GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cons_hypoth95 - Conserved hypothetical protein 95
Pfam: PF03602 (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: CL0063
Length: 183
Sequences: 5351
Seq/Len: 29.24
HH_delta: 0.171 (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
57_G70_F1.162013.392
45_R67_S1.108933.237
116_D144_N1.072973.132
143_L147_G1.039333.033
72_E78_I0.946462.762
67_S95_R0.930232.715
47_L115_F0.928372.710
51_A70_F0.900092.627
69_V115_F0.889162.595
75_R98_K0.879472.567
69_V97_I0.834712.436
51_A81_I0.807012.355
45_R115_F0.749972.189
78_I96_V0.726092.119
58_L85_L0.668121.950
73_K100_D0.598031.745
99_G104_F0.571641.668
78_I98_K0.570491.665
57_G68_V0.570471.665
75_R79_K0.569151.661
85_L96_V0.564431.647
85_L94_I0.562781.643
30_E34_N0.560631.636
46_V56_L0.542291.583
69_V95_R0.515591.505
29_R55_A0.51461.502
45_R69_V0.511111.492
49_L71_V0.51081.491
79_K83_K0.49751.452
100_D103_K0.490321.431
79_K82_K0.488821.427
58_L84_N0.47951.400
132_E135_E0.476151.390
131_E135_E0.453031.322
50_F133_L0.447111.305
144_N147_G0.444391.297
83_K86_E0.444311.297
72_E77_A0.436891.275
70_F81_I0.434971.270
31_A34_N0.432351.262
51_A72_E0.427421.247
46_V119_F0.423621.236
71_V104_F0.421561.230
104_F108_L0.42111.229
61_L94_I0.420251.227
118_I147_G0.419171.223
112_G141_N0.418831.222
86_E91_E0.416091.214
28_V31_A0.414721.210
46_V117_I0.410461.198
56_L119_F0.410371.198
70_F94_I0.406411.186
51_A57_G0.403061.176
41_L44_A0.399071.165
48_D54_G0.391291.142
47_L118_I0.390661.140
125_A154_S0.372371.087
61_L68_V0.366631.070
61_L70_F0.357221.043
115_F118_I0.350041.022
81_I96_V0.348261.016
97_I104_F0.347461.014
44_A116_D0.345911.010
45_R114_K0.341680.997
50_F123_P0.340550.994
49_L101_A0.339040.990
128_L133_L0.33580.980
82_K86_E0.335260.979
45_R116_D0.334690.977
78_I82_K0.328440.959
80_I84_N0.326950.954
48_D57_G0.325150.949
45_R66_K0.322390.941
154_S157_E0.320170.934
120_L149_I0.318370.929
124_Y152_E0.317070.925
45_R113_E0.316190.923
125_A156_K0.313170.914
31_A35_I0.311330.909
27_R30_E0.311050.908
71_V97_I0.311030.908
46_V60_A0.310430.906
83_K87_K0.307080.896
38_P44_A0.306260.894
68_V94_I0.301250.879
67_S113_E0.300360.877
137_L147_G0.298620.872
21_T24_T0.295530.863
32_L56_L0.29210.853
45_R144_N0.290850.849
43_G66_K0.288580.842
41_L65_A0.284790.831
59_E62_S0.28280.825
35_I150_I0.281920.823
21_T77_A0.281180.821
99_G103_K0.280710.819
90_L94_I0.278680.813
114_K141_N0.275090.803
84_N87_K0.274510.801
48_D71_V0.268770.784
117_I150_I0.268640.784
74_N77_A0.268570.784
50_F100_D0.267810.782
114_K144_N0.265890.776
44_A117_I0.263710.770
121_D124_Y0.26360.769
21_T80_I0.260680.761
46_V68_V0.259580.758
21_T35_I0.256910.750
27_R31_A0.256310.748
76_K79_K0.256310.748
137_L149_I0.255630.746
114_K142_L0.251970.735
71_V101_A0.249920.729
70_F96_V0.249260.728
82_K85_L0.24840.725
126_K154_S0.245160.716
48_D51_A0.242760.709
44_A65_A0.242610.708
75_R82_K0.24080.703
103_K106_L0.239890.700
61_L85_L0.23940.699
134_L138_A0.239010.698
29_R33_F0.237860.694
99_G107_K0.237270.693
20_N24_T0.235360.687
153_H157_E0.235290.687
29_R56_L0.235140.686
99_G105_L0.231330.675
47_L69_V0.230310.672
118_I143_L0.229810.671
136_L141_N0.227480.664
141_N145_E0.226890.662
53_S84_N0.226370.661
29_R59_E0.225310.658
78_I81_I0.224960.657
102_F132_E0.218790.639
48_D52_G0.218090.637
133_L136_L0.217650.635
108_L142_L0.216790.633
120_L151_I0.216780.633
56_L121_D0.216570.632
56_L123_P0.216020.630
61_L90_L0.215890.630
120_L125_A0.214330.626
46_V65_A0.212340.620
59_E63_R0.212080.619
118_I149_I0.211940.619
24_T121_D0.211320.617
91_E94_I0.208110.607
86_E89_G0.205820.601
73_K98_K0.20580.601
82_K98_K0.205230.599
24_T28_V0.204960.598
26_D152_E0.20480.598
33_F63_R0.204740.598
37_Q63_R0.203940.595
57_G96_V0.203280.593
34_N37_Q0.202750.592
87_K90_L0.201950.589
49_L102_F0.201230.587
123_P126_K0.201030.587
73_K126_K0.198990.581
71_V99_G0.198250.579
115_F142_L0.196640.574
127_G130_Y0.196090.572
95_R113_E0.195960.572
58_L94_I0.195630.571
51_A54_G0.195270.570
25_T28_V0.194730.568
121_D152_E0.192890.563
23_P56_L0.192720.562
24_T27_R0.192590.562
125_A155_K0.192470.562
53_S80_I0.191970.560
121_D125_A0.19190.560
136_L142_L0.191380.559
101_A133_L0.190450.556
134_L157_E0.190010.555
70_F85_L0.189960.554
73_K102_F0.189210.552
33_F62_S0.187650.548
81_I84_N0.186360.544
120_L150_I0.186250.544
77_A80_I0.18620.543
123_P152_E0.185040.540
114_K145_E0.184940.540
29_R32_L0.184370.538
48_D68_V0.183640.536
87_K95_R0.182720.533
143_L149_I0.181990.531
130_Y133_L0.181680.530
22_R152_E0.181020.528
23_P26_D0.180910.528
29_R50_F0.180590.527
127_G131_E0.180410.527
20_N32_L0.180030.525
123_P127_G0.179620.524
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
3p9nA0.978199.90.171
2fhpA0.989199.90.194
2iftA0.972799.90.196
2fpoA0.967299.90.197
1ws6A0.923599.90.279
2esrA0.91899.90.296
1o9gA0.961799.70.399
4dcmA0.950899.70.406
3dmgA0.945499.70.41
3lpmA0.92999.70.411

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