GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Beta_elim_lyase - Beta-eliminating lyase
Pfam: PF01212 (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: CL0061
Length: 290
Sequences: 40406
Seq/Len: 139.33
HH_delta: 0.278 (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
151_S155_R2.975883.799
255_H259_M2.316512.957
112_E156_E2.311092.950
37_R247_E2.279152.909
108_P149_A2.20842.819
262_R266_G2.021772.581
146_E149_A1.932212.467
110_D113_A1.882162.403
257_N261_K1.828452.334
70_S96_I1.822522.327
151_S161_L1.82182.326
266_G269_A1.809322.310
70_S116_E1.693422.162
149_A152_E1.659832.119
110_D114_A1.639412.093
70_S94_K1.634342.086
264_A268_E1.600452.043
261_K265_A1.593022.034
148_R152_E1.570882.005
69_E126_A1.560461.992
144_L148_R1.528821.952
112_E153_L1.510521.928
112_E116_E1.502641.918
207_G212_I1.4861.897
50_V56_A1.475681.884
152_E156_E1.461771.866
254_R258_A1.461411.866
70_S124_Q1.432211.828
251_E254_R1.415321.807
112_E157_H1.414681.806
127_V162_H1.401971.790
266_G270_L1.388371.772
37_R243_L1.385611.769
112_E149_A1.37951.761
108_P153_L1.37591.756
65_L93_A1.364531.742
259_M262_R1.359521.736
58_Q62_R1.358131.734
143_S146_E1.354131.729
153_L157_H1.338081.708
154_A159_L1.331411.700
32_A36_E1.32431.691
107_T110_D1.297461.656
51_P55_M1.296111.655
265_A269_A1.285981.642
154_A161_L1.269731.621
66_R69_E1.268111.619
36_E40_E1.268041.619
37_R40_E1.252251.599
255_H258_A1.24671.591
191_F204_V1.24411.588
145_E148_R1.243671.588
38_I204_V1.226311.565
115_I159_L1.214741.551
70_S125_P1.193711.524
262_R265_A1.177321.503
155_R185_G1.174451.499
109_E113_A1.162531.484
241_A244_R1.155751.475
60_A162_H1.149521.467
258_A262_R1.127241.439
115_I153_L1.117921.427
99_P110_D1.116831.426
265_A268_E1.110731.418
260_A264_A1.108681.415
128_V154_A1.104341.410
33_R243_L1.097841.401
244_R248_L1.083621.383
116_E157_H1.075061.372
37_R244_R1.069861.366
109_E149_A1.066431.361
244_R247_E1.065581.360
60_A188_S1.065271.360
109_E112_E1.045541.335
75_D99_P1.03141.317
254_R257_N1.010191.290
57_N190_S1.001581.279
130_L150_I0.988541.262
75_D97_P0.982051.254
61_L129_S0.980171.251
34_L242_A0.977171.247
64_H160_P0.973271.242
128_V159_L0.97271.242
129_S162_H0.950121.213
162_H190_S0.950021.213
33_R37_R0.931481.189
111_L150_I0.925491.181
152_E155_R0.913781.167
30_T33_R0.901811.151
213_A217_R0.898631.147
153_L159_L0.893681.141
105_K146_E0.892571.139
98_L114_A0.882911.127
145_E149_A0.880021.123
73_C95_L0.877831.121
130_L147_L0.873381.115
151_S154_A0.863271.102
113_A117_E0.862361.101
128_V150_I0.859191.097
261_K264_A0.853481.090
33_R36_E0.853321.089
37_R41_L0.851641.087
241_A245_A0.841071.074
39_A47_A0.838991.071
209_K213_A0.838091.070
250_L254_R0.835441.066
115_I157_H0.829521.059
96_I114_A0.829431.059
116_E125_P0.822281.050
62_R91_S0.821451.049
263_L266_G0.816591.042
108_P112_E0.811931.036
50_V59_L0.806861.030
155_R187_D0.805191.028
263_L267_L0.799761.021
69_E124_Q0.799731.021
258_A261_K0.79971.021
72_I125_P0.796141.016
56_A205_L0.793231.013
42_F206_A0.787721.006
36_E39_A0.785431.003
259_M263_L0.783561.000
72_I114_A0.781710.998
67_P92_G0.778910.994
160_P211_F0.763170.974
153_L156_E0.755790.965
127_V160_P0.755590.965
114_A117_E0.755530.964
243_L247_E0.752780.961
45_E208_N0.752410.961
166_A192_G0.750860.959
116_E124_Q0.749260.956
29_P33_R0.745380.952
180_A183_A0.737540.942
64_H127_V0.737030.941
34_L49_F0.733540.936
115_I125_P0.732660.935
149_A153_L0.72470.925
212_I215_A0.722830.923
224_G227_R0.718270.917
35_E49_F0.717280.916
56_A190_S0.716130.914
245_A248_L0.715110.913
130_L161_L0.712710.910
256_A259_M0.704630.900
252_R255_H0.700720.895
53_G190_S0.700540.894
111_L153_L0.692430.884
195_K201_G0.691560.883
112_E152_E0.691110.882
46_A209_K0.690460.881
101_D107_T0.681580.870
125_P159_L0.678180.866
45_E209_K0.678160.866
40_E247_E0.678060.866
250_L253_A0.674430.861
222_L225_G0.673390.860
116_E156_E0.66970.855
154_A157_H0.656430.838
35_E39_A0.656370.838
65_L127_V0.653130.834
249_W252_R0.651970.832
150_I161_L0.650990.831
268_E271_G0.645670.824
61_L65_L0.6430.821
165_G189_V0.640230.817
252_R256_A0.63590.812
44_K206_A0.6330.808
