GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2824 - Protein of unknown function (DUF2824)
Pfam: PF11039 (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: 151
Sequences: 13711
Seq/Len: 90.8
HH_delta: 0.319 (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
78_L114_L2.100253.046
99_T112_C1.972162.860
119_R122_H1.901352.757
85_C117_A1.888232.738
110_V113_R1.606522.330
113_R119_R1.565892.271
42_G49_L1.447992.100
83_L86_K1.439692.088
101_V109_R1.435672.082
87_W91_N1.4172.055
50_G73_F1.411762.047
109_R113_R1.368451.984
85_C97_V1.303431.890
81_G115_L1.297271.881
86_K90_E1.294731.878
78_L115_L1.265581.835
53_V80_I1.241271.800
109_R119_R1.193161.730
63_V94_F1.132791.643
101_V112_C1.13151.641
11_D71_P1.127231.635
53_V84_F1.101491.597
55_V88_L1.093551.586
88_L97_V1.030491.494
70_D73_F1.030281.494
108_G112_C1.018891.478
22_I26_S1.001881.453
69_Y77_A0.99551.444
21_D24_A0.986681.431
106_R110_V0.980061.421
96_N120_V0.973991.412
103_D122_H0.961261.394
78_L82_R0.930411.349
111_I115_L0.92461.341
106_R109_R0.923291.339
82_R115_L0.908561.318
44_Y47_G0.908041.317
52_I68_M0.906881.315
76_Y79_E0.881651.279
55_V84_F0.881131.278
48_Q72_G0.88021.276
83_L87_W0.875771.270
26_S30_D0.864921.254
85_C115_L0.856411.242
79_E83_L0.85451.239
120_V124_D0.839881.218
9_N71_P0.835561.212
44_Y49_L0.83361.209
82_R86_K0.824831.196
69_Y76_Y0.803711.166
99_T108_G0.797281.156
43_V80_I0.791661.148
41_L87_W0.783011.135
51_G69_Y0.778461.129
43_V76_Y0.777971.128
99_T117_A0.777631.128
67_A112_C0.776511.126
87_W92_S0.756611.097
78_L111_I0.750811.089
77_A111_I0.741561.075
45_E50_G0.734381.065
11_D14_E0.723531.049
65_C81_G0.716371.039
48_Q73_F0.708821.028
81_G117_A0.69171.003
74_R107_Y0.678880.984
71_P74_R0.670450.972
25_G28_N0.66680.967
43_V51_G0.661860.960
105_T108_G0.659350.956
43_V69_Y0.656040.951
88_L94_F0.655850.951
48_Q70_D0.653580.948
27_N31_G0.64560.936
88_L92_S0.637420.924
41_L83_L0.624890.906
101_V108_G0.624040.905
82_R85_C0.61370.890
112_C117_A0.610020.885
121_G124_D0.603840.876
110_V114_L0.595430.863
20_A25_G0.592810.860
64_E98_I0.584950.848
86_K91_N0.584310.847
9_N13_I0.584040.847
50_G76_Y0.582010.844
67_A108_G0.580120.841
79_E82_R0.577740.838
100_F123_I0.571220.828
23_I26_S0.560510.813
101_V105_T0.555630.806
12_L74_R0.54530.791
73_F76_Y0.543810.789
23_I27_N0.530970.770
59_Q62_V0.530450.769
64_E100_F0.524140.760
75_G111_I0.519380.753
40_Y54_Y0.517160.750
21_D25_G0.50820.737
120_V123_I0.507950.737
76_Y80_I0.505440.733
25_G30_D0.504860.732
64_E68_M0.502270.728
20_A24_A0.481210.698
10_I14_E0.481130.698
75_G110_V0.47910.695
55_V92_S0.47860.694
45_E73_F0.477540.693
103_D109_R0.47690.692
69_Y74_R0.475740.690
27_N30_D0.475030.689
98_I120_V0.46960.681
107_Y110_V0.469410.681
40_Y44_Y0.466360.676
107_Y111_I0.463960.673
57_E94_F0.462040.670
69_Y80_I0.461140.669
81_G111_I0.458750.665
13_I18_N0.447690.649
10_I13_I0.446830.648
49_L52_I0.445840.647
41_L44_Y0.445450.646
108_G111_I0.440210.638
106_R113_R0.438690.636
75_G107_Y0.434990.631
41_L84_F0.432350.627
67_A81_G0.425520.617
67_A77_A0.423120.614
63_V97_V0.422310.612
39_L87_W0.421650.611
85_C90_E0.415010.602
45_E48_Q0.412270.598
64_E67_A0.410850.596
97_V117_A0.409740.594
105_T109_R0.404170.586
18_N22_I0.403930.586
66_H108_G0.401850.583
80_I83_L0.401180.582
77_A112_C0.400670.581
44_Y50_G0.397120.576
81_G97_V0.396620.575
21_D29_G0.395210.573
24_A28_N0.393370.570
77_A80_I0.387840.562
58_I62_V0.385560.559
22_I25_G0.378020.548
96_N124_D0.377280.547
81_G112_C0.377080.547
54_Y66_H0.376490.546
40_Y68_M0.375810.545
63_V98_I0.372530.540
52_I66_H0.369290.536
58_I61_S0.36880.535
17_G20_A0.368540.534
65_C108_G0.365730.530
69_Y73_F0.365140.530
79_E86_K0.36170.525
53_V81_G0.360930.523
11_D74_R0.35920.521
52_I101_V0.356880.518
77_A81_G0.351620.510
38_Q54_Y0.347420.504
45_E76_Y0.346220.502
20_A23_I0.345340.501
23_I30_D0.341410.495
102_P105_T0.341180.495
39_L92_S0.339370.492
65_C112_C0.338030.490
57_E63_V0.336140.487
75_G114_L0.335660.487
20_A28_N0.332960.483
36_P39_L0.331960.481
75_G78_L0.331670.481
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
3tcvA199.70.319
3pzjA0.966999.70.337
3shpA0.960399.70.339
4k4lA0.980199.70.346
3eg7A0.980199.70.346
2vzyA0.993499.60.35
2z10A199.60.356
2zw5A0.986899.60.357
2qmlA0.980199.60.36
3tthA0.94799.60.361

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