GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thioesterase - Thioesterase domain
Pfam: PF00975 (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: CL0028
Length: 229
Sequences: 37458
Seq/Len: 163.57
HH_delta: 0.038 (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
69_V96_R3.423834.972
84_A97_L1.725522.506
70_L80_A1.711242.485
26_D226_A1.651752.399
204_H224_K1.64092.383
202_E206_V1.596872.319
36_P54_R1.578662.292
177_L207_P1.564142.271
69_V95_S1.55912.264
2_P29_G1.555492.259
177_L205_D1.442552.095
19_L222_A1.441322.093
77_G102_S1.436412.086
67_P95_S1.429252.075
217_H220_E1.423812.068
2_P31_Y1.408162.045
83_M87_L1.311471.904
101_D179_D1.279681.858
99_L102_S1.238541.799
5_C71_A1.19671.738
69_V98_I1.181181.715
82_E85_R1.1771.709
8_P74_S1.175971.708
56_A60_R1.161221.686
71_A100_I1.151661.672
224_K227_E1.148051.667
82_E86_Q1.125361.634
80_A97_L1.121181.628
13_A34_E1.101041.599
96_R172_T1.078041.565
206_V224_K1.067141.550
100_I221_I1.067131.550
223_E227_E1.056511.534
3_L28_I1.054691.532
175_Y184_M1.034791.503
220_E224_K1.030671.497
81_F99_L1.030081.496
20_A32_G1.028911.494
58_A62_R1.020191.481
6_F80_A1.012721.471
53_S86_Q1.0121.470
6_F35_Y1.009151.465
22_A222_A1.004281.458
47_S50_E0.990231.438
56_A87_L0.989381.437
97_L171_I0.979771.423
220_E223_E0.975341.416
5_C30_V0.973671.414
191_D195_D0.970851.410
56_A83_M0.963471.399
34_E39_G0.961521.396
6_F33_I0.958621.392
171_I197_T0.956051.388
59_I68_Y0.953111.384
56_A90_A0.937961.362
192_R196_Y0.927691.347
3_L71_A0.923841.342
184_M205_D0.919931.336
9_A75_F0.917011.332
98_I225_I0.91111.323
99_L173_L0.910461.322
22_A25_D0.910231.322
22_A26_D0.902211.310
202_E224_K0.900591.308
98_I172_T0.899771.307
7_P35_Y0.899721.307
177_L184_M0.898181.304
57_E61_A0.891271.294
58_A61_A0.880821.279
221_I225_I0.855321.242
72_G80_A0.852841.238
22_A226_A0.852251.238
11_G15_S0.84741.231
172_T204_H0.842921.224
52_A82_E0.842491.223
175_Y205_D0.837491.216
60_R90_A0.835431.213
28_I69_V0.834831.212
57_E60_R0.822341.194
96_R170_P0.815911.185
190_A193_W0.812871.180
6_F70_L0.810281.177
80_A84_A0.806221.171
20_A24_P0.797921.159
177_L206_V0.793981.153
190_A194_W0.792121.150
68_Y94_V0.792011.150
194_W201_V0.789781.147
219_A223_E0.78661.142
179_D182_V0.784041.139
35_Y79_L0.782421.136
54_R58_A0.782181.136
7_P38_R0.778751.131
194_W200_D0.776571.128
72_G76_G0.772711.122
71_A98_I0.768831.116
74_S210_H0.767061.114
172_T202_E0.762451.107
54_R57_E0.759841.103
24_P30_V0.757061.099
49_E86_Q0.754531.096
175_Y203_V0.752321.092
73_W101_D0.749781.089
10_G74_S0.748811.087
18_P21_R0.737441.071
22_A219_A0.735391.068
192_R195_D0.723871.051
53_S57_E0.711131.033
5_C16_Y0.710531.032
13_A32_G0.706691.026
54_R61_A0.70061.017
193_W197_T0.698111.014
87_L90_A0.691941.005
175_Y190_A0.689471.001
2_P68_Y0.686220.996
3_L30_V0.68250.991
72_G77_G0.681520.990
73_W100_I0.680380.988
191_D203_V0.667260.969
3_L69_V0.665960.967
174_F221_I0.664550.965
4_F68_Y0.663140.963
101_D176_A0.661340.960
191_D205_D0.658460.956
70_L94_V0.652350.947
184_M191_D0.645270.937
73_W211_F0.641310.931
178_D208_G0.636230.924
35_Y75_F0.633920.921
50_E53_S0.629480.914
173_L190_A0.625480.908
20_A30_V0.624870.907
50_E54_R0.623190.905
212_S215_K0.62070.901
223_E226_A0.619370.899
35_Y38_R0.6190.899
191_D194_W0.614730.893
60_R63_Q0.61140.888
21_R25_D0.611010.887
10_G75_F0.607430.882
17_R21_R0.605620.879
2_P64_P0.60560.879
206_V220_E0.60240.875
175_Y182_V0.601430.873
194_W197_T0.600870.873
59_I64_P0.596990.867
52_A56_A0.596250.866
174_F206_V0.595180.864
75_F79_L0.594960.864
154_Q158_N0.593760.862
55_Y83_M0.593330.862
64_P68_Y0.590390.857
176_A179_D0.586130.851
178_D207_P0.584660.849
56_A86_Q0.582120.845
194_W199_G0.581540.844
97_L169_V0.580380.843
8_P73_W0.57890.841
201_V206_V0.577070.838
31_Y58_A0.574470.834
177_L208_G0.574340.834
222_A226_A0.574070.834
3_L23_L0.572490.831
