GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MEDS - MEDS MEthanogenmethylotroph DcmR Sensory domain
Pfam: PF14417 (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: CL0023
Length: 191
Sequences: 4040
Seq/Len: 21.15
HH_delta: 0.503 (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
7_K14_G0.839773.542
43_G123_R0.751563.170
49_R122_L0.716573.022
40_I125_I0.703962.969
48_E122_L0.672282.835
18_W154_P0.593162.502
8_S16_I0.589072.484
111_L124_V0.588882.484
21_H62_E0.525492.216
73_D76_Q0.48822.059
40_I50_C0.443761.872
36_L160_A0.432311.823
109_A113_Q0.417961.763
9_G14_G0.414071.746
150_F157_A0.397191.675
125_I158_L0.392211.654
36_L125_I0.376171.587
35_V39_F0.35751.508
22_I146_L0.354741.496
103_M107_W0.354031.493
54_A63_L0.352491.487
143_E159_C0.337711.424
37_V67_L0.332581.403
149_L153_H0.32191.358
7_K46_R0.321061.354
27_D30_E0.317861.341
42_E46_R0.316591.335
124_V155_F0.313841.324
39_F43_G0.313211.321
22_I147_N0.309051.303
8_S14_G0.307931.299
27_D32_L0.304361.284
112_E153_H0.304191.283
17_P21_H0.30071.268
49_R90_E0.295341.246
51_L124_V0.294881.244
27_D31_E0.294731.243
16_I158_L0.291121.228
98_F102_R0.289331.220
31_E127_E0.289131.219
59_R62_E0.286131.207
44_L50_C0.285781.205
76_Q82_Q0.28491.202
48_E123_R0.281611.188
44_L91_W0.279641.179
156_T161_Y0.271071.143
86_L89_E0.269721.138
103_M132_L0.268261.131
32_L57_P0.267671.129
103_M110_A0.267421.128
107_W111_L0.266981.126
76_Q87_D0.26581.121
18_W122_L0.264711.116
43_G48_E0.264411.115
108_R145_L0.26391.113
107_W124_V0.262691.108
84_E119_Y0.260371.098
43_G50_C0.259291.094
124_V157_A0.256971.084
7_K11_D0.256251.081
64_R68_R0.255561.078
123_R158_L0.252771.066
50_C123_R0.251881.062
34_E66_E0.250031.055
40_I52_Y0.249861.054
33_L162_D0.249671.053
40_I44_L0.248111.046
57_P162_D0.247581.044
106_F110_A0.24691.041
10_I38_P0.243851.028
102_R107_W0.24341.027
39_F123_R0.24241.022
52_Y125_I0.242061.021
32_L127_E0.241511.019
110_A113_Q0.240831.016
98_F106_F0.240391.014
42_E45_A0.238611.006
156_T160_A0.238541.006
104_I109_A0.238391.005
108_R152_E0.236140.996
146_L157_A0.234770.990
103_M106_F0.234490.989
20_D154_P0.234480.989
51_L110_A0.233490.985
130_W161_Y0.233040.983
149_L155_F0.231330.976
49_R120_R0.229980.970
41_R45_A0.228090.962
104_I107_W0.227450.959
75_E80_S0.226730.956
112_E152_E0.225230.950
60_V64_R0.225050.949
25_F158_L0.21990.927
107_W132_L0.217710.918
145_L148_R0.214030.903
76_Q84_E0.211310.891
34_E38_P0.210520.888
9_G42_E0.209550.884
120_R153_H0.209110.882
75_E79_D0.20880.881
157_A160_A0.208590.880
55_P131_A0.20760.876
49_R119_Y0.206730.872
38_P41_R0.206290.870
50_C125_I0.205270.866
105_A109_A0.204230.861
99_D102_R0.203550.858
69_K79_D0.201860.851
24_A58_R0.200810.847
29_E164_R0.199760.843
