GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATP-synt_A - ATP synthase A chain
Pfam: PF00119 (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. )
Length: 215
Sequences: 3696
Seq/Len: 17.19
HH_delta: 0.288 (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
90_T95_F0.608343.187
66_F103_V0.569262.982
75_L199_F0.553022.897
124_V137_V0.472392.475
140_E143_S0.454712.382
81_G88_S0.445412.334
35_R38_N0.440882.310
87_F92_H0.402892.111
37_Q41_E0.399872.095
96_T156_F0.394322.066
70_L74_I0.374871.964
108_M144_E0.353081.850
88_S159_I0.350881.838
77_S89_P0.349861.833
46_F49_N0.34511.808
202_A206_T0.337421.768
38_N42_M0.334921.755
67_I206_T0.321271.683
173_I184_F0.319421.673
128_T136_M0.314041.645
190_F193_F0.309751.623
48_R64_F0.299181.567
109_I113_K0.298851.566
134_P138_P0.294531.543
124_V133_I0.291421.527
200_I204_V0.28021.468
112_I120_F0.276671.450
41_E45_D0.274591.439
33_P37_Q0.274481.438
162_G194_E0.274081.436
97_L101_L0.272641.428
93_L153_L0.271931.425
74_I99_L0.270411.417
194_E197_V0.26771.403
103_V209_T0.265331.390
52_K64_F0.264251.384
149_L152_S0.263411.380
100_A152_S0.262691.376
52_K57_K0.261341.369
75_L79_L0.25871.355
33_P41_E0.258491.354
79_L199_F0.254771.335
47_V71_F0.252741.324
30_K34_S0.252531.323
208_L212_Y0.252471.323
82_L195_L0.25241.322
67_I209_T0.249421.307
163_H194_E0.246321.291
49_N53_S0.244221.279
71_F202_A0.240771.261
74_I155_L0.239221.253
202_A205_F0.237881.246
147_R215_E0.236471.239
205_F208_L0.233391.223
54_N207_L0.233091.221
67_I210_S0.232961.221
135_F138_P0.232761.219
150_S166_L0.232641.219
160_F164_I0.231741.214
132_L136_M0.229181.201
166_L170_S0.226461.186
112_I119_F0.225111.179
82_L198_A0.223091.169
79_L195_L0.222041.163
93_L152_S0.221631.161
97_L152_S0.220571.156
107_I213_I0.219611.151
131_P134_P0.215261.128
149_L153_L0.215041.127
137_V141_L0.21171.109
169_L187_P0.211581.108
128_T133_I0.210341.102
105_L109_I0.210051.100
156_F160_F0.209611.098
91_S163_H0.20061.051
140_E144_E0.199361.044
138_P142_I0.19881.042
79_L198_A0.197731.036
96_T152_S0.197421.034
49_N52_K0.196861.031
73_F77_S0.196141.028
210_S214_S0.196041.027
51_V54_N0.193051.011
204_V214_S0.192921.011
40_V72_F0.191761.005
118_K121_S0.191141.001
161_A197_V0.190750.999
79_L83_F0.18930.992
58_K61_K0.18830.987
153_L157_G0.186980.980
193_F196_F0.186740.978
55_I210_S0.185960.974
104_W148_P0.183490.961
63_F110_S0.180430.945
190_F194_E0.180190.944
171_G175_S0.179850.942
74_I205_F0.179540.941
30_K61_K0.179160.939
117_F121_S0.177070.928
182_V186_L0.17650.925
151_L158_N0.175710.921
71_F162_G0.174710.915
147_R151_L0.174520.914
93_L97_L0.174050.912
133_I137_V0.173610.910
115_H122_H0.173180.907
130_L133_I0.172950.906
115_H118_K0.172740.905
110_S114_K0.171890.901
197_V204_V0.171430.898
91_S159_I0.171330.898
95_F98_A0.171010.896
126_P138_P0.170960.896
43_I72_F0.170950.896
211_L215_E0.170850.895
167_S171_G0.170660.894
125_P134_P0.170540.893
36_F40_V0.170030.891
45_D49_N0.169530.888
189_F193_F0.168910.885
125_P129_P0.168720.884
138_P141_L0.168580.883
141_L145_L0.168480.883
92_H156_F0.168390.882
123_F144_E0.168360.882
42_M45_D0.168250.881
52_K55_I0.16750.878
55_I59_S0.167370.877
104_W143_S0.167290.876
66_F102_I0.166530.872
146_I211_L0.166430.872
75_L202_A0.166380.872
58_K114_K0.166110.870
38_N45_D0.165840.869
169_L190_F0.165040.865
130_L138_P0.165030.865
47_V68_L0.164950.864
