GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oxidored_q1 - NADH-Ubiquinoneplastoquinone (complex I) various chains
Pfam: PF00361 (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: CL0425
Length: 270
Sequences: 14428
Seq/Len: 53.44
HH_delta: -0.009 (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
210_L247_G1.257054.148
37_K104_D0.994683.282
64_N67_D0.942323.110
203_S258_S0.846652.794
166_D225_R0.799762.639
7_F128_G0.783672.586
200_Y262_S0.768612.536
171_L215_A0.728082.403
62_S67_D0.666672.200
122_K175_S0.649292.143
106_Y114_S0.648242.139
90_L95_L0.646472.133
90_L149_L0.639652.111
52_G84_L0.630282.080
224_T229_K0.614282.027
226_N229_K0.595751.966
165_K228_S0.594651.962
148_I152_I0.58851.942
106_Y122_K0.556321.836
52_G88_G0.554111.828
95_L183_L0.542981.792
106_Y118_S0.530261.750
1_S6_L0.517471.708
170_L227_I0.508051.677
4_L132_F0.506571.672
33_E37_K0.494661.632
94_G102_L0.49331.628
237_M240_L0.482521.592
91_I98_F0.482151.591
86_L146_L0.479561.582
103_P173_Y0.477671.576
199_F262_S0.477171.575
104_D169_R0.476921.574
244_F248_L0.475931.571
144_N148_I0.473771.563
158_S177_S0.46981.550
96_F152_I0.468071.545
234_F241_S0.465971.538
211_L247_G0.46321.529
55_L81_G0.461041.521
130_L197_A0.454881.501
156_Y160_M0.453061.495
89_F128_G0.453011.495
150_G187_L0.452441.493
200_Y203_S0.452041.492
4_L68_L0.443261.463
17_S20_L0.442681.461
2_S66_S0.441631.457
157_G180_G0.441.452
22_I109_A0.439491.450
150_G185_G0.436511.440
118_S212_F0.435171.436
185_G266_I0.435081.436
164_Q169_R0.432121.426
160_M173_Y0.426721.408
18_S21_L0.425691.405
182_I197_A0.423131.396
196_G269_S0.42091.389
21_L113_V0.414491.368
165_K226_N0.413841.366
150_G180_G0.413331.364
214_L244_F0.40811.347
49_L88_G0.404551.335
157_G160_M0.404171.334
34_A108_S0.40261.329
83_I87_L0.400781.323
55_L59_F0.397691.312
143_S147_L0.395991.307
57_Y63_L0.395841.306
209_A213_L0.394921.303
115_A209_A0.393161.297
3_D63_L0.388131.281
17_S21_L0.384141.268
86_L90_L0.377491.246
18_S121_Q0.376071.241
264_W268_S0.374241.235
3_D64_N0.373771.233
54_I58_A0.373741.233
178_Q200_Y0.369491.219
41_I100_F0.36151.193
242_L246_L0.360361.189
45_G91_I0.359761.187
144_N147_L0.359131.185
196_G265_L0.358581.183
154_I180_G0.35851.183
249_L254_L0.357971.181
102_L106_Y0.357881.181
49_L53_I0.356311.176
24_F35_A0.355511.173
19_F35_A0.34881.151
52_G81_G0.348481.150
14_M121_Q0.347671.147
207_S259_G0.347221.146
204_H208_K0.342991.132
112_P220_R0.341991.129
7_F65_F0.337711.114
239_F243_L0.337571.114
95_L149_L0.335351.107
126_L201_L0.335221.106
8_W50_L0.333931.102
157_G177_S0.332351.097
110_P113_V0.331441.094
243_L247_G0.331041.092
250_S257_F0.331031.092
62_S68_L0.33051.091
67_D70_L0.329841.088
145_I148_I0.327981.082
205_S209_A0.327651.081
68_L81_G0.326971.079
203_S262_S0.324611.071
211_L248_L0.323151.066
126_L179_M0.320521.058
158_S174_S0.320251.057
221_R237_M0.318331.050
186_I197_A0.3181.049
152_I156_Y0.314461.038
239_F242_L0.312761.032
224_T230_L0.312381.031
111_P168_K0.309381.021
