GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4442 - Domain of unknown function (DUF4442)
Pfam: PF14539 (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: CL0050
Length: 132
Sequences: 5864
Seq/Len: 44.42
HH_delta: 0.104 (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
32_V95_T1.42132.881
24_E34_R1.300282.636
114_E122_V1.174822.381
78_K108_E1.119042.268
95_T116_T1.09922.228
54_F80_A1.096762.223
30_R95_T1.081132.192
25_E30_R1.075042.179
86_K121_E1.026972.082
25_E32_V1.02632.080
79_S83_D1.015562.059
33_V60_A1.009342.046
34_R93_T0.985361.997
34_R91_D0.965881.958
30_R97_E0.95451.935
58_E77_D0.954231.934
22_R34_R0.950731.927
85_L125_E0.921531.868
32_V93_T0.911941.849
53_L124_A0.860541.744
57_A126_A0.845051.713
116_T122_V0.843271.709
88_A123_V0.833581.690
117_D121_E0.803991.630
27_D30_R0.792911.607
112_P125_E0.787071.595
54_F84_F0.756131.533
24_E32_V0.754231.529
54_F82_I0.753571.528
61_Y113_V0.75331.527
116_T120_G0.748161.517
97_E114_E0.733311.486
114_E125_E0.71661.453
61_Y128_I0.714711.449
97_E112_P0.701241.421
65_L109_L0.699711.418
57_A113_V0.679031.376
35_L52_A0.678941.376
99_T112_P0.675681.370
57_A115_I0.656231.330
110_T129_T0.645221.308
81_E127_T0.636751.291
60_A94_A0.624921.267
88_A92_V0.59641.209
112_P127_T0.584791.185
79_S129_T0.578511.173
38_R41_N0.570581.157
29_G67_S0.554051.123
37_L48_I0.550941.117
83_D125_E0.539151.093
100_E110_T0.530521.075
100_E108_E0.52331.061
41_N52_A0.519321.053
82_I124_A0.508821.031
37_L42_R0.505531.025
110_T127_T0.496321.006
93_T116_T0.494141.002
61_Y111_V0.49150.996
56_L94_A0.481580.976
39_P42_R0.477590.968
35_L56_L0.469970.953
91_D118_A0.469380.951
43_N47_T0.467620.948
53_L115_I0.460680.934
122_V125_E0.459480.931
77_D128_I0.454720.922
94_A113_V0.447170.906
64_L96_A0.425930.863
51_G55_T0.421130.854
61_Y130_W0.417150.846
36_P91_D0.415650.843
79_S127_T0.409540.830
85_L122_V0.409260.830
28_P68_N0.405210.821
64_L111_V0.405050.821
95_T114_E0.400520.812
48_I88_A0.392560.796
23_I63_L0.391950.795
56_L115_I0.386880.784
80_A126_A0.378530.767
78_K129_T0.371080.752
80_A128_I0.365020.740
94_A98_L0.364510.739
23_I33_V0.36250.735
53_L123_V0.361520.733
47_T76_W0.359880.730
43_N50_A0.355150.720
57_A82_I0.352380.714
44_H62_G0.349120.708
93_T117_D0.344440.698
43_N49_H0.3430.695
82_I126_A0.342730.695
92_V98_L0.340780.691
93_T118_A0.337090.683
21_I33_V0.336650.682
96_A113_V0.328080.665
65_L130_W0.325510.660
31_V64_L0.322180.653
77_D130_W0.32080.650
22_R36_P0.318880.646
52_A55_T0.317740.644
57_A124_A0.314820.638
21_I35_L0.312510.633
96_A111_V0.310490.629
80_A84_F0.308960.626
59_P63_L0.307730.624
53_L84_F0.304960.618
39_P90_G0.304480.617
26_V67_S0.302590.613
28_P67_S0.301460.611
113_V128_I0.299380.607
65_L111_V0.299280.607
77_D80_A0.298950.606
31_V67_S0.293830.596
109_L130_W0.292490.593
47_T87_P0.292090.592
64_L98_L0.291380.591
50_A84_F0.290690.589
83_D127_T0.288780.585
98_L111_V0.287870.584
92_V100_E0.286760.581
94_A100_E0.28480.577
49_H52_A0.284790.577
33_V63_L0.284750.577
70_G73_Y0.284620.577
49_H56_L0.283970.576
108_E129_T0.281730.571
66_M75_V0.27950.567
21_I59_P0.275030.558
54_F128_I0.274570.557
66_M74_R0.270970.549
99_T125_E0.270920.549
67_S71_D0.269070.545
20_G40_R0.268350.544
62_G65_L0.266970.541
48_I92_V0.264870.537
118_A121_E0.263310.534
75_V130_W0.262390.532
45_V74_R0.25990.527
117_D123_V0.259240.525
61_Y65_L0.258470.524
29_G97_E0.258040.523
33_V56_L0.257420.522
33_V59_P0.256670.520
51_G58_E0.255740.518
65_L75_V0.254730.516
86_K100_E0.254710.516
20_G38_R0.254340.516
37_L41_N0.254320.516
42_R45_V0.253370.514
50_A77_D0.251350.510
43_N51_G0.250980.509
115_I124_A0.250960.509
77_D84_F0.248460.504
49_H59_P0.244110.495
41_N49_H0.240720.488
36_P41_N0.240380.487
49_H58_E0.239960.486
97_E116_T0.239590.486
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
1yocA0.969799.80.104
1sc0A0.962199.80.14
3gekA0.886499.80.146
3hduA0.977399.80.158
3e8pA0.977399.80.163
1sh8A0.969799.80.167
3f1tA0.969799.80.175
3e1eA0.969799.80.179
1t82A0.984899.80.18
3dkzA0.969799.80.184

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