GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
WaaY - Lipopolysaccharide core biosynthesis protein (WaaY)
Pfam: PF06176 (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: CL0016
Length: 229
Sequences: 10765
Seq/Len: 47.01
HH_delta: 0.162 (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
167_L176_I1.627563.424
141_A209_G1.601833.370
37_K49_L1.530723.220
49_L56_K1.475573.104
50_I57_Y1.392552.929
38_V46_Y1.368012.878
123_E174_R1.282742.698
143_K173_I1.254052.638
50_I59_L1.115172.346
145_V206_K1.10862.332
166_F173_I1.083242.279
38_V41_N1.046352.201
149_K153_K1.041072.190
148_I161_P0.980152.062
185_N188_K0.978592.059
49_L124_Y0.973922.049
144_I166_F0.972912.047
131_N164_G0.965042.030
148_I206_K0.961582.023
93_R99_E0.952432.004
94_N150_Q0.907041.908
161_P208_F0.885411.863
34_K51_E0.86821.826
147_A175_I0.863221.816
141_A212_L0.857091.803
160_D165_N0.856381.801
140_L173_I0.830541.747
126_E170_N0.823961.733
189_A201_I0.804541.692
141_A206_K0.801891.687
101_A123_E0.791141.664
129_E132_D0.786061.654
142_E146_E0.779211.639
36_I51_E0.775631.632
38_V48_A0.764891.609
156_F181_K0.751231.580
59_L121_L0.737211.551
189_A192_M0.715911.506
51_E56_K0.706471.486
47_V58_I0.703261.479
148_I152_H0.695171.462
125_I169_S0.680751.432
168_V173_I0.669341.408
42_T45_N0.658981.386
61_E119_V0.650961.369
169_S174_R0.646311.360
57_Y121_L0.646151.359
33_Y102_D0.640571.347
163_P208_F0.636491.339
165_N177_D0.632011.329
99_E123_E0.629631.324
131_N135_D0.624221.313
166_F208_F0.617371.299
125_I174_R0.614431.292
36_I49_L0.60441.271
162_H177_D0.602731.268
98_T125_I0.586591.234
85_L88_N0.584191.229
139_D143_K0.576651.213
159_G197_R0.574121.208
41_N46_Y0.565021.189
51_E54_G0.561411.181
146_E149_K0.559431.177
127_G172_G0.5481.153
161_P175_I0.543591.143
96_G147_A0.538281.132
144_I161_P0.53191.119
85_L92_I0.53121.117
158_H161_P0.529091.113
162_H165_N0.528981.113
85_L89_T0.52861.112
48_A61_E0.527531.110
144_I173_I0.520191.094
160_D179_Q0.519411.093
211_Y217_K0.519331.092
206_K209_G0.511341.076
151_L178_T0.509381.072
144_I147_A0.502631.057
144_I208_F0.500391.053
61_E117_S0.49981.051
150_Q153_K0.494371.040
88_N181_K0.492761.037
197_R201_I0.491991.035
131_N211_Y0.485191.021
163_P211_Y0.482931.016
55_K101_A0.472360.994
58_I124_Y0.469140.987
96_G146_E0.467350.983
192_M201_I0.466260.981
91_K154_H0.45620.960
201_I205_Y0.451650.950
148_I175_I0.447590.942
210_Y219_F0.444880.936
39_F124_Y0.443710.933
40_K47_V0.443110.932
50_I121_L0.44050.927
83_S87_N0.440090.926
133_I168_V0.436210.918
124_Y128_V0.434780.915
92_I156_F0.433390.912
94_N97_F0.430660.906
100_P122_M0.427690.900
151_L156_F0.42570.895
191_D204_P0.423360.891
145_V203_N0.423340.891
96_G99_E0.423060.890
56_K124_Y0.419120.882
93_R150_Q0.414510.872
98_T122_M0.412830.868
169_S172_G0.41110.865
36_I56_K0.407850.858
33_Y121_L0.406880.856
158_H165_N0.403330.848
105_L108_E0.400480.842
160_D177_D0.398920.839
203_N207_N0.398590.838
125_I167_L0.397480.836
46_Y63_R0.396590.834
155_G199_Y0.394940.831
105_L119_V0.392950.827
150_Q154_H0.391440.823
35_I61_E0.391070.823
88_N156_F0.390870.822
202_K205_Y0.389350.819
128_V132_D0.388960.818
190_N204_P0.388490.817
159_G182_R0.387640.815
35_I38_V0.387090.814
35_I50_I0.386940.814
