GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thiolase_N - Thiolase N-terminal domain
Pfam: PF00108 (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: CL0046
Length: 264
Sequences: 7501
Seq/Len: 28.41
HH_delta: 0.144 (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
181_R185_R1.669073.864
180_V226_L1.545893.579
3_D263_E1.447383.351
107_A110_V1.358233.144
188_A192_E1.345573.115
36_A39_E1.3313.081
175_Q242_T1.312383.038
181_R184_Q1.294572.997
191_D222_P1.135532.629
37_A259_L1.126962.609
34_V111_L1.126312.607
2_R264_E1.097332.540
102_I260_L1.0892.521
219_G250_P1.086132.514
10_V40_R1.055792.444
166_K237_R1.054242.441
190_Q220_I1.048682.428
44_D47_D1.01382.347
102_I262_S1.000432.316
196_D215_D0.995362.304
98_A110_V0.990922.294
173_E177_E0.967332.239
109_V261_M0.947322.193
229_L246_G0.918722.127
7_V261_M0.917172.123
171_S174_E0.910552.108
30_A53_V0.888942.058
164_L170_I0.87752.031
32_E202_V0.86622.005
187_A191_D0.863381.999
20_S214_V0.847851.963
196_D216_R0.834631.932
190_Q199_I0.830831.923
30_A69_A0.823141.906
158_G236_F0.797871.847
177_E181_R0.790231.829
187_A220_I0.788091.824
108_D262_S0.786261.820
5_V261_M0.78061.807
37_A41_A0.767741.777
82_T97_L0.753571.745
228_K231_K0.752841.743
53_V113_G0.746631.728
5_V263_E0.728151.686
36_A200_V0.724331.677
101_A107_A0.720911.669
28_D72_A0.717741.662
34_V69_A0.713571.652
98_A260_L0.709881.643
180_V184_Q0.705081.632
117_S120_R0.697511.615
190_Q216_R0.687091.591
174_E177_E0.686231.589
32_E200_V0.67941.573
100_M106_E0.677831.569
35_K39_E0.674311.561
36_A40_R0.668721.548
51_V70_A0.65071.506
33_A257_A0.639781.481
55_N58_Q0.635621.471
8_G37_A0.632131.463
8_G41_A0.622281.441
31_A72_A0.607891.407
33_A255_A0.605511.402
10_V200_V0.593331.374
184_Q188_A0.586291.357
187_A223_D0.584371.353
53_V257_A0.583751.351
65_I115_V0.581931.347
49_D108_D0.566651.312
177_E226_L0.564431.307
49_D107_A0.561921.301
124_G142_S0.559191.295
170_I175_Q0.543061.257
224_T229_L0.540711.252
95_V258_V0.540561.251
184_Q223_D0.534711.238
48_I109_V0.532671.233
98_A112_A0.52921.225
95_V260_L0.527941.222
21_L214_V0.527391.221
111_L259_L0.524551.214
93_Q97_L0.521651.208
159_I237_R0.5191.202
52_I110_V0.511991.185
226_L230_A0.508771.178
24_V32_E0.493921.143
8_G40_R0.491.134
172_R244_T0.482471.117
188_A191_D0.480461.112
4_V260_L0.479071.109
2_R262_S0.476561.103
14_F252_N0.47131.091
38_L43_I0.467081.081
186_A220_I0.463731.074
187_A222_P0.46271.071
12_T33_A0.462621.071
54_G90_S0.462481.071
184_Q187_A0.460831.067
38_L75_L0.458781.062
15_G218_E0.458211.061
34_V75_L0.455541.055
180_V229_L0.453411.050
13_P214_V0.452261.047
9_A258_V0.451131.044
158_G235_A0.44661.034
232_L246_G0.446571.034
103_A106_E0.446331.033
180_V223_D0.44521.031
31_A35_K0.44311.026
25_S28_D0.443021.026
71_L77_E0.441051.021
75_L79_V0.440921.021
84_V97_L0.439291.017
33_A37_A0.436441.010
112_A258_V0.432721.002
