GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HMGL-like - HMGL-like
Pfam: PF00682 (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: CL0036
Length: 237
Sequences: 13015
Seq/Len: 54.92
HH_delta: 0.054 (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
12_S15_E1.312592.798
111_E115_K1.190482.538
144_E148_E1.172922.500
21_K52_A1.164582.483
173_R177_E1.114582.376
70_E116_Y1.081422.305
118_K152_D1.053562.246
169_A205_A0.995592.122
201_A204_E0.975452.079
173_R205_A0.965182.058
24_D55_N0.961382.049
108_E112_E0.952272.030
74_E78_E0.945762.016
75_A78_E0.941692.008
145_A148_E0.930521.984
174_A178_A0.886251.889
169_A201_A0.885021.887
48_R51_E0.875171.866
136_P174_A0.874531.864
71_R74_E0.849151.810
44_E47_R0.848681.809
144_E178_A0.826961.763
140_L178_A0.794941.695
145_A149_A0.792191.689
75_A79_A0.785251.674
17_L48_R0.783961.671
176_R184_L0.777431.657
169_A204_E0.77451.651
70_E74_E0.768921.639
44_E48_R0.752231.604
43_F75_A0.750261.599
176_R208_D0.743961.586
74_E120_L0.742391.583
111_E145_A0.741611.581
140_L144_E0.740181.578
47_R51_E0.735331.568
174_A177_E0.734051.565
22_A25_E0.732471.561
17_L21_K0.730461.557
186_F202_A0.725481.547
169_A173_R0.719891.535
112_E115_K0.709821.513
115_K119_E0.709331.512
18_E22_A0.706541.506
116_Y120_L0.697591.487
24_D56_A0.697181.486
135_D138_E0.696641.485
77_K122_Y0.693391.478
13_T48_R0.682741.455
140_L174_A0.68111.452
15_E18_E0.676391.442
138_E141_E0.669441.427
116_Y119_E0.668071.424
21_K25_E0.667881.424
141_E145_A0.658691.404
147_A180_P0.654661.396
200_L204_E0.654091.394
144_E147_A0.653871.394
70_E119_E0.651081.388
21_K24_D0.638571.361
17_L52_A0.637911.360
147_A182_I0.634341.352
197_A201_A0.634321.352
183_P208_D0.631161.346
114_V124_V0.622561.327
48_R52_A0.610961.302
141_E144_E0.608631.297
201_A205_A0.603581.287
170_E174_A0.601791.283
13_T17_L0.598431.276
195_A198_N0.592741.264
109_R112_E0.591861.262
77_K120_L0.586371.250
22_A26_A0.58631.250
74_E116_Y0.579671.236
108_E111_E0.576291.229
18_E21_K0.573781.223
73_V77_K0.554711.183
170_E173_R0.551811.176
199_A210_I0.551351.175
14_E18_E0.54381.159
111_E149_A0.541051.153
172_V184_L0.540691.153
114_V118_K0.529341.128
114_V149_A0.524811.119
50_R82_D0.522621.114
36_P60_A0.519851.108
203_L210_I0.511841.091
47_R79_A0.511041.089
90_V134_T0.507471.082
71_R75_A0.501581.069
117_A124_V0.496361.058
13_T44_E0.495951.057
110_I142_L0.490791.046
123_E152_D0.489511.044
143_A179_L0.487911.040
167_D170_E0.483061.030
107_L111_E0.48191.027
107_L148_E0.481121.026
43_F47_R0.478721.021
197_A200_L0.478561.020
136_P170_E0.476231.015
115_K149_A0.475721.014
156_L171_L0.471361.005
144_E179_L0.467790.997
112_E116_Y0.466260.994
35_F39_S0.462080.985
166_E204_E0.459660.980
24_D54_P0.45730.975
166_E170_E0.457280.975
92_D135_D0.455440.971
172_V205_A0.454120.968
23_L28_V0.453550.967
137_E141_E0.45170.963
34_G49_L0.450070.959
137_E140_L0.449130.957
83_I123_E0.448280.956
143_A154_I0.447480.954
186_F210_I0.444990.949
179_L182_I0.440620.939
168_V186_F0.438480.935
57_R82_D0.435260.928
172_V207_A0.428660.914
136_P139_L0.428580.914
40_E44_E0.428240.913
19_I22_A0.423050.902
47_R78_E0.422790.901
126_F142_L0.417230.889
136_P140_L0.416710.888
70_E120_L0.416130.887
146_L151_A0.411850.878
74_E77_K0.411610.877
43_F79_A0.411030.876
186_F207_A0.407590.869
76_A81_I0.404420.862
23_L31_I0.399150.851
172_V186_F0.398990.851
156_L175_L0.392260.836