190_A197_T0.569270.827
56_A59_I0.568770.826
198_S201_V0.568740.826
2_P28_I0.56620.822
40_D43_P0.564010.819
55_Y59_I0.557290.809
5_C23_L0.554420.805
221_I224_K0.553930.804
28_I226_A0.553430.804
33_I55_Y0.551850.801
60_R64_P0.545240.792
58_A64_P0.540880.785
4_F55_Y0.539160.783
55_Y58_A0.538550.782
70_L83_M0.537510.781
208_G217_H0.53690.780
189_E192_R0.536590.779
211_F215_K0.536170.779
71_A225_I0.533530.775
53_S56_A0.533260.774
59_I83_M0.532990.774
62_R65_E0.532880.774
154_Q157_E0.532290.773
173_L201_V0.531070.771
163_P166_K0.529990.770
76_G80_A0.527250.766
209_D215_K0.526570.765
98_I174_F0.525710.763
4_F31_Y0.524510.762
84_A169_V0.522330.758
29_G64_P0.522020.758
83_M90_A0.521130.757
95_S98_I0.520140.755
36_P51_L0.518850.753
29_G32_G0.518660.753
148_A152_D0.518150.752
35_Y51_L0.514270.747
143_A147_R0.514120.747
61_A65_E0.513910.746
164_I167_Q0.513210.745
5_C20_A0.513010.745
202_E227_E0.512480.744
5_C32_G0.511530.743
94_V97_L0.509430.740
49_E82_E0.50840.738
100_I174_F0.507790.737
59_I63_Q0.507310.737
138_D141_L0.50650.736
7_P33_I0.505930.735
102_S105_P0.505540.734
197_T200_D0.50540.734
60_R87_L0.50280.730
47_S54_R0.502470.730
7_P12_S0.501830.729
68_Y95_S0.501760.729
17_R32_G0.500950.727
75_F78_I0.500410.727
16_Y73_W0.498110.723
10_G37_G0.494930.719
19_L23_L0.491620.714
209_D212_S0.489850.711
12_S15_S0.489010.710
147_R151_D0.488690.710
174_F224_K0.488570.709
51_L55_Y0.487520.708
161_I164_I0.487230.708
23_L71_A0.485960.706
172_T224_K0.483420.702
148_A151_D0.483190.702
135_S138_D0.48250.701
168_K199_G0.482340.700
101_D175_Y0.481970.700
47_S51_L0.481830.700
174_F204_H0.480970.698
123_E126_R0.48090.698
24_P29_G0.480870.698
124_E127_R0.480440.698
83_M94_V0.480110.697
96_R99_L0.477220.693
52_A83_M0.476630.692
6_F83_M0.474430.689
49_E53_S0.473650.688
218_V222_A0.473480.688
64_P67_P0.472920.687
121_F124_E0.471580.685
144_R147_R0.469130.681
2_P69_V0.468940.681
193_W196_Y0.467180.678
21_R24_P0.467080.678
124_E128_I0.465340.676
101_D212_S0.465110.675
201_V204_H0.464150.674
8_P11_G0.463630.673
51_L58_A0.463580.673
123_E127_R0.463230.673
222_A225_I0.462370.671
16_Y19_L0.460650.669
9_A35_Y0.460380.669
73_W213_M0.459140.667
146_L150_R0.459030.667
6_F55_Y0.459030.667
161_I165_D0.457570.664
88_E168_K0.457410.664
77_G99_L0.454330.660
103_P182_V0.453490.659
152_D155_A0.453150.658
112_R116_P0.452650.657
121_F125_L0.451880.656
138_D145_L0.451840.656
30_V33_I0.45140.655
19_L22_A0.45090.655
4_F70_L0.450230.654
179_D210_H0.44910.652
70_L97_L0.44850.651
78_I81_F0.448030.651
59_I62_R0.447930.650
72_G84_A0.447390.650
139_E142_L0.44670.649
208_G212_S0.446510.648
51_L75_F0.445690.647
33_I58_A0.44550.647
138_D142_L0.445290.647
201_V205_D0.443650.644
14_S17_R0.443430.644
69_V73_W0.442870.643
162_R165_D0.442810.643
48_I51_L0.442490.643
51_L54_R0.442460.643
159_Y163_P0.441050.640
74_S101_D0.439850.639
204_H220_E0.437660.636
149_L152_D0.435750.633
173_L203_V0.4350.632
13_A40_D0.431860.627
143_A146_L0.431610.627
140_E144_R0.430550.625
61_A64_P0.430330.625
44_P47_S0.430170.625
172_T175_Y0.42920.623
6_F79_L0.428770.623
151_D154_Q0.428330.622
51_L79_L0.426470.619
78_I82_E0.425660.618
49_E52_A0.420990.611
145_L148_A0.419070.609
145_L152_D0.418690.608
15_S73_W0.417810.607
204_H227_E0.417440.606
10_G38_R0.417110.606
52_A86_Q0.416630.605
54_R62_R0.415640.604
15_S213_M0.415550.603
127_R130_G0.415140.603
81_F102_S0.414030.601
42_E45_P0.413120.600
142_L145_L0.412520.599
147_R150_R0.41250.599
160_S163_P0.412460.599
122_I126_R0.412410.599
150_R153_F0.412050.598
133_D137_E0.412040.598
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
3om8A0.956399.90.038
3qmvA0.978299.90.044
3v48A0.960799.90.06
3w06A0.960799.90.063
1b6gA0.95299.90.067
3flaA0.973899.90.068
3w04A0.960799.90.073
2xuaA0.95299.90.076
1zoiA0.960799.90.079
2xt0A0.943299.90.083

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