.771
13_V43_L0.2060.769
106_L110_G0.202880.757
51_F130_V0.202630.756
15_A101_A0.201450.752
18_E90_R0.200740.749
53_R57_G0.199230.743
136_R139_G0.198170.740
16_K19_G0.196090.732
8_R12_T0.195930.731
22_D83_A0.195640.730
131_I134_Y0.194840.727
83_A86_L0.194420.726
46_V50_W0.193950.724
37_G82_V0.193870.723
52_G92_A0.19240.718
6_L9_Q0.192250.717
47_E50_W0.191920.716
136_R142_D0.190870.712
77_A81_T0.190840.712
50_W130_V0.190780.712
8_R11_D0.190470.711
95_R98_A0.189880.709
10_R13_V0.189180.706
80_E84_D0.188510.703
44_A89_Y0.186430.696
13_V141_A0.185950.694
14_L18_E0.185550.692
10_R14_L0.185110.691
98_A101_A0.183410.684
48_R52_G0.181240.676
28_R35_S0.180810.675
125_W129_H0.180280.673
96_T99_Y0.180250.673
108_A127_L0.178360.666
52_G95_R0.177910.664
104_L109_P0.177750.663
84_D88_E0.177450.662
11_D90_R0.176270.658
54_V99_Y0.175740.656
41_K81_T0.17460.652
33_S136_R0.174140.650
30_V33_S0.173230.646
40_V86_L0.172960.645
28_R33_S0.172710.645
110_G123_L0.171780.641
6_L131_I0.170520.636
52_G96_T0.170280.635
70_R74_F0.170090.635
29_P35_S0.169440.632
62_P109_P0.169050.631
132_E138_A0.169030.631
136_R140_H0.168620.629
12_T16_K0.168080.627
73_E76_V0.168070.627
19_G22_D0.167950.627
47_E130_V0.166940.623
43_L93_R0.166610.622
94_A97_R0.163060.609
113_P120_P0.162960.608
77_A80_E0.162140.605
57_G99_Y0.161870.604
18_E83_A0.161550.603
33_S36_I0.160750.600
97_R100_L0.158790.593
71_D75_R0.158740.592
11_D78_D0.157680.588
25_L36_I0.156860.585
41_K77_A0.156340.583
10_R20_L0.15630.583
24_Q29_P0.155710.581
103_A107_D0.155660.581
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
1rxqA0.993399.80.221
3gorA0.9299.80.23
3e4xA0.9299.70.242
3dkaA0.9299.70.243
3di5A0.913399.70.258
2rd9A0.9899.70.262
2ou6A0.9499.70.27
3cexA0.986799.70.279
2p1aA0.9499.70.285
2yqyA0.9699.70.292

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