GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DHQ_synthase - 3-dehydroquinate synthase
Pfam: PF01761 (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: CL0224
Length: 260
Sequences: 6440
Seq/Len: 24.77
HH_delta: 0.08 (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
20_D24_E1.113313.537
33_I45_A0.882222.803
18_I48_A0.854682.715
168_D171_E0.827392.628
110_R200_E0.822672.614
42_G60_Q0.770552.448
164_I171_E0.744212.364
21_A25_A0.705632.242
57_P95_E0.683812.172
15_V44_L0.681682.166
7_E14_T0.679982.160
229_E233_K0.674392.142
105_K172_K0.670482.130
35_A45_A0.655772.083
17_K20_D0.650152.065
22_L27_L0.645022.049
5_A17_K0.644472.047
19_Y51_T0.643582.045
232_E238_T0.627121.992
225_E229_E0.622641.978
135_E226_R0.617211.961
239_S242_D0.615761.956
109_P113_R0.611021.941
21_A24_E0.597391.898
22_L56_I0.596841.896
108_P111_E0.584591.857
221_E225_E0.580291.843
185_G201_A0.557921.772
145_R148_D0.550611.749
167_Q174_L0.543371.726
182_H190_S0.539631.714
128_P132_E0.536931.706
15_V48_A0.532171.691
50_S90_T0.525411.669
14_T17_K0.52341.663
59_I96_A0.508191.614
12_L16_E0.485991.544
171_E174_L0.478811.521
7_E11_S0.471631.498
196_I201_A0.470981.496
73_I76_K0.467681.486
27_L31_D0.467341.485
228_E232_E0.467111.484
226_R229_E0.464781.477
102_S105_K0.464661.476
72_S76_K0.46371.473
114_S200_E0.460691.464
163_R167_Q0.460111.462
220_D223_D0.459661.460
47_F51_T0.459031.458
180_F206_M0.458131.455
42_G71_S0.454431.444
163_R233_K0.449711.429
122_Y157_S0.448371.424
107_L111_E0.4411.401
123_A146_D0.43391.378
207_V228_E0.432711.375
32_L59_I0.431251.370
211_R214_V0.427781.359
156_R171_E0.422911.344
114_S197_S0.418921.331
35_A42_G0.416061.322
112_I175_R0.411511.307
185_G189_E0.410331.304
155_K233_K0.405551.288
213_S223_D0.403551.282
15_V19_Y0.40141.275
16_E20_D0.400521.272
13_E16_E0.397561.263
33_I49_A0.392951.248
35_A60_Q0.384151.220
84_G87_L0.379431.205
20_D23_L0.379331.205
196_I204_I0.376981.198
214_V224_V0.375841.194
185_G202_V0.371511.180
22_L33_I0.369221.173
120_I147_P0.368391.170
11_S195_K0.366811.165
32_L57_P0.360391.145
174_L177_I0.360111.144
17_K21_A0.359111.141
104_L175_R0.354791.127
129_E132_E0.354571.126
9_S195_K0.354431.126
18_I44_L0.353051.122
229_E232_E0.35231.119
121_K206_M0.352021.118
102_S172_K0.351491.117
147_P212_L0.348471.107
72_S75_G0.340811.083
189_E201_A0.340361.081
35_A58_F0.340021.080
119_I150_L0.338971.077
148_D152_E0.33871.076
203_A236_L0.337941.074
152_E156_R0.334381.062
184_F205_G0.333511.060
12_L79_V0.332491.056
15_V51_T0.331981.055
225_E228_E0.33091.051
182_H189_E0.326871.038
49_A55_G0.325931.035
169_E175_R0.325791.035
182_H185_G0.325121.033
140_D143_E0.324261.030
222_D225_E0.32031.018
162_A166_E0.318361.011
197_S200_E0.315481.002
5_A9_S0.315121.001
109_P145_R0.313880.997
124_L227_I0.31370.997
9_S40_V0.313520.996
62_P99_I0.313430.996
13_E17_K0.310820.987
93_Q169_E0.309640.984
153_I156_R0.307730.978
74_G78_G0.30510.969
164_I168_D0.304710.968
11_S14_T0.304020.966
211_R215_R0.302480.961
33_I56_I0.301760.959
149_A152_E0.301680.958
237_P242_D0.300380.954
7_E17_K0.299980.953
163_R166_E0.296670.942
212_L223_D0.29620.941
59_I98_L0.295290.938
49_A56_I0.294280.935
200_E236_L0.293220.932
139_K233_K0.292250.928
122_Y130_L0.291930.927
116_L119_I0.290690.923
115_G178_L0.290150.922
238_T242_D0.288860.918
112_I169_E0.287640.914
124_L223_D0.287550.914
137_H140_D0.284280.903
145_R149_A0.282240.897
101_P154_I0.279870.889
228_E238_T0.279710.889
19_Y23_L0.278830.886
45_A58_F0.277610.882
22_L48_A0.277130.880
204_I207_V0.276980.880
214_V220_D0.274440.872
224_V228_E0.272770.867
130_L153_I0.272030.864
137_H143_E0.271090.861
203_A231_L0.270970.861
109_P235_G0.270770.860
129_E143_E0.269830.857
200_E237_P0.267990.851
44_L48_A0.267680.850
207_V231_L0.2660.845
81_F88_I0.265910.845
167_Q233_K0.265820.844
184_F187_A0.264850.841
165_V169_E0.263640.838
184_F208_F0.263450.837
42_G62_P0.262840.835
151_E216_L0.262330.833
13_E82_P0.260490.828
214_V222_D0.260110.826
9_S41_V0.25940.824
16_E19_Y0.259380.824