167_L215_A0.308761.019
127_Y131_R0.307491.015
32_I35_A0.307381.014
52_G85_I0.304461.005
80_L84_L0.300430.991
53_I85_I0.299810.989
103_P164_Q0.29940.988
5_F63_L0.29880.986
126_L182_I0.297950.983
150_G188_S0.296950.980
59_F81_G0.294310.971
96_F156_Y0.294280.971
175_S204_H0.29340.968
199_F203_S0.292210.964
16_L20_L0.292080.964
19_F42_Q0.291240.961
83_I145_I0.29080.960
253_G263_K0.290260.958
155_L159_I0.289580.956
22_I105_V0.288140.951
129_L183_L0.287030.947
4_L53_I0.285980.944
106_Y109_A0.285940.944
1_S10_F0.285070.941
48_L84_L0.28180.930
65_F69_F0.28020.925
265_L268_S0.28010.924
107_E166_D0.279670.923
48_L87_L0.27950.922
30_S108_S0.278430.919
11_L124_L0.278280.918
115_A213_L0.276490.912
15_S18_S0.276350.912
10_F13_L0.275170.908
222_Y233_L0.274890.907
111_P114_S0.274380.905
52_G56_L0.274340.905
93_L126_L0.273660.903
255_P260_F0.272260.898
147_L185_G0.271740.897
253_G257_F0.269510.889
208_K212_F0.269130.888
211_L214_L0.269040.888
96_F157_G0.268220.885
79_P83_I0.267140.882
111_P215_A0.26710.881
199_F261_F0.266040.878
167_L230_L0.265630.877
187_L197_A0.265570.876
215_A230_L0.264980.874
166_D226_N0.263660.870
8_W12_E0.263270.869
80_L83_I0.262610.867
28_S31_S0.262420.866
164_Q173_Y0.26240.866
250_S259_G0.26110.862
43_S46_S0.260760.860
41_I105_V0.260020.858
178_Q251_L0.258750.854
154_I184_L0.25830.852
107_E169_R0.25820.852
30_S107_E0.258090.852
160_M163_K0.255710.844
123_K179_M0.255540.843
126_L197_A0.254880.841
109_A113_V0.254630.840
174_S178_Q0.254490.840
109_A112_P0.254490.840
147_L150_G0.254080.838
31_S107_E0.253770.837
18_S117_L0.253640.837
151_L155_L0.253210.836
15_S46_S0.252830.834
150_G154_I0.252280.832
95_L98_F0.251690.831
120_V124_L0.250840.828
81_G85_I0.250560.827
165_K174_S0.250010.825
222_Y237_M0.249770.824
195_T199_F0.249560.824
147_L187_L0.249560.824
60_T64_N0.248770.821
123_K127_Y0.248380.820
66_S70_L0.248040.819
171_L211_L0.247890.818
25_S28_S0.247850.818
86_L129_L0.246860.815
178_Q208_K0.246630.814
181_W266_I0.24660.814
109_A114_S0.24660.814
201_L205_S0.24630.813
178_Q181_W0.24610.812
200_Y207_S0.245440.810
55_L58_A0.244520.807
100_F103_P0.243980.805
261_F265_L0.243750.804
102_L118_S0.24370.804
148_I151_L0.24370.804
93_L125_G0.243490.803
2_S64_N0.242580.800
11_L49_L0.241980.799
185_G189_L0.241870.798
250_S258_S0.241820.798
196_G266_I0.239930.792
15_S20_L0.239860.792
167_L225_R0.239830.791
12_E92_K0.239170.789
6_L9_V0.239090.789
222_Y230_L0.238780.788
130_L186_I0.238360.787
7_F49_L0.237830.785
207_S250_S0.237540.784
99_H103_P0.23720.783
202_I205_S0.237060.782
265_L269_S0.235820.778
49_L85_I0.235650.778
114_S212_F0.234710.775
214_L247_G0.234440.774
62_S65_F0.234240.773
3_D6_L0.234020.772
57_Y60_T0.233910.772
8_W19_F0.233210.770
112_P115_A0.231470.764
172_A175_S0.230550.761
42_Q121_Q0.230190.760
146_L187_L0.230010.759
150_G184_L0.229130.756
233_L237_M0.226910.749
188_S191_S0.226540.748
82_L86_L0.22630.747
109_A117_L0.226090.746
13_L17_S0.225090.743
119_G123_K0.224820.742