96_G143_K0.38540.811
131_N163_P0.381180.802
126_E169_S0.37880.797
57_Y60_K0.378060.795
204_P207_N0.37590.791
46_Y61_E0.375850.791
97_F151_L0.373340.785
98_T176_I0.371160.781
40_K58_I0.368780.776
35_I48_A0.368620.775
210_Y214_L0.367910.774
59_L119_V0.364420.767
42_T58_I0.363760.765
141_A145_V0.361650.761
163_P187_R0.361350.760
32_N52_I0.360740.759
125_I176_I0.360560.758
152_H202_K0.358510.754
129_E164_G0.358440.754
99_E174_R0.354850.746
133_I140_L0.351760.740
45_N60_K0.350990.738
197_R200_N0.350880.738
41_N63_R0.350110.736
156_F183_M0.349550.735
86_I90_D0.347370.731
36_I50_I0.345680.727
87_N91_K0.345110.726
144_I175_I0.344920.726
100_P120_L0.341560.718
100_P104_Y0.341150.718
202_K207_N0.338990.713
192_M197_R0.33870.712
178_T181_K0.338430.712
192_M196_E0.331960.698
89_T122_M0.33110.696
97_F150_Q0.330680.696
134_E211_Y0.327570.689
85_L179_Q0.326750.687
42_T47_V0.32570.685
140_L168_V0.324960.684
208_F212_L0.321830.677
91_K183_M0.32180.677
144_I206_K0.32170.677
98_T123_E0.320650.675
151_L175_I0.318190.669
43_K160_D0.316880.667
140_L212_L0.316430.666
97_F100_P0.314720.662
80_S83_S0.313930.660
143_K146_E0.313430.659
157_Y184_S0.313230.659
92_I150_Q0.311980.656
94_N98_T0.30910.650
57_Y101_A0.308410.649
108_E116_S0.308380.649
189_A205_Y0.306850.645
104_Y107_A0.306290.644
33_Y57_Y0.305430.642
85_L178_T0.303250.638
97_F102_D0.303070.638
145_V149_K0.300340.632
147_A174_R0.299810.631
159_G192_M0.29970.630
200_N203_N0.297590.626
192_M205_Y0.297210.625
187_R211_Y0.296950.625
209_G212_L0.296010.623
147_A150_Q0.294720.620
31_N34_K0.293020.616
184_S187_R0.292820.616
84_R87_N0.291010.612
152_H199_Y0.288820.608
97_F147_A0.287090.604
191_D201_I0.287030.604
86_I100_P0.286870.603
39_F49_L0.284820.599
157_Y197_R0.279370.588
134_E163_P0.278960.587
65_E91_K0.278810.586
87_N90_D0.278730.586
104_Y108_E0.277490.584
165_N179_Q0.276190.581
128_V176_I0.276150.581
42_T179_Q0.274970.578
47_V160_D0.2740.576
127_G169_S0.273630.576
42_T177_D0.27110.570
62_P82_Y0.269240.566
82_Y85_L0.268810.565
62_P118_Y0.268810.565
130_L134_E0.267480.563
56_K126_E0.266760.561
95_E146_E0.266170.560
64_E67_R0.265750.559
92_I151_L0.264530.556
157_Y201_I0.263770.555
125_I128_V0.262450.552
128_V136_I0.261670.550
148_I203_N0.260910.549
204_P219_F0.260660.548
102_D105_L0.260610.548
211_Y218_K0.260420.548
158_H175_I0.259850.547
34_K37_K0.257470.542
98_T174_R0.255910.538
143_K166_F0.25390.534
175_I178_T0.253090.532
160_D181_K0.252540.531
167_L177_D0.251270.529
130_L212_L0.248170.522
35_I59_L0.248030.522
36_I48_A0.247130.520
42_T165_N0.24660.519
190_N205_Y0.246190.518
153_K199_Y0.245960.517
60_K177_D0.245550.517
143_K147_A0.244970.515
52_I56_K0.244830.515
173_I206_K0.244480.514
123_E169_S0.243830.513
159_G178_T0.243720.513
140_L144_I0.243250.512
141_A213_I0.242830.511
139_D172_G0.241910.509
106_A117_S0.238720.502
93_R154_H0.238390.501
214_L217_K0.238350.501
94_N147_A0.237910.500
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
3fpqA0.92141000.162
3ubdA0.89081000.166
3omvA0.90391000.171
4g3fA0.89961000.176
3v5wA0.9521000.178
4im0A0.86031000.179
4fieA0.92581000.183
3hyhA0.85591000.187
4f9cA0.87341000.19
4g31A0.83411000.191

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