GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DAHP_synth_1 - DAHP synthetase I family
Pfam: PF00793 (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: 270
Sequences: 3857
Seq/Len: 14.29
HH_delta: 0.134 (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
238_D241_K0.993743.895
29_E82_E0.913873.582
179_N182_D0.796023.120
81_S85_E0.791513.102
113_I127_A0.745182.921
19_V259_L0.647792.539
251_T254_Q0.595512.334
37_E87_L0.58252.283
82_E85_E0.558172.188
40_K44_E0.557072.183
45_K256_I0.54452.134
110_W164_I0.538322.110
164_I232_M0.529542.076
18_L90_P0.519232.035
105_A111_L0.508381.993
93_T108_V0.50781.990
256_I260_C0.500841.963
38_R41_E0.479791.881
246_G249_Q0.474741.861
154_H160_N0.473691.857
136_F154_H0.46811.835
82_E86_G0.451351.769
34_E237_P0.449551.762
34_E37_E0.446831.751
124_L154_H0.445381.746
35_Y237_P0.441791.732
37_E41_E0.435581.707
17_L266_T0.431171.690
102_E126_A0.422921.658
262_L265_I0.420171.647
75_P78_D0.411471.613
238_D254_Q0.409621.605
33_L37_E0.408481.601
30_E34_E0.407161.596
239_P262_L0.405411.589
205_N219_L0.40521.588
221_R261_I0.396671.555
40_K87_L0.390271.530
118_M142_A0.386841.516
29_E33_L0.383451.503
20_I92_A0.378221.482
99_E126_A0.373591.464
257_T261_I0.372961.462
220_A258_L0.372121.459
20_I198_I0.372061.458
196_P229_D0.371511.456
73_L103_Y0.371031.454
155_L163_N0.368941.446
33_L83_V0.36721.439
33_L87_L0.360261.412
127_A134_V0.35491.391
238_D251_T0.350331.373
97_D100_Q0.347691.363
51_P110_W0.341921.340
189_M193_T0.339031.329
18_L51_P0.338191.326
32_A79_I0.334291.310
93_T104_V0.333731.308
257_T260_C0.33351.307
151_A165_L0.330961.297
34_E38_R0.330641.296
17_L224_I0.329681.292
21_A266_T0.328191.286
83_V87_L0.327461.283
125_E157_L0.326281.279
101_A130_T0.326071.278
148_L152_E0.324981.274
155_L195_L0.324641.272
33_L86_G0.316211.239
208_K254_Q0.313531.229
74_D78_D0.311251.220
152_E156_F0.309691.214
43_G51_P0.30611.200
98_P101_A0.305761.198
104_V108_V0.305381.197
219_L222_A0.30511.196
217_P261_I0.304691.194
37_E86_G0.304211.192
37_E83_V0.301671.182
147_W189_M0.30051.178
126_A130_T0.30021.177
134_V154_H0.300081.176
38_R42_L0.300021.176
22_G27_E0.29991.175
103_Y106_D0.29891.172
81_S107_L0.298451.170
38_R253_G0.295921.160
121_Q153_K0.293851.152
129_G157_L0.293761.151
209_D215_L0.29151.143
105_A130_T0.290981.140
24_C27_E0.288821.132
40_K89_L0.288731.132
111_L132_K0.288281.130
101_A111_L0.286391.122
36_A80_L0.286181.122
41_E256_I0.284941.117
95_V101_A0.283591.112
39_L44_E0.280551.100
183_I219_L0.279441.095
103_Y107_L0.2791.094
84_K91_V0.27771.088
101_A127_A0.276611.084
126_A129_G0.275741.081
148_L192_K0.275071.078
151_A155_L0.272991.070
41_E44_E0.272291.067
186_V199_V0.272271.067
52_L89_L0.267861.050
78_D107_L0.265711.041
81_S84_K0.265121.039
28_S31_Q0.264891.038