96_F99_H0.22480.742
145_I149_L0.224630.741
95_L179_M0.224430.741
49_L89_F0.222840.735
214_L243_L0.222170.733
22_I114_S0.221950.732
241_S245_L0.221650.731
34_A105_V0.221150.730
130_L198_L0.220890.729
225_R229_K0.220730.728
30_S33_E0.220640.728
28_S107_E0.220590.728
106_Y168_K0.220560.728
198_L202_I0.220290.727
182_I201_L0.219440.724
4_L56_L0.218970.723
15_S21_L0.218280.720
36_L40_I0.217730.718
50_L54_I0.217290.717
92_K168_K0.217080.716
238_P241_S0.215980.713
56_L68_L0.215640.712
55_L84_L0.215580.711
185_G196_G0.214780.709
232_G235_R0.214370.707
253_G259_G0.214110.707
2_S6_L0.21340.704
214_L240_L0.212580.701
157_G176_I0.212170.700
99_H176_I0.212160.700
114_S117_L0.210960.696
123_K205_S0.210680.695
92_K263_K0.209630.692
87_L90_L0.209250.691
204_H212_F0.209040.690
103_P176_I0.208690.689
159_I163_K0.208490.688
82_L136_L0.208380.688
132_F136_L0.208320.687
41_I45_G0.207960.686
168_K175_S0.207860.686
233_L238_P0.207550.685
147_L151_L0.207140.684
70_L134_S0.206970.683
234_F242_L0.206820.682
22_I117_L0.206750.682
200_Y266_I0.20660.682
221_R240_L0.206570.682
27_T32_I0.204890.676
105_V172_A0.204740.676
174_S208_K0.204610.675
45_G88_G0.204510.675
107_E118_S0.204290.674
178_Q207_S0.203940.673
248_L252_A0.203610.672
129_L186_I0.203440.671
119_G205_S0.20340.671
173_Y176_I0.202880.669
197_A200_Y0.201190.664
57_Y61_G0.200640.662
151_L154_I0.200590.662
69_F134_S0.200240.661
137_F190_N0.20020.661
260_F264_W0.199330.658
191_S195_T0.198590.655
15_S42_Q0.198580.655
119_G208_K0.19820.654
100_F104_D0.197820.653
168_K204_H0.196950.650
256_P261_F0.196950.650
8_W46_S0.196880.650
185_G197_A0.196410.648
164_Q170_L0.196390.648
11_L14_M0.195780.646
42_Q92_K0.195730.646
115_A212_F0.195520.645
114_S168_K0.195210.644
174_S204_H0.194420.642
11_L125_G0.19440.641
247_G258_S0.194210.641
160_M167_L0.1940.640
41_I91_I0.193760.639
14_M124_L0.19370.639
119_G204_H0.193510.639
122_K204_H0.19310.637
85_I135_L0.192590.636
118_S208_K0.192490.635
39_F43_S0.192170.634
234_F245_L0.191790.633
177_S257_F0.191750.633
236_K239_F0.191150.631
259_G263_K0.190450.628
185_G188_S0.18940.625
110_P114_S0.188710.623
168_K172_A0.188520.622
124_L177_S0.188190.621
154_I181_W0.187930.620
8_W53_I0.187880.620
245_L249_L0.187850.620
236_K240_L0.187540.619
211_L244_F0.187460.619
66_S69_F0.186690.616
147_L184_L0.186550.616
86_L149_L0.186370.615
108_S169_R0.186210.614
175_S208_K0.185430.612
134_S137_F0.185230.611
117_L121_Q0.185010.611
38_Y42_Q0.184130.608
147_L188_S0.183910.607
41_I104_D0.183610.606
118_S204_H0.183520.606
132_F135_L0.18330.605
8_W57_Y0.183120.604
49_L128_G0.182910.604
102_L117_L0.18280.603
56_L81_G0.182730.603
30_S104_D0.182570.602
12_E116_L0.182550.602
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
3rkoM1100-0.009
3rkoN1100-0.004
3rkoL0.9889100-0
4he8L0.98891000.001
4he8M0.99631000.021
4he8N0.93331000.071
4he8H0.82962.10.966
3rkoK0.27041.80.968
4he8K0.26671.40.97
4he8J0.44071.30.97

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