175_L179_L0.390280.832
198_N201_A0.3860.823
171_L174_A0.384340.819
107_L145_A0.382740.816
140_L179_L0.38270.816
171_L175_L0.377180.804
143_A175_L0.375550.801
59_Q83_I0.374150.798
17_L45_Q0.371410.792
115_K118_K0.370460.790
167_D171_L0.369910.789
20_A49_L0.369740.788
27_G55_N0.369030.787
128_C139_L0.363050.774
33_V58_L0.361960.772
199_A203_L0.361070.770
14_E17_L0.359570.767
35_F38_A0.358450.764
78_E120_L0.357890.763
92_D138_E0.354890.757
66_E112_E0.352490.751
142_L145_A0.352480.751
125_A185_G0.348490.743
137_E178_A0.346830.739
164_T167_D0.344650.735
73_V84_I0.344070.733
152_D183_P0.343510.732
66_E70_E0.343070.731
131_A134_T0.342790.731
117_A122_Y0.342350.730
13_T45_Q0.340780.726
14_E48_R0.337080.719
155_Y185_G0.336690.718
163_M168_V0.333660.711
20_A31_I0.328530.700
139_L171_L0.327510.698
69_I72_A0.32570.694
90_V142_L0.325340.694
196_V199_A0.324750.692
30_Y59_Q0.323920.691
77_K116_Y0.321080.684
184_L207_A0.32050.683
140_L177_E0.317680.677
202_A207_A0.317590.677
65_N68_D0.316850.675
134_T139_L0.315730.673
57_R123_E0.315230.672
16_K49_L0.312790.667
137_E174_A0.311740.665
111_E148_E0.311340.664
70_E112_E0.308580.658
73_V117_A0.307220.655
168_V171_L0.307080.655
40_E43_F0.305840.652
128_C131_A0.303980.648
147_A179_L0.303970.648
82_D122_Y0.303360.647
133_R167_D0.302720.645
110_I146_L0.301780.643
73_V120_L0.300410.640
143_A147_A0.300390.640
166_E169_A0.300190.640
86_I109_R0.298840.637
185_G209_R0.298590.637
45_Q49_L0.298510.636
46_V60_A0.297630.634
23_L26_A0.294070.627
202_A206_G0.293990.627
203_L206_G0.292770.624
134_T138_E0.29220.623
161_G165_P0.291890.622
199_A212_G0.289940.618
52_A55_N0.289180.616
203_L208_D0.288420.615
39_S42_D0.287480.613
73_V116_Y0.286760.611
89_S92_D0.286730.611
143_A178_A0.285910.610
85_R155_Y0.28590.609
144_E180_P0.285080.608
128_C143_A0.283630.605
133_R163_M0.283140.604
147_A183_P0.282780.603
64_A113_A0.282750.603
182_I186_F0.281730.601
13_T16_K0.28160.600
203_L213_T0.281220.600
11_F15_E0.278490.594
11_F16_K0.277910.592
73_V121_G0.277520.592
37_F41_D0.277480.592
37_F40_E0.276870.590
85_R125_A0.27610.589
85_R127_G0.273350.583
88_I126_F0.272750.581
84_I117_A0.271980.580
125_A129_E0.27080.577
107_L142_L0.268320.572
20_A58_L0.267920.571
88_I110_I0.267670.571
138_E142_L0.266780.569
173_R201_A0.266020.567
74_E119_E0.265870.567
185_G212_G0.265440.566
107_L149_A0.265030.565
143_A146_L0.264350.564
36_P41_D0.263070.561
170_E177_E0.261450.557
173_R176_R0.261090.557
123_E153_I0.260440.555
118_K121_G0.260020.554
31_I56_A0.258640.551
66_E116_Y0.258630.551
166_E201_A0.258380.551
136_P167_D0.257920.550
30_Y83_I0.257230.548
86_I90_V0.256890.548
83_I125_A0.256120.546
132_S163_M0.255530.545
140_L147_A0.255510.545
133_R171_L0.255330.544
86_I124_V0.255210.544
43_F46_V0.255170.544
24_D27_G0.255090.544
176_R205_A0.255060.544
50_R58_L0.254040.542
110_I114_V0.254020.542
42_D45_Q0.253490.540
38_A43_F0.252560.538
57_R83_I0.252430.538
136_P171_L0.252240.538
72_A75_A0.251610.536
80_G122_Y0.251440.536
17_L49_L0.251170.535
17_L20_A0.250630.534
60_A81_I0.246140.525
30_Y57_R0.245330.523
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
3rmjA11000.054
3eegA11000.071
3bleA0.97891000.074
3ewbX11000.078
3ivsA0.97891000.112
2ztjA0.97471000.113
1rqbA0.94091000.123
1nvmA0.93671000.124
4jn6A0.93671000.126
3hq1A11000.127

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