GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1570 - Protein of unknown function (DUF1570)
Pfam: PF07607 (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: CL0126
Length: 128
Sequences: 2874
Seq/Len: 22.45
HH_delta: 0.23 (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
116_R120_E0.642592.835
8_E11_H0.558732.465
41_P107_M0.557782.461
7_H11_H0.516232.278
107_M112_E0.497242.194
36_T39_E0.478612.112
7_H96_Y0.47852.111
37_Y107_M0.474092.092
32_E96_Y0.428511.891
116_R119_R0.394991.743
11_H32_E0.391421.727
7_H32_E0.387731.711
36_T100_W0.382771.689
33_G103_V0.362051.597
113_E117_Y0.357831.579
8_E32_E0.352391.555
115_A119_R0.34751.533
3_A39_E0.339281.497
11_H96_Y0.334071.474
102_L105_F0.32621.439
8_E96_Y0.324841.433
61_A64_R0.319941.412
10_T38_F0.30321.338
62_W65_A0.3021.333
28_R31_S0.299681.322
113_E116_R0.293411.295
13_L98_E0.289021.275
33_G99_S0.286691.265
110_R113_E0.283281.250
48_R51_G0.279511.233
10_T35_A0.278131.227
93_L97_A0.275981.218
37_Y41_P0.275331.215
114_F118_L0.274551.211
34_L103_V0.273651.207
71_R74_D0.267721.181
53_G56_N0.263431.162
86_F95_A0.262981.160
60_L64_R0.260961.151
12_Q35_A0.253941.120
39_E43_M0.250731.106
50_S53_G0.249941.103
15_F25_D0.249511.101
114_F117_Y0.247361.091
104_H108_E0.246021.086
13_L18_G0.245481.083
16_N31_S0.243451.074
29_W48_R0.240751.062
58_M61_A0.239941.059
41_P44_S0.236751.045
79_L84_D0.235931.041
6_A39_E0.234111.033
29_W76_L0.233091.028
38_F42_G0.23221.025
79_L82_S0.23081.018
15_F31_S0.230061.015
80_L83_D0.227751.005
6_A42_G0.225620.996
14_A34_L0.224990.993
9_A12_Q0.22310.984
44_S107_M0.222980.984
34_L114_F0.219750.970
104_H107_M0.219190.967
98_E105_F0.217760.961
15_F98_E0.212810.939
14_A18_G0.211890.935
15_F19_L0.211410.933
3_A36_T0.210770.930
19_L25_D0.210510.929
41_P50_S0.209220.923
19_L31_S0.208740.921
106_L110_R0.205180.905
31_S86_F0.204740.903
106_L114_F0.204190.901
23_L27_P0.204140.901
39_E42_G0.202640.894
51_G54_R0.202380.893
115_A118_L0.200750.886
100_W104_H0.200530.885
36_T97_A0.20030.884
98_E110_R0.199940.882
25_D31_S0.197080.870
16_N19_L0.196320.866
3_A43_M0.194720.859
6_A12_Q0.19370.855
117_Y120_E0.193680.855
55_V58_M0.193590.854
112_E115_A0.193020.852
29_W33_G0.189380.836
92_A95_A0.186920.825
58_M62_W0.185950.820
16_N35_A0.18350.810
39_E44_S0.182130.804
56_N97_A0.180060.794
23_L26_W0.180040.794
59_R114_F0.17980.793
13_L110_R0.17770.784
41_P45_S0.176650.779
27_P73_G0.176260.778
101_A104_H0.176130.777
40_T100_W0.176110.777
51_G62_W0.175970.776
28_R95_A0.17550.774
105_F109_T0.175460.774
57_R60_L0.174030.768
52_I55_V0.1740.768
41_P112_E0.173770.767
13_L34_L0.173660.766
52_I57_R0.173080.764
79_L83_D0.173070.764
67_L76_L0.173030.763
78_Q81_Q0.170580.753
43_M53_G0.17050.752
17_T31_S0.170.750
45_S112_E0.169050.746
65_A68_R0.168980.746
6_A9_A0.168790.745
15_F28_R0.16790.741
76_L79_L0.167580.739
103_V107_M0.167380.739
57_R61_A0.166720.736
5_I114_F0.166210.733
52_I56_N0.164630.726
41_P115_A0.16450.726
59_R67_L0.164070.724
17_T33_G0.1640.724
62_W97_A0.162560.717
15_F18_G0.162310.716
114_F119_R0.161350.712
63_F67_L0.161240.711
77_E81_Q0.160910.710
61_A93_L0.160650.709
6_A43_M0.160160.707
103_V106_L0.160040.706
56_N61_A0.159280.703
3_A40_T0.159170.702
49_W81_Q0.158970.701
24_A31_S0.158050.697
44_S50_S0.155220.685
13_L111_P0.154340.681
65_A71_R0.153890.679
23_L121_L0.152910.675
66_Y71_R0.151650.669
63_F66_Y0.151250.667
69_G74_D0.151050.666
79_L85_A0.150480.664
35_A92_A0.150150.663
3_A78_Q0.149340.659
59_R62_W0.148970.657
95_A99_S0.148880.657
30_V117_Y0.148780.656
10_T13_L0.148710.656
94_D99_S0.148570.656
18_G110_R0.14830.654
40_T97_A0.147420.650
53_G57_R0.14710.649
82_S86_F0.147080.649
59_R97_A0.146710.647
16_N28_R0.146610.647
44_S56_N0.146560.647
44_S51_G0.145390.642
59_R108_E0.145260.641
30_V99_S0.144950.640
33_G105_F0.144780.639
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
3u9wA0.984499.70.23
4gaaA0.976699.70.238
4fkeA0.937599.70.241
2xdtA0.945399.70.249
3se6A0.945399.70.254
1z5hA0.945399.70.261
2xq0A0.937599.70.264
3ciaA0.914199.70.276
3ebhA0.914199.70.278
3b34A0.914199.70.29

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