33_A36_A0.428840.993
32_E36_A0.426970.988
191_D216_R0.424690.983
86_R93_Q0.421160.975
37_A111_L0.417840.967
99_A103_A0.417790.967
4_V262_S0.416910.965
52_I94_A0.41450.960
162_E166_K0.414360.959
16_K219_G0.412650.955
160_T163_N0.410.949
37_A257_A0.409920.949
10_V36_A0.408540.946
47_D109_V0.408540.946
100_M104_S0.406920.942
149_Y154_G0.405980.940
163_N167_K0.404830.937
180_V225_T0.403110.933
52_I98_A0.401140.929
162_E237_R0.400030.926
176_D247_N0.391890.907
101_A106_E0.388130.899
190_Q196_D0.387540.897
186_A190_Q0.385280.892
173_E226_L0.385150.892
185_R188_A0.383980.889
52_I82_T0.383120.887
49_D110_V0.380590.881
144_L156_P0.380130.880
183_H219_G0.380040.880
35_K45_P0.379280.878
38_L48_I0.379030.877
12_T29_L0.376550.872
12_T32_E0.374530.867
180_V224_T0.374130.866
180_V228_K0.372890.863
111_L257_A0.371560.860
4_V103_A0.36850.853
82_T93_Q0.367960.852
97_L101_A0.365980.847
4_V99_A0.364960.845
93_Q96_H0.364690.844
98_A107_A0.361910.838
53_V66_A0.357780.828
35_K73_A0.355530.823
75_L111_L0.354710.821
188_A194_R0.353510.818
216_R220_I0.350480.811
28_D31_A0.34790.805
50_A101_A0.347250.804
48_I111_L0.346780.803
24_V117_S0.345030.799
173_E230_A0.344430.797
225_T228_K0.343380.795
232_L244_T0.343260.795
163_N166_K0.342160.792
38_L45_P0.339660.786
183_H220_I0.339560.786
30_A113_G0.336890.780
224_T228_K0.335550.777
161_A165_A0.335490.777
35_K74_G0.33410.773
51_V79_V0.334040.773
10_V37_A0.332580.770
170_I174_E0.331510.767
6_I260_L0.331040.766
24_V120_R0.329660.763
13_P32_E0.327620.758
2_R108_D0.326730.756
27_E72_A0.325430.753
70_A75_L0.324720.752
53_V69_A0.324080.750
69_A115_V0.323840.750
46_E78_S0.323110.748
161_A243_V0.323060.748
157_M160_T0.319270.739
219_G252_N0.318660.738
50_A93_Q0.317060.734
190_Q222_P0.315750.731
123_M132_A0.314790.729
55_N61_E0.314750.729
5_V262_S0.312610.724
7_V109_V0.312310.723
233_K245_A0.311180.720
10_V33_A0.311160.720
144_L149_Y0.309910.717
183_H187_A0.309380.716
12_T202_V0.308460.714
143_L146_D0.307960.713
159_I163_N0.30430.704
18_G119_S0.303860.703
147_G150_D0.303470.703
50_A86_R0.300720.696
55_N65_I0.300660.696
142_S146_D0.299260.693
160_T164_L0.29920.693
144_L154_G0.299020.692
97_L100_M0.298440.691
134_L143_L0.296640.687
13_P215_D0.296450.686
52_I97_L0.295790.685
58_Q83_T0.294920.683
225_T229_L0.294590.682
61_E120_R0.293630.680
57_L121_V0.293210.679
23_D120_R0.292450.677
100_M103_A0.289480.670
235_A245_A0.289240.670
31_A73_A0.288410.668
27_E31_A0.288120.667
60_G124_G0.287540.666
214_V217_D0.286650.664
243_V248_S0.286490.663
38_L42_G0.286340.663
121_V142_S0.285940.662
56_V87_A0.283920.657
224_T246_G0.283710.657
52_I101_A0.283310.656
94_A112_A0.283270.656
27_E61_E0.283220.656
162_E241_G0.282220.653
194_R197_D0.282190.653
95_V112_A0.280070.648
166_K242_T0.279710.648
125_L132_A0.279640.647
26_P117_S0.278790.645
184_Q226_L0.278540.645
164_L168_Y0.278430.645
32_E35_K0.27820.644