162_G197_V0.164910.864
42_M46_F0.163890.859
108_M112_I0.163830.858
201_Q204_V0.163090.854
47_V50_M0.162780.853
136_M139_I0.162320.850
69_T184_F0.161610.847
65_P69_T0.160570.841
31_V45_D0.159810.837
41_E53_S0.159720.837
150_S212_Y0.159460.835
88_S91_S0.15930.835
41_E186_L0.159130.834
39_F42_M0.158950.833
201_Q208_L0.15830.829
104_W107_I0.158190.829
108_M119_F0.157970.828
169_L186_L0.157780.827
200_I203_Y0.157710.826
72_F99_L0.157110.823
100_A148_P0.156580.820
146_I165_L0.156570.820
125_P140_E0.156490.820
124_V128_T0.1560.817
107_I212_Y0.155830.816
168_L193_F0.155660.816
116_G120_F0.154240.808
165_L190_F0.154060.807
32_V41_E0.153390.804
97_L100_A0.15320.803
155_L158_N0.153090.802
106_S213_I0.153010.802
64_F68_L0.152340.798
55_I135_F0.152280.798
151_L209_T0.152170.797
104_W144_E0.151690.795
84_P194_E0.151360.793
39_F43_I0.150970.791
190_F197_V0.150690.789
88_S147_R0.150670.789
40_V76_F0.150580.789
160_F163_H0.150250.787
207_L210_S0.149710.784
93_L98_A0.149260.782
51_V206_T0.14910.781
172_F206_T0.1490.781
201_Q205_F0.148750.779
44_V80_L0.148330.777
121_S130_L0.147420.772
207_L212_Y0.14620.766
81_G163_H0.145840.764
41_E44_V0.145620.763
100_A151_L0.145430.762
111_G119_F0.145310.761
30_K174_W0.144990.760
89_P113_K0.144820.759
90_T96_T0.14480.759
56_G65_P0.144130.755
77_S80_L0.142680.748
142_I146_I0.142470.746
160_F207_L0.14180.743
63_F213_I0.141620.742
122_H140_E0.141250.740
94_S98_A0.141220.740
122_H136_M0.141060.739
147_R168_L0.140710.737
50_M207_L0.140530.736
44_V72_F0.139560.731
157_G163_H0.13940.730
84_P147_R0.139060.729
73_F169_L0.138950.728
201_Q212_Y0.138770.727
50_M204_V0.13870.727
108_M111_G0.138510.726
139_I148_P0.138440.725
32_V175_S0.138170.724
121_S125_P0.137640.721
181_I184_F0.137050.718
72_F76_F0.136590.716
75_L103_V0.136590.716
196_F200_I0.136290.714
88_S163_H0.134930.707
97_L149_L0.134650.705
107_I144_E0.134510.705
71_F75_L0.134480.705
147_R169_L0.134330.704
134_P137_V0.134130.703
153_L203_Y0.134060.702
189_F192_I0.133950.702
82_L165_L0.133930.702
180_G183_P0.13380.701
76_F174_W0.133450.699
52_K61_K0.133010.697
88_S198_A0.132950.697
103_V107_I0.132860.696
76_F213_I0.13280.696
73_F95_F0.132620.695
32_V38_N0.132380.694
191_F195_L0.132030.692
175_S195_L0.131840.691
74_I199_F0.131730.690
173_I185_L0.131610.690
116_G119_F0.131540.689
35_R39_F0.131390.688
127_G131_P0.130970.686
194_E201_Q0.130340.683
111_G164_I0.130060.681
192_I195_L0.129650.679
66_F209_T0.129590.679
51_V210_S0.129390.678
199_F202_A0.129320.678
152_S165_L0.129310.677
194_E198_A0.128480.673
77_S97_L0.128440.673
143_S204_V0.128440.673
146_I150_S0.128410.673
96_T104_W0.128280.672
48_R52_K0.128180.672
58_K62_G0.128120.671
150_S191_F0.127710.669
66_F69_T0.127460.668
71_F206_T0.127420.668
63_F67_I0.127350.667
76_F184_F0.127340.667
82_L191_F0.127140.666
154_R158_N0.126960.665
148_P168_L0.126950.665
172_F175_S0.126950.665
146_I168_L0.126880.665
32_V49_N0.126850.665
51_V55_I0.126630.663
163_H197_V0.126130.661
37_Q142_I0.125990.660
80_L86_S0.125790.659
53_S207_L0.125710.659
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
1c17M0.71161000.288
3dl8C0.2142.30.967
2l6wA0.167420.968
2rddB0.17211.60.97
3dinD0.2141.40.971
2jpkA0.16281.20.972
1jdmA0.14421.10.973
3qbrA0.302310.973
4ainA0.28840.90.974
3lssA0.26980.90.974

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