GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MdcE - Malonate decarboxylase gamma subunit (MdcE)
Pfam: PF06833 (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: CL0127
Length: 234
Sequences: 2380
Seq/Len: 10.17
HH_delta: 0.397 (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
19_V51_L0.447212.828
192_Q195_E0.444332.810
71_V110_G0.398112.518
33_A60_R0.372332.355
32_I68_V0.355622.249
143_G146_S0.351412.222
28_D198_A0.346032.188
61_S101_A0.335122.119
110_G128_A0.333492.109
183_E196_A0.32642.064
111_L193_P0.32282.041
49_W90_A0.310691.965
161_L168_F0.30781.946
186_D191_D0.304481.925
68_V111_L0.298561.888
109_I204_A0.293081.853
157_E160_E0.289611.831
164_S167_V0.281391.779
163_K168_F0.277181.753
24_A34_V0.266861.688
133_A137_A0.259131.639
68_V101_A0.25781.630
109_I200_Q0.257511.628
85_L90_A0.254181.607
81_R85_L0.2521.594
132_I183_E0.251361.590
81_R84_L0.241881.530
161_L165_V0.240971.524
135_P186_D0.238531.508
55_V101_A0.233981.480
132_I200_Q0.231921.467
21_D55_V0.231911.467
165_V168_F0.229131.449
31_F65_R0.214131.354
98_Y108_V0.212011.341
202_Q206_A0.211731.339
142_M146_S0.211691.339
111_L197_L0.209151.323
71_V125_G0.209111.322
99_A126_L0.207481.312
56_L97_A0.207161.310
164_S168_F0.207131.310
23_E65_R0.20351.287
75_S120_A0.203231.285
61_S102_R0.203111.284
163_K167_V0.202441.280
117_M140_H0.200981.271
80_R84_L0.200881.270
77_A81_R0.19691.245
43_V48_A0.194961.233
28_D202_Q0.193591.224
91_L141_V0.193121.221
45_L90_A0.191721.212
28_D195_E0.190191.203
193_P197_L0.189831.200
76_Q123_A0.188751.194
138_M166_P0.187791.188
117_M123_A0.187511.186
33_A55_V0.186041.176
89_Q93_H0.185661.174
176_A181_L0.185251.171
33_A65_R0.184591.167
149_R153_R0.184171.165
136_G190_A0.183751.162
70_L111_L0.182261.153
25_G31_F0.181481.148
134_L193_P0.178991.132
68_V197_L0.178731.130
55_V67_I0.177751.124
195_E199_A0.177361.122
69_A108_V0.176981.119
112_V125_G0.176381.115
112_V131_L0.175431.109
38_A41_G0.174621.104
35_V61_S0.174451.103
161_L164_S0.172181.089
186_D190_A0.17161.085
30_R202_Q0.171051.082
132_I185_W0.170371.077
186_D192_Q0.170341.077
62_G65_R0.169681.073
194_A197_L0.167461.059
37_D124_H0.164861.043
64_K205_L0.163711.035
51_L94_L0.163571.034
142_M147_A0.162831.030
56_L100_L0.161741.023
87_I91_L0.161531.021
200_Q205_L0.160731.016
158_L165_V0.160681.016
125_G131_L0.160251.013
133_A175_Y0.161.012
116_A121_F0.159441.008
200_Q204_A0.158741.004
110_G131_L0.157780.998
202_Q205_L0.155020.980
26_G198_A0.155020.980
22_G43_V0.154810.979
130_R182_D0.153380.970
111_L185_W0.153290.969
62_G130_R0.15320.969
199_A203_E0.153090.968
112_V137_A0.152590.965
158_L161_L0.149810.947
115_K138_M0.148540.939
45_L85_L0.148440.939
181_L184_L0.148240.937
135_P190_A0.147110.930
22_G34_V0.146930.929
65_R106_H0.145970.923
109_I130_R0.145770.922
144_K147_A0.144570.914
109_I201_V0.14350.907
134_L190_A0.143010.904
23_E63_P0.14260.902
53_K94_L0.141970.898
83_E86_G0.141690.896
109_I175_Y0.140640.889
160_E165_V0.140610.889
197_L201_V0.140170.886
195_E202_Q0.139840.884
131_L181_L0.139730.884
30_R206_A0.138660.877
26_G32_I0.137780.871
131_L175_Y0.137590.870
185_W193_P0.13740.869
176_A184_L0.137080.867
70_L113_Y0.136730.865
22_G39_N0.136520.863
28_D31_F0.136490.863
