GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_trans_1_3 - Glycosyl transferase family 1
Pfam: PF13528 (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: CL0113
Length: 318
Sequences: 17646
Seq/Len: 55.49
HH_delta: 0.324 (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
197_V251_A2.125024.839
218_Q235_H1.961724.467
2_K29_E1.926024.385
31_T93_F1.604863.654
254_V266_A1.499193.414
31_T95_P1.498373.412
211_L219_F1.212152.760
4_L33_I1.206662.748
4_L95_P1.180972.689
220_I237_R1.167532.658
193_P218_Q1.159082.639
31_T49_R1.105612.517
243_D246_E1.104452.515
99_I120_I1.101642.508
195_I220_I1.067572.431
254_V271_K1.061562.417
3_I28_H1.010742.301
220_I235_H1.003722.285
222_F247_L0.945372.153
277_P282_D0.943862.149
240_S243_D0.936252.132
87_I112_R0.933312.125
240_S247_L0.920782.097
157_R174_P0.91962.094
2_K31_T0.901012.052
100_S117_V0.896582.041
195_I218_Q0.88512.015
5_F22_A0.863161.965
196_L253_L0.832291.895
194_K252_D0.831771.894
202_G221_V0.819911.867
222_F237_R0.818381.863
91_R113_A0.797311.815
224_P228_D0.794961.810
4_L90_L0.790131.799
5_F99_I0.778221.772
195_I250_A0.768331.749
199_F244_F0.754641.718
244_F248_M0.747871.703
196_L255_I0.721811.644
195_I252_D0.721621.643
87_I113_A0.716691.632
14_H17_R0.711351.620
5_F101_D0.700821.596
227_A230_R0.68971.570
220_I247_L0.680031.548
98_V110_A0.676991.541
207_L255_I0.667691.520
5_F25_L0.66671.518
88_R92_E0.650781.482
87_I91_R0.649651.479
2_K95_P0.643581.465
251_A271_K0.639191.455
22_A32_F0.634731.445
110_A117_V0.626411.426
108_L112_R0.61661.404
97_L118_I0.603831.375
89_W93_F0.598931.364
266_A273_A0.594821.354
207_L219_F0.593551.351
2_K93_F0.591241.346
245_A269_L0.588641.340
20_A23_R0.58521.332
194_K253_L0.584861.332
263_I281_Q0.582211.326
84_R88_R0.577061.314
220_I251_A0.573551.306
199_F248_M0.568731.295
18_C101_D0.565531.288
163_F166_P0.564411.285
220_I250_A0.561321.278
28_H96_D0.561261.278
222_F240_S0.556481.267
256_S262_T0.549021.250
5_F30_V0.545961.243
119_V155_A0.543181.237
81_R85_R0.542321.235
203_G226_A0.542241.235
206_D210_A0.539031.227
211_L217_Y0.538111.225
266_A271_K0.537781.224
2_K96_D0.532791.213
246_E249_A0.532131.212
101_D122_N0.53171.211
197_V222_F0.527731.202
169_P172_R0.527161.200
249_A269_L0.524311.194
33_I89_W0.524081.193
199_F222_F0.523941.193
198_Y254_V0.516331.176
267_L273_A0.514951.173
209_E212_K0.514821.172
254_V262_T0.514271.171
122_N261_T0.509651.160
31_T47_P0.506441.153
84_R112_R0.505521.151
248_M269_L0.504011.148
237_R247_L0.503631.147
181_R185_R0.503331.146
90_L95_P0.502311.144
257_K276_I0.501851.143
195_I251_A0.500711.140
109_A113_A0.500311.139
245_A249_A0.500081.139
275_V299_V0.497281.132
4_L93_F0.495561.128
206_D276_I0.491441.119
25_L28_H0.483221.100
262_T266_A0.482451.099
237_R240_S0.479281.091
206_D209_E0.477961.088
248_M262_T0.475581.083
29_E47_P0.47431.080
22_A30_V0.472411.076
275_V297_G0.464361.057
197_V247_L0.463111.054
190_E193_P0.460651.049
176_V179_I0.458741.045
256_S263_I0.457991.043
194_K217_Y0.45761.042
224_P239_F0.454711.035
100_S119_V0.449981.025
101_D120_I0.446311.016
80_A84_R0.44611.016
275_V281_Q0.444841.013
253_L274_L0.443721.010
246_E250_A0.442951.009
155_A158_R0.442621.008
19_L23_R0.440371.003
198_Y221_V0.439371.000
25_L30_V0.43460.990
99_I118_I0.433140.986
192_E218_Q0.431990.984
201_G205_G0.431780.983
279_P282_D0.427430.973
85_R88_R0.426290.971
224_P238_P0.425040.968
193_P216_D0.423690.965
160_A173_V0.421380.959
90_L113_A0.419570.955
194_K218_Q0.418090.952
23_R45_R0.41730.950
210_A213_A0.416190.948
31_T89_W0.415780.947
3_I97_L0.414990.945
274_L298_I0.41210.938
277_P299_V0.409490.932
83_I87_I0.409020.931
