GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF756 - Domain of unknown function (DUF756)
Pfam: PF05506 (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: 89
Sequences: 573
Seq/Len: 6.44
HH_delta: 0.812 (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
73_D85_R0.447013.218
54_A57_Q0.37722.716
72_Y88_G0.360562.596
51_Y61_L0.298552.149
16_D19_T0.248961.792
75_T83_L0.234431.688
25_T60_S0.227921.641
40_D49_W0.225541.624
36_F53_V0.214051.541
41_N75_T0.211981.526
7_Y39_Y0.211761.525
13_A22_L0.211121.520
9_P36_F0.206341.485
36_F76_V0.205981.483
77_T83_L0.198241.427
37_T50_T0.187231.348
21_N65_L0.178411.284
65_L70_G0.174971.260
71_W89_R0.174641.257
14_R17_P0.171411.234
35_T48_P0.16871.215
33_A55_A0.16851.213
10_E84_R0.162651.171
36_F57_Q0.161931.166
49_W63_W0.161271.161
78_G81_G0.161241.161
35_T39_Y0.160831.158
51_Y78_G0.159161.146
51_Y59_V0.154041.109
43_Y46_G0.152531.098
11_V82_F0.1511.087
71_W87_A0.146881.057
49_W61_L0.145581.048
43_Y68_S0.1451.044
33_A59_V0.144921.043
39_Y79_P0.14411.037
26_L76_V0.143631.034
16_D82_F0.141681.020
38_V51_Y0.140841.014
7_Y80_N0.139521.004
24_L74_L0.138871.000
16_D20_G0.137780.992
44_G68_S0.136860.985
23_R62_T0.136750.984
34_V48_P0.135320.974
73_D87_A0.134430.968
27_S58_T0.133430.961
26_L34_V0.133330.960
63_W74_L0.132820.956
18_A27_S0.132570.954
35_T84_R0.132210.952
15_Y65_L0.130840.942
16_D85_R0.128920.928
12_T74_L0.12850.925
37_T77_T0.126550.911
38_V44_G0.125890.906
26_L53_V0.125290.902
10_E29_P0.124940.899
27_S63_W0.123890.892
40_D43_Y0.123120.886
75_T85_R0.123070.886
35_T50_T0.123050.886
10_E57_Q0.120890.870
24_L58_T0.120450.867
18_A21_N0.120440.867
20_G65_L0.118540.853
7_Y81_G0.118320.852
41_N74_L0.116770.841
36_F49_W0.113950.820
78_G89_R0.113740.819
43_Y71_W0.113380.816
32_A51_Y0.113250.815
40_D46_G0.112870.813
51_Y80_N0.11250.810
65_L87_A0.111910.806
58_T89_R0.111840.805
65_L68_S0.110810.798
38_V61_L0.109620.789
7_Y79_P0.108520.781
7_Y51_Y0.108480.781
9_P34_V0.108380.780
40_D44_G0.108270.779
24_L38_V0.107860.777
39_Y51_Y0.106370.766
54_A61_L0.106070.764
65_L71_W0.105870.762
77_T81_G0.10540.759
51_Y79_P0.105340.758
81_G86_F0.105050.756
31_S76_V0.104390.752
22_L28_N0.104340.751
28_N53_V0.10420.750
39_Y84_R0.103950.748
36_F82_F0.10370.747
30_G34_V0.102770.740
11_V26_L0.102570.738
32_A79_P0.10250.738
10_E27_S0.102280.736
9_P13_A0.101710.732
38_V50_T0.101220.729
16_D71_W0.100950.727
32_A35_T0.100760.725
42_A71_W0.100620.724
38_V49_W0.100490.723
24_L68_S0.100270.722
53_V67_A0.099830.719
34_V78_G0.099710.718
12_T79_P0.099590.717
58_T66_A0.099540.717
11_V18_A0.098640.710
16_D25_T0.097920.705
40_D77_T0.097820.704
26_L61_L0.097520.702
70_G86_F0.097240.700
43_Y89_R0.096820.697
46_G64_P0.096550.695
16_D23_R0.096130.692
15_Y21_N0.095940.691
19_T23_R0.094660.681
35_T52_T0.094420.680
38_V83_L0.094390.680
42_A47_G0.094040.677
18_A22_L0.094010.677
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
2x3cA0.921391.70.812
1sddA0.955157.10.865
2ccwA0.966350.70.87
2ys4A148.40.871
3abzA0.988843.50.875
4enzA0.932641.90.876
2wnwA0.707941.40.877
2dv6A0.910138.70.878
2r7eA0.955134.80.881
2nt0A0.696632.70.883
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