9_S14_T0.255020.810
129_E140_D0.254990.810
18_I21_A0.254690.809
7_E195_K0.254680.809
164_I173_G0.254120.807
39_G43_D0.253020.804
181_G202_V0.2530.804
116_L231_L0.251950.800
147_P150_L0.251120.798
184_F190_S0.250980.797
164_I177_I0.250750.797
181_G189_E0.250670.796
104_L107_L0.250390.795
210_A214_V0.24920.792
76_K79_V0.248820.790
186_H198_H0.248410.789
149_A153_I0.247570.786
101_P176_R0.24710.785
121_K202_V0.246920.784
135_E140_D0.246890.784
141_L145_R0.245350.779
219_L223_D0.244640.777
34_I59_I0.244520.777
50_S92_Y0.244170.776
118_E198_H0.243240.773
180_F183_T0.242690.771
210_A227_I0.242650.771
206_M231_L0.240990.766
61_V98_L0.240360.764
185_G190_S0.239580.761
181_G185_G0.237550.755
116_L162_A0.237330.754
231_L238_T0.235930.750
60_Q94_P0.235430.748
99_I104_L0.234950.746
180_F227_I0.234890.746
214_V221_E0.23470.746
105_K170_F0.234650.745
35_A41_V0.233470.742
43_D199_G0.233420.742
120_I230_L0.231630.736
111_E197_S0.231630.736
120_I227_I0.231080.734
16_E23_L0.230940.734
110_R197_S0.230750.733
209_A213_S0.230150.731
6_G44_L0.230080.731
78_G81_F0.229170.728
120_I124_L0.228450.726
111_E114_S0.228070.725
39_G198_H0.227920.724
36_I60_Q0.227790.724
112_I165_V0.227730.723
133_L137_H0.227410.722
110_R114_S0.227030.721
120_I234_L0.225980.718
143_E146_D0.225420.716
146_D150_L0.225350.716
21_A27_L0.225040.715
43_D198_H0.225010.715
11_S15_V0.224990.715
153_I157_S0.224640.714
184_F209_A0.222040.705
22_L25_A0.221960.705
109_P169_E0.221870.705
136_D139_K0.221380.703
146_D149_A0.221050.702
196_I200_E0.218580.694
178_L186_H0.218490.694
130_L133_L0.218490.694
164_I174_L0.218480.694
182_H191_L0.217480.691
197_S201_A0.216850.689
212_L216_L0.216740.689
58_F95_E0.216680.688
20_D83_G0.216450.688
113_R116_L0.216280.687
169_E174_L0.215620.685
60_Q97_V0.215270.684
113_R200_E0.214770.682
58_F92_Y0.214540.682
133_L153_I0.214220.681
148_D151_E0.213540.678
137_H141_L0.213420.678
202_V205_G0.212890.676
14_T44_L0.212830.676
72_S77_T0.21210.674
183_T187_A0.211630.672
182_H198_H0.21150.672
124_L131_F0.211420.672
43_D118_E0.210140.668
12_L15_V0.209740.666
152_E155_K0.209650.666
150_L154_I0.209630.666
63_T103_F0.209080.664
109_P166_E0.207130.658
151_E155_K0.206590.656
142_L145_R0.205970.654
116_L234_L0.20580.654
138_A142_L0.205720.654
213_S218_L0.205720.654
131_F135_E0.205540.653
54_R91_F0.203780.647
185_G188_L0.203680.647
131_F226_R0.203520.647
10_K118_E0.203390.646
166_E234_L0.202610.644
230_L234_L0.202510.643
135_E139_K0.201770.641
124_L206_M0.201640.641
72_S78_G0.201130.639
104_L112_I0.200470.637
120_I231_L0.200170.636
85_K186_H0.199230.633
132_E136_D0.198550.631
188_L240_L0.198340.630
7_E44_L0.198060.629
12_L47_F0.197770.628
119_I122_Y0.197720.628
212_L227_I0.197620.628
150_L153_I0.197340.627
124_L212_L0.197010.626
165_V174_L0.196980.626
109_P167_Q0.196960.626
113_R235_G0.196540.624
62_P97_V0.196080.623
218_L222_D0.196020.623
71_S76_K0.19590.622
183_T186_H0.19560.621
116_L178_L0.195420.621
153_I173_G0.195260.620
227_I231_L0.194870.619
76_K85_K0.194590.618
171_E175_R0.19360.615
147_P151_E0.193130.614
111_E119_I0.193060.613
121_K181_G0.19290.613
184_F189_E0.192060.610
113_R236_L0.191640.609
231_L234_L0.191480.608
182_H188_L0.191260.608
173_G176_R0.188830.600
45_A48_A0.18870.599
165_V175_R0.188560.599
181_G184_F0.187980.597
228_E239_S0.18780.597
31_D56_I0.187110.594
138_A141_L0.186370.592
232_E242_D0.186290.592
118_E121_K0.185880.591
15_V79_V0.185020.588
22_L52_Y0.184570.586
15_V47_F0.184550.586
20_D25_A0.184520.586
55_G92_Y0.183940.584
34_I61_V0.183550.583
49_A58_F0.182980.581
184_F188_L0.182980.581
154_I157_S0.182630.580
130_L157_S0.182380.579
169_E172_K0.182190.579
32_L35_A0.181970.578
19_Y22_L0.181970.578
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
3qbeA0.99231000.08
3okfA0.99621000.081
3clhA0.96921000.09
1xahA0.96921000.106
2gruA0.99621000.107
1ujnA0.951000.109
1sg6A11000.129
3bfjA0.93081000.238
1rrmA0.92311000.253
3ox4A0.93081000.255

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