196_A199_A0.134260.849
67_I106_H0.133790.846
186_D196_A0.133220.842
64_K195_E0.13310.842
35_V73_V0.132890.840
101_A106_H0.132670.839
133_A181_L0.132640.839
50_A54_A0.132090.835
79_G83_E0.131580.832
72_D114_G0.13130.830
26_G68_V0.130830.827
162_A167_V0.130620.826
76_Q119_G0.129040.816
144_K148_A0.128680.814
201_V206_A0.128250.811
31_F202_Q0.128130.810
110_G124_H0.127760.808
111_L194_A0.127290.805
156_E160_E0.127010.803
67_I101_A0.126720.801
30_R205_L0.126470.800
183_E186_D0.126390.799
63_P106_H0.126360.799
192_Q196_A0.126080.797
24_A68_V0.125860.796
68_V109_I0.125670.795
64_K102_R0.124570.788
53_K97_A0.124070.785
52_A55_V0.124060.785
162_A165_V0.123930.784
203_E206_A0.123680.782
119_G146_S0.123570.781
71_V113_Y0.123090.778
158_L166_P0.1230.778
179_G183_E0.122580.775
130_R183_E0.12240.774
201_V205_L0.121840.770
46_E81_R0.120620.763
44_G47_E0.120460.762
84_L89_Q0.120150.760
46_E82_E0.11920.754
38_A74_P0.118840.752
91_L95_A0.117980.746
24_A32_I0.117960.746
91_L144_K0.117680.744
109_I183_E0.117660.744
201_V204_A0.117170.741
45_L49_W0.116980.740
21_D33_A0.116750.738
19_V37_D0.116750.738
59_I106_H0.115930.733
48_A91_L0.115040.727
161_L166_P0.114970.727
139_I175_Y0.114630.725
96_K100_L0.114260.723
48_A52_A0.113880.720
152_K164_S0.113860.720
85_L156_E0.113720.719
71_V74_P0.112940.714
56_L93_H0.112720.713
108_V128_A0.112620.712
81_R159_E0.112360.711
87_I144_K0.112160.709
155_V158_L0.112080.709
18_Q168_F0.112070.709
112_V166_P0.112050.709
44_G48_A0.111440.705
184_L190_A0.111320.704
112_V133_A0.110620.700
52_A93_H0.110440.698
112_V139_I0.11010.696
97_A101_A0.110030.696
68_V106_H0.109370.692
110_G120_A0.10930.691
25_G191_D0.10930.691
76_Q94_L0.109160.690
96_K156_E0.109120.690
20_L155_V0.109050.690
160_E163_K0.108920.689
78_Y143_G0.108790.688
88_N116_A0.108580.687
48_A94_L0.10820.684
130_R177_K0.108180.684
135_P184_L0.10810.684
191_D202_Q0.107960.683
61_S158_L0.107910.682
74_P98_Y0.107180.678
26_G197_L0.107080.677
40_H128_A0.106940.676
69_A122_L0.106880.676
25_G28_D0.106760.675
45_L72_D0.106760.675
152_K160_E0.106610.674
176_A183_E0.106480.673
73_V117_M0.106420.673
128_A179_G0.106380.673
24_A191_D0.106330.672
60_R97_A0.106220.672
119_G122_L0.10620.672
139_I181_L0.105980.670
75_S119_G0.105920.670
98_Y122_L0.10590.670
80_R145_P0.105520.667
56_L136_G0.105440.667
88_N92_A0.105340.666
162_A168_F0.105310.666
78_Y119_G0.105210.665
132_I154_P0.105120.665
50_A194_A0.10510.665
62_G96_K0.105010.664
150_V153_R0.104970.664
47_E79_G0.104860.663
123_A140_H0.104830.663
82_E90_A0.104620.662
28_D186_D0.10440.660
64_K106_H0.104370.660
73_V116_A0.104320.660
79_G82_E0.104280.659
39_N184_L0.104160.659
153_R156_E0.103960.657
121_F133_A0.103880.657
29_G194_A0.103810.656
33_A83_E0.103680.656
117_M138_M0.103640.655
198_A206_A0.103610.655
157_E165_V0.103530.655
67_I108_V0.103340.653
159_E163_K0.103070.652
195_E198_A0.102690.649
34_V68_V0.102650.649
20_L24_A0.102530.648
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
2f9iA0.93161000.397
2f9yA0.92311000.405
3hrxA0.86751000.414
3n6rB0.9061000.414
4fzwA0.88891000.419
1on3A0.9061000.421
1pixA0.91031000.421
2bzrA0.9061000.422
3iavA0.9061000.426
4fzwC0.93161000.426

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