GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2753 - Protein of unknown function (DUF2753)
Pfam: PF10952 (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: 140
Sequences: 21716
Seq/Len: 155.11
HH_delta: 0.092 (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
16_D19_R3.278462.833
96_I115_N3.259642.817
108_D111_K3.217782.781
53_C72_Y3.124122.700
65_D68_Y3.087222.668
4_H23_H3.051332.637
57_A73_L2.791912.413
56_L72_Y2.755762.382
8_A24_Y2.726792.357
41_E44_D2.632012.275
74_Q99_L2.607082.253
99_L115_N2.461112.127
100_G116_P2.366322.045
7_L23_H2.295231.984
11_A19_R2.202881.904
60_W68_Y2.132261.843
103_K115_N2.065031.785
103_K111_K1.968771.701
60_W72_Y1.953421.688
21_I25_Q1.935211.672
11_A23_H1.926771.665
70_L106_L1.787441.545
70_L74_Q1.781211.539
73_L98_S1.762761.523
53_C75_L1.751331.514
113_H117_E1.675431.448
60_W65_D1.650151.426
59_F63_Q1.546051.336
10_Q14_E1.534641.326
97_D101_C1.449981.253
70_L103_K1.429041.235
103_K108_D1.427761.234
58_D98_S1.421411.228
11_A16_D1.40331.213
4_H26_Q1.384881.197
67_D106_L1.378061.191
111_K114_P1.32471.145
54_H98_S1.31491.136
61_R105_A1.304171.127
7_L11_A1.303531.127
31_S34_I1.274261.101
118_I121_L1.271951.099
26_Q29_S1.248621.079
70_L99_L1.247851.078
70_L102_C1.235141.067
99_L103_K1.234561.067
68_Y71_K1.230341.063
50_V84_I1.217131.052
5_T9_D1.202621.039
80_V95_F1.201561.038
56_L60_W1.144830.989
75_L82_T1.144820.989
87_C95_F1.126980.974
81_L95_F1.120910.969
26_Q30_L1.117690.966
81_L96_I1.113060.962
96_I118_I1.089030.941
73_L102_C1.06210.918
66_S105_A1.060910.917
50_V80_V1.055670.912
100_G119_A1.049440.907
9_D24_Y1.04420.902
61_R102_C1.039890.899
9_D12_F1.028370.889
102_C106_L1.025730.886
84_I87_C1.01970.881
70_L108_D1.014520.877
66_S102_C1.014480.877
12_F17_P1.004380.868
19_R22_L0.990990.856
104_K116_P0.985350.852
8_A27_A0.977230.845
54_H58_D0.977210.845
115_N118_I0.975450.843
100_G112_R0.974150.842
75_L83_L0.957410.827
61_R98_S0.953520.824
4_H27_A0.950040.821
72_Y75_L0.945020.817
116_P120_R0.93920.812
98_S101_C0.937280.810
61_R66_S0.936030.809
61_R73_L0.932990.806
22_L26_Q0.929240.803
118_I122_V0.928020.802
4_H30_L0.920380.795
54_H95_F0.903110.780
17_P21_I0.887160.767
21_I39_E0.884530.764
43_E63_Q0.883670.764
101_C104_K0.883670.764
27_A30_L0.872840.754
23_H26_Q0.853560.738
9_D13_K0.852610.737
58_D61_R0.836410.723
66_S106_L0.830780.718
42_L59_F0.826540.714
101_C116_P0.826390.714
96_I119_A0.815180.704
23_H27_A0.81490.704
7_L10_Q0.802850.694
104_K109_F0.798870.690
57_A80_V0.796470.688
6_L9_D0.795280.687
25_Q29_S0.793540.686
5_T27_A0.792790.685
69_E102_C0.791650.684
58_D62_S0.777210.672
71_K75_L0.773150.668
8_A20_S0.772320.667
74_Q103_K0.771820.667
101_C105_A0.759790.657
12_F24_Y0.750890.649
74_Q115_N0.747610.646
11_A14_E0.744530.643
112_R116_P0.737740.638
117_E121_L0.735560.636
88_P123_Q0.733330.634
39_E42_L0.731740.632
96_I122_V0.72770.629
25_Q28_L0.702470.607
80_V84_I0.692050.598
81_L99_L0.689820.596
73_L95_F0.686610.593
18_L39_E0.684960.592
58_D73_L0.683930.591
109_F113_H0.683120.590
50_V53_C0.679030.587
117_E120_R0.675220.584
22_L25_Q0.674830.583
31_S35_D0.673060.582
107_L112_R0.672090.581
19_R23_H0.668790.578
71_K74_Q0.662710.573
114_P118_I0.655930.567
111_K115_N0.645070.557
97_D119_A0.640350.553
54_H87_C0.633590.548
12_F20_S0.632940.547
80_V83_L0.630410.545
85_P88_P0.628250.543
23_H72_Y0.626840.542
62_S105_A0.622390.538
104_K112_R0.61430.531
84_I88_P0.613020.530
103_K106_L0.611820.529
50_V83_L0.60930.527
18_L22_L0.599310.518
74_Q82_T0.598390.517
20_S24_Y0.596310.515
53_C83_L0.592710.512
61_R69_E0.591090.511
66_S70_L0.590860.511
119_A122_V0.590440.510
110_M113_H0.589520.509
116_P119_A0.588720.509
61_R104_K0.584880.505
28_L32_E0.58380.505
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
4i2zA0.864399.50.092
4gywA0.935799.50.108
4gywA0.935799.50.125
3gyzA0.821499.40.175
1kt0A0.935799.30.188
1p5qA0.935799.30.191
4ga2A0.828699.30.204
3zheB0.828699.30.206
2h6fA0.935799.30.213
2pziA0.821499.30.214

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