91_V108_V0.264821.038
185_A189_M0.264471.037
22_G25_S0.262221.028
95_V111_L0.260021.019
97_D122_D0.259331.016
250_L258_L0.25841.013
42_L45_K0.257281.008
125_E156_F0.256281.004
98_P126_A0.255451.001
190_K229_D0.249580.978
39_L255_S0.249480.978
183_I199_V0.249420.978
128_S157_L0.248670.975
42_L256_I0.248240.973
164_I196_P0.247470.970
148_L193_T0.246040.964
222_A225_A0.245760.963
31_Q237_P0.245740.963
34_E252_Y0.245720.963
100_Q122_D0.244620.959
71_L75_P0.244560.959
178_Y207_R0.242230.949
98_P122_D0.241870.948
31_Q243_L0.24150.947
125_E129_G0.240640.943
56_A93_T0.23630.926
136_F150_A0.235080.921
123_L127_A0.235060.921
77_L256_I0.235040.921
142_A150_A0.234980.921
188_I215_L0.234920.921
72_G75_P0.234140.918
261_I264_E0.233440.915
102_E129_G0.233090.914
188_I192_K0.233060.913
95_V104_V0.232930.913
181_L185_A0.230520.904
131_G162_G0.230450.903
92_A110_W0.229920.901
37_E40_K0.227080.890
199_V219_L0.227060.890
263_W266_T0.226130.886
40_K88_G0.225960.886
84_K107_L0.225960.886
101_A126_A0.22590.885
198_I204_A0.225390.883
253_G257_T0.225310.883
21_A233_I0.22460.880
84_K87_L0.223870.877
218_P222_A0.223290.875
145_D177_N0.222460.872
254_Q257_T0.222220.871
145_D192_K0.222010.870
233_I258_L0.221720.869
222_A226_A0.221020.866
188_I191_K0.219910.862
220_A262_L0.219230.859
183_I223_A0.218950.858
255_S258_L0.217760.853
40_K43_G0.217580.853
155_L161_S0.217470.852
30_E37_E0.21730.852
102_E106_D0.217250.851
20_I232_M0.215630.845
258_L262_L0.215540.845
79_I83_V0.214970.843
33_L79_I0.214240.840
163_N195_L0.213290.836
20_I53_R0.21310.835
78_D81_S0.211410.829
39_L52_L0.211190.828
35_Y39_L0.210580.825
157_L160_N0.209850.822
255_S259_L0.20940.821
176_P182_D0.209010.819
18_L53_R0.208170.816
191_K209_D0.206540.810
147_W150_A0.206370.809
122_D125_E0.205360.805
199_V223_A0.204370.801
102_E130_T0.204040.800
255_S260_C0.203960.799
151_A195_L0.203720.798
31_Q35_Y0.203390.797
245_D248_Q0.202470.794
118_M139_G0.20170.791
26_I56_A0.200130.784
152_E155_L0.199950.784
235_S255_S0.199830.783
186_V197_V0.199640.782
18_L198_I0.199390.781
260_C263_W0.19910.780
83_V86_G0.198730.779
78_D82_E0.198470.778
21_A235_S0.198280.777
122_D126_A0.19740.774
26_I80_L0.196840.772
187_P226_A0.19670.771
111_L127_A0.196350.770
217_P257_T0.195970.768
57_Y116_R0.19560.767
240_G243_L0.195470.766
185_A188_I0.194880.764
43_G89_L0.193640.759
188_I207_R0.193390.758
244_S256_I0.193270.758
180_V184_A0.192180.753
180_V219_L0.19210.753
253_G256_I0.192020.753
221_R262_L0.191620.751
73_L106_D0.190910.748
241_K251_T0.190850.748
145_D149_A0.190580.747
144_I148_L0.190530.747
253_G260_C0.18970.744
239_P265_I0.189680.743
199_V220_A0.189620.743
105_A132_K0.188810.740
181_L219_L0.187950.737
35_Y38_R0.187790.736
184_A187_P0.187780.736
25_S68_F0.187420.735