57_N129_S0.631430.806
31_T35_E0.630460.805
113_A116_E0.629560.804
71_V127_V0.627510.801
251_E255_H0.618480.790
64_H188_S0.616680.787
72_I111_L0.613250.783
197_G245_A0.606470.774
148_R185_G0.601790.768
184_A187_D0.599440.765
96_I116_E0.597060.762
34_L37_R0.594440.759
34_L243_L0.592720.757
98_L110_D0.59150.755
154_A158_G0.590930.754
205_L215_A0.59080.754
253_A257_N0.588480.751
131_E135_E0.58730.750
50_V202_G0.582260.743
108_P146_E0.581590.742
65_L71_V0.572150.730
65_L69_E0.572140.730
61_L127_V0.572070.730
89_E95_L0.570670.728
101_D105_K0.569020.726
77_A131_E0.566770.724
173_A178_S0.566770.724
178_S181_E0.565050.721
58_Q90_L0.564690.721
210_E214_K0.56060.716
179_L182_I0.557790.712
60_A190_S0.556980.711
242_A245_A0.556750.711
126_A160_P0.556220.710
78_H81_F0.555110.709
214_K217_R0.547750.699
142_Y147_L0.547640.699
163_M186_A0.546270.697
96_I125_P0.5460.697
108_P150_I0.542610.693
166_A174_A0.541670.691
147_L163_M0.541080.691
256_A260_A0.540740.690
208_N211_F0.537610.686
151_S185_G0.537410.686
253_A256_A0.535730.684
47_A206_A0.535120.683
38_I191_F0.534780.683
111_L128_V0.534380.682
71_V74_A0.533310.681
212_I216_R0.533240.681
186_A189_V0.529090.675
174_A178_S0.526730.672
80_H83_E0.526030.672
32_A35_E0.523860.669
33_R247_E0.523470.668
46_A213_A0.521630.666
221_R224_G0.519840.664
207_G211_F0.519430.663
183_A186_A0.517050.660
182_I185_G0.516830.660
188_S207_G0.516620.660
40_E43_G0.516110.659
249_W253_A0.515320.658
108_P111_L0.510330.651
146_E150_I0.508150.649
106_L111_L0.504390.644
152_E185_G0.501870.641
189_V206_A0.501550.640
213_A216_R0.500230.639
34_L38_I0.49890.637
193_G198_G0.49630.634
101_D110_D0.493790.630
85_G89_E0.49280.629
112_E115_I0.492460.629
41_L197_G0.491780.628
188_S211_F0.488280.623
50_V55_M0.48790.623
53_G166_A0.487740.623
231_V234_A0.48740.622
70_S126_A0.487170.622
155_R184_A0.483410.617
60_A64_H0.482920.616
57_N162_H0.48090.614
77_A80_H0.480540.613
117_E124_Q0.479680.612
199_A202_G0.479170.612
174_A177_V0.479070.612
267_L270_L0.478380.611
175_L181_E0.476770.609
77_A81_F0.473880.605
39_A42_F0.472660.603
257_N260_A0.472580.603
68_G94_K0.471480.602
162_H188_S0.465140.594
187_D208_N0.464070.592
192_G195_K0.463340.591
132_N163_M0.458520.585
42_F189_V0.45650.583
79_I82_D0.454150.580
148_R151_S0.453970.580
222_L226_M0.453450.579
245_A249_W0.452770.578
160_P188_S0.452670.578
42_F191_F0.449670.574
82_D97_P0.448970.573
248_L251_E0.448480.573
223_G226_M0.447360.571
111_L115_I0.446840.570
211_F214_K0.445170.568
117_E125_P0.444790.568
28_D31_T0.444060.567
66_R126_A0.44380.567
155_R161_L0.442730.565
207_G213_A0.441340.563
133_T136_L0.438060.559
195_K203_A0.43730.558
38_I49_F0.437210.558
55_M219_R0.436540.557
214_K218_Q0.434650.555
142_Y146_E0.43420.554
246_L249_W0.433070.553
268_E272_G0.432220.552
267_L272_G0.430760.550
83_E86_A0.430740.550
130_L163_M0.430350.549
177_V182_I0.427640.546
54_T58_Q0.427360.546
96_I99_P0.426860.545
67_P70_S0.426690.545
40_E44_K0.426350.544
180_A189_V0.425780.544
173_A176_G0.42320.540
37_R246_L0.423190.540
175_L178_S0.420840.537
66_R93_A0.418840.535
72_I98_L0.418560.534
211_F215_A0.418450.534
210_E213_A0.418320.534
30_T34_L0.418140.534
71_V75_D0.417690.533
30_T243_L0.41720.533
81_F129_S0.416230.531
219_R223_G0.415910.531
190_S205_L0.415880.531
77_A82_D0.415390.530
155_R158_G0.415150.530
259_M266_G0.414660.529
53_G56_A0.413780.528
26_G31_T0.411770.526
50_V219_R0.410480.524
248_L252_R0.410010.523
219_R222_L0.407950.521
41_L246_L0.407830.521
70_S73_C0.406370.519
199_A242_A0.406350.519
132_N147_L0.40610.518
42_F204_V0.403630.515
114_A125_P0.403470.515
52_S55_M0.401180.512
201_G242_A0.399530.510
217_R221_R0.399470.510
74_A142_Y0.398140.508
166_A195_K0.397360.507
81_F84_T0.397310.507
52_S56_A0.397260.507
86_A89_E0.397030.507
177_V181_E0.396930.507
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
1jg8A0.97591000.278
3b46A0.94831000.287
3lwsA0.94831000.29
1v2dA0.94831000.294
1b5pA0.94831000.302
3pj0A0.94831000.303
1yizA0.94831000.303
2o1bA0.94831000.304
2douA0.94481000.307
3fvsA0.94831000.308

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