48_E120_R0.197130.831
148_R152_E0.196410.828
103_M111_L0.194020.818
47_G90_E0.193620.817
16_I39_F0.193320.815
15_D128_M0.193160.815
90_E99_D0.19190.809
147_N159_C0.191480.808
22_I143_E0.189530.799
98_F164_R0.189520.799
39_F42_E0.189230.798
136_W140_L0.188850.796
128_M131_A0.186060.785
12_A75_E0.185270.781
17_P79_D0.185210.781
139_L142_Y0.185180.781
29_E138_E0.183840.775
109_A112_E0.183840.775
139_L143_E0.183650.775
128_M162_D0.181650.766
52_Y91_W0.181370.765
61_E84_E0.179340.756
146_L149_L0.179250.756
49_R82_Q0.178770.754
65_D75_E0.178270.752
11_D47_G0.17670.745
100_P111_L0.175170.739
54_A161_Y0.175030.738
33_L66_E0.17480.737
29_E32_L0.174540.736
15_D18_W0.173820.733
32_L162_D0.173780.733
44_L47_G0.173640.732
73_D83_L0.173630.732
12_A71_G0.173490.732
144_A147_N0.172690.728
129_T163_R0.17260.728
27_D33_L0.172580.728
41_R70_A0.172570.728
107_W126_G0.172520.728
12_A69_K0.172320.727
33_L57_P0.171790.725
105_A108_R0.171690.724
149_L157_A0.171440.723
102_R106_F0.170580.719
75_E82_Q0.170290.718
128_M161_Y0.170170.718
100_P103_M0.170090.717
13_I16_I0.16780.708
31_E57_P0.167750.707
27_D128_M0.167710.707
156_T162_D0.167530.707
102_R110_A0.167270.705
25_F35_V0.16720.705
133_R148_R0.166840.704
104_I145_L0.166250.701
98_F103_M0.165770.699
51_L119_Y0.165530.698
157_A161_Y0.164740.695
11_D71_G0.163840.691
53_V124_V0.163110.688
32_L160_A0.163040.688
26_Y161_Y0.162910.687
33_L127_E0.161690.682
157_A163_R0.161620.682
9_G113_Q0.161060.679
146_L158_L0.161040.679
33_L36_L0.160420.677
68_R73_D0.160260.676
136_W143_E0.159510.673
104_I110_A0.159290.672
64_R140_L0.158840.670
39_F48_E0.158820.670
57_P66_E0.158810.670
121_G155_F0.158770.670
40_I123_R0.158120.667
26_Y163_R0.157730.665
49_R121_G0.157720.665
64_R136_W0.157160.663
39_F158_L0.156460.660
9_G46_R0.156270.659
98_F135_G0.156260.659
128_M139_L0.155850.657
101_A110_A0.154570.652
131_A147_N0.154320.651
64_R67_L0.154040.650
152_E156_T0.153440.647
100_P145_L0.153420.647
136_W139_L0.153420.647
129_T142_Y0.153360.647
75_E85_L0.153250.646
34_E160_A0.152390.643
54_A130_W0.152210.642
11_D65_D0.151510.639
128_M160_A0.151350.638
147_N151_A0.150960.637
66_E163_R0.150850.636
44_L83_L0.15030.634
7_K48_E0.150120.633
84_E87_D0.150050.633
137_E153_H0.149970.633
69_K77_Y0.149650.631
58_R129_T0.149550.631
147_N150_F0.149440.630
11_D89_E0.149290.630
71_G119_Y0.149240.629
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
3bs4A0.963499.70.503
2ztsA0.963499.60.536
3bgwA0.958199.60.542
3bh0A0.958199.60.548
1q57A0.963499.60.548
4a1fA0.958199.60.552
3cmuA0.874399.50.562
3cmwA0.874399.50.564
2dr3A0.963499.50.567
2q6tA0.958199.50.568
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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