262_L266_T0.187320.734
25_S67_S0.186580.731
151_A163_N0.185140.726
105_A131_G0.185120.726
36_A89_L0.18460.724
115_A140_T0.184440.723
36_A87_L0.183760.720
224_I262_L0.183670.720
186_V226_A0.183660.720
39_L42_L0.18360.720
223_A228_I0.1830.717
143_A146_E0.182550.715
187_P191_K0.182460.715
20_I51_P0.182160.714
114_G120_N0.181230.710
102_E131_G0.181170.710
24_C70_G0.17920.702
38_R237_P0.178880.701
68_F71_L0.177920.697
57_Y103_Y0.177280.695
215_L218_P0.177210.695
170_L185_A0.176720.693
90_P110_W0.176010.690
35_Y54_M0.175330.687
243_L246_G0.17290.678
53_R110_W0.172760.677
28_S243_L0.172440.676
178_Y264_E0.17160.673
160_N163_N0.171560.672
167_E170_L0.171520.672
29_E79_I0.171220.671
237_P252_Y0.170460.668
96_L100_Q0.169880.666
147_W168_R0.169870.666
117_L120_N0.169470.664
36_A91_V0.169150.663
51_P92_A0.168880.662
257_T264_E0.168660.661
98_P102_E0.168590.661
175_G182_D0.168430.660
100_Q103_Y0.167630.657
18_L45_K0.167420.656
25_S71_L0.167390.656
66_Y152_E0.166780.654
198_I229_D0.166480.653
43_G52_L0.1660.651
32_A52_L0.164270.644
38_R256_I0.164050.643
190_K197_V0.163170.640
110_W167_E0.163120.639
261_I265_I0.162730.638
144_I188_I0.162060.635
145_D148_L0.162010.635
208_K251_T0.161940.635
165_L189_M0.161620.633
33_L82_E0.161070.631
85_E107_L0.160770.630
250_L255_S0.160590.629
135_G232_M0.160580.629
96_L122_D0.160220.628
78_D106_D0.159770.626
224_I228_I0.15960.626
32_A35_Y0.15940.625
22_G245_D0.159360.625
135_G166_C0.159140.624
41_E45_K0.158820.622
21_A174_Y0.158780.622
38_R252_Y0.158590.622
180_V226_A0.158590.622
17_L262_L0.158180.620
94_E117_L0.157910.619
118_M150_A0.157530.617
26_I32_A0.157530.617
34_E253_G0.157380.617
113_I123_L0.157210.616
144_I185_A0.157010.615
180_V222_A0.156790.615
72_G77_L0.155660.610
51_P90_P0.155650.610
260_C264_E0.15550.609
53_R141_F0.155470.609
124_L134_V0.154780.607
173_G177_N0.15470.606
143_A177_N0.154640.606
238_D264_E0.154640.606
22_G70_G0.153390.601
128_S154_H0.15270.598
158_G162_G0.152570.598
205_N215_L0.15220.597
258_L266_T0.151980.596
128_S156_F0.151930.595
94_E114_G0.151550.594
101_A123_L0.151540.594
22_G71_L0.151070.592
62_R68_F0.150440.590
218_P264_E0.150250.589
221_R265_I0.149960.588
35_Y56_A0.149950.588
124_L139_G0.149790.587
111_L130_T0.149710.587
181_L199_V0.149610.586
175_G207_R0.149080.584
204_A219_L0.148430.582
68_F75_P0.148160.581
241_K254_Q0.147770.579
121_Q125_E0.147290.577
95_V127_A0.147290.577
32_A86_G0.147150.577
133_P162_G0.146710.575
23_P35_Y0.146290.573
222_A265_I0.146040.572
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
1vliA0.90371000.134
2wqpA0.91000.151
3nvtA0.9371000.169
1vs1A0.92591000.178
1vr6A0.9371000.18
3fs2A0.97411000.199
3tmlA0.97411000.201
2qkfA0.97781000.209
3sz8A0.98151000.211
1zcoA0.92591000.211

Page generated in 0.0176 seconds.