193_G196_D0.278070.644
134_L144_L0.277940.643
178_Y185_R0.275590.638
93_Q101_A0.275340.637
64_N87_A0.275230.637
123_M133_P0.275030.637
125_L131_G0.274680.636
50_A107_A0.274460.635
143_L148_L0.273660.634
119_S253_D0.273650.634
51_V111_L0.273370.633
146_D150_D0.272910.632
101_A104_S0.272840.632
45_P76_P0.271630.629
34_V73_A0.270130.625
66_A83_T0.26920.623
50_A110_V0.267740.620
183_H250_P0.267710.620
25_S120_R0.267540.619
249_S252_N0.26740.619
217_D220_I0.267370.619
21_L24_V0.266240.616
38_L41_A0.265240.614
20_S218_E0.26490.613
15_G21_L0.263490.610
165_A175_Q0.261140.605
236_F241_G0.260550.603
3_D103_A0.260340.603
222_P225_T0.259830.602
149_Y153_A0.25910.600
26_P115_V0.25750.596
66_A81_A0.257230.595
2_R103_A0.256950.595
223_D228_K0.256470.594
4_V102_I0.256290.593
177_E230_A0.255620.592
30_A33_A0.254980.590
41_A259_L0.254550.589
63_Q68_Q0.253990.588
226_L229_L0.253130.586
177_E180_V0.251670.583
179_A229_L0.250710.580
179_A183_H0.248910.576
24_V28_D0.248780.576
183_H223_D0.247040.572
37_A40_R0.246780.571
18_G123_M0.245570.569
155_Q159_I0.244980.567
70_A81_A0.244950.567
50_A82_T0.244710.567
227_E231_K0.244610.566
244_T247_N0.243730.564
162_E236_F0.243540.564
179_A247_N0.243110.563
180_V230_A0.242580.562
34_V51_V0.242510.561
93_Q100_M0.242480.561
232_L245_A0.242070.560
175_Q243_V0.24160.559
55_N83_T0.241250.559
34_V257_A0.241190.558
237_R241_G0.240750.557
187_A190_Q0.24010.556
178_Y181_R0.23980.555
181_R188_A0.239640.555
101_A110_V0.239610.555
142_S145_R0.239590.555
8_G258_V0.23870.553
145_R148_L0.235680.546
142_S154_G0.23520.544
146_D154_G0.23420.542
4_V7_V0.233850.541
52_I84_V0.233540.541
162_E243_V0.233470.540
69_A257_A0.23310.540
8_G259_L0.232750.539
30_A34_V0.23210.537
89_A162_E0.231660.536
183_H225_T0.230370.533
89_A93_Q0.230360.533
176_D226_L0.229870.532
49_D80_P0.227620.527
108_D261_M0.227380.526
227_E230_A0.227230.526
113_G257_A0.227090.526
142_S147_G0.226750.525
187_A225_T0.226710.525
26_P120_R0.225810.523
247_N252_N0.225250.521
224_T227_E0.225070.521
221_R225_T0.224490.520
10_V41_A0.223990.519
30_A115_V0.223680.518
146_D151_P0.223380.517
166_K169_G0.223020.516
41_A48_I0.222740.516
3_D264_E0.222030.514
43_I109_V0.221780.513
12_T21_L0.221760.513
160_T243_V0.221590.513
156_P159_I0.22140.513
43_I259_L0.221360.512
201_P215_D0.221210.512
225_T230_A0.220360.510
69_A73_A0.218940.507
47_D261_M0.21860.506
145_R149_Y0.218230.505
16_K221_R0.218130.505
73_A76_P0.217210.503
51_V69_A0.216960.502
25_S72_A0.216780.502
26_P61_E0.216580.501
14_F254_G0.216520.501
110_V260_L0.216360.501
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
4dd5A0.99241000.144
4e1lA0.99621000.15
3ss6A0.98861000.155
1ulqA0.98861000.173
3goaA0.95081000.177
1wl4A0.99241000.182
2vu1A0.98481000.186
2wu9A0.95081000.199
1afwA0.95451000.218
3svkA0.93941000.224

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