174_P177_G0.406060.925
89_W92_E0.405520.923
100_S106_A0.405470.923
107_A117_V0.404830.922
27_G30_V0.40330.918
95_P115_I0.402290.916
258_G275_V0.4020.915
197_V248_M0.401610.914
215_P233_N0.40140.914
263_I273_A0.398080.906
4_L31_T0.397330.905
212_K231_P0.397140.904
219_F234_I0.396940.904
83_I112_R0.389870.888
4_L98_V0.387820.883
111_R114_G0.386870.881
3_I25_L0.385170.877
209_E213_A0.384440.875
181_R184_I0.383730.874
244_F247_L0.383490.873
247_L250_A0.382330.871
225_N228_D0.380410.866
158_R162_S0.380390.866
160_A166_P0.376290.857
84_R87_I0.37610.856
198_Y257_K0.375870.856
49_R89_W0.375430.855
152_F155_A0.373270.850
6_Y106_A0.370240.843
263_I275_V0.369820.842
248_M271_K0.368290.839
222_F244_F0.367140.836
218_Q233_N0.365520.832
240_S244_F0.365520.832
214_L217_Y0.365010.831
23_R46_F0.364930.831
266_A275_V0.362630.826
217_Y252_D0.360760.821
116_P156_D0.358680.817
185_R188_P0.357710.814
112_R115_I0.356910.813
83_I108_L0.355990.811
194_K197_V0.352790.803
14_H19_L0.352340.802
177_G283_E0.351530.800
208_I234_I0.347220.791
193_P252_D0.343030.781
123_Q205_G0.341960.779
256_S281_Q0.340150.775
7_V15_A0.338820.771
3_I30_V0.336820.767
205_G260_Y0.334040.761
21_L25_L0.333670.760
206_D259_G0.332980.758
40_E44_P0.332690.758
118_I159_L0.330.751
196_L211_L0.329690.751
216_D233_N0.329040.749
98_V115_I0.32890.749
202_G225_N0.328890.749
194_K216_D0.327450.746
94_R115_I0.325330.741
196_L274_L0.324470.739
88_R91_R0.324040.738
22_A27_G0.323820.737
11_G14_H0.323720.737
4_L89_W0.322730.735
200_G203_G0.322170.734
248_M254_V0.322090.733
47_P93_F0.32020.729
163_F283_E0.319640.728
204_P259_G0.319630.728
110_A115_I0.319050.726
156_D160_A0.318250.725
142_L146_Y0.316220.720
33_I86_E0.314860.717
253_L272_P0.314810.717
245_A248_M0.313690.714
48_V52_P0.313220.713
196_L251_A0.311820.710
278_R281_Q0.30940.704
211_L233_N0.309320.704
168_P171_F0.307880.701
142_L145_R0.306440.698
190_E218_Q0.305060.695
163_F175_F0.304970.694
123_Q128_H0.304890.694
194_K250_A0.304230.693
189_P192_E0.303250.690
144_E147_I0.301310.686
195_I253_L0.30.683
22_A46_F0.299150.681
16_S239_F0.298070.679
21_L101_D0.297990.679
247_L251_A0.297620.678
221_V234_I0.296570.675
28_H97_L0.295250.672
157_R161_L0.294390.670
113_A116_P0.293240.668
166_P175_F0.293180.668
117_V155_A0.292680.666
110_A156_D0.292640.666
159_L176_V0.292310.666
192_E216_D0.291870.665
153_P156_D0.291440.664
17_R101_D0.291270.663
172_R176_V0.288850.658
256_S273_A0.288680.657
50_E53_G0.288120.656
240_S246_E0.287430.654
13_G17_R0.28710.654
17_R20_A0.286530.652
18_C122_N0.286450.652
52_P85_R0.285560.650
20_A24_A0.285430.650
261_T264_S0.283410.645
12_L17_R0.283380.645
228_D236_V0.282910.644
120_I123_Q0.282090.642
184_I245_A0.280760.639
163_F167_L0.280290.638
189_P193_P0.279910.637
221_V236_V0.279710.637
95_P98_V0.279660.637
248_M266_A0.279480.636
83_I109_A0.279010.635
199_F262_T0.27830.634
12_L15_A0.278160.633
97_L116_P0.278070.633
166_P173_V0.278040.633
33_I95_P0.277140.631
243_D247_L0.277080.631
29_E96_D0.277050.631
101_D261_T0.276760.630
34_T48_V0.276740.630
255_I274_L0.276450.629
210_A214_L0.276270.629
254_V273_A0.276170.629
84_R92_E0.275370.627
168_P172_R0.274690.625
120_I261_T0.274670.625
198_Y207_L0.273940.624
14_H18_C0.273790.623
207_L210_A0.272480.620
110_A113_A0.270640.616
182_P268_A0.269850.614
7_V32_F0.267980.610
161_L165_P0.267940.610
2_K28_H0.267910.610
6_Y33_I0.266210.606
85_R89_W0.264060.601
210_A255_I0.263660.600
39_P43_K0.263250.599
201_G262_T0.263110.599
191_D194_K0.261280.595
202_G228_D0.261240.595
8_Q102_F0.261080.594
141_R144_E0.260880.594
81_R84_R0.260710.594
124_Y127_L0.260550.593
249_A271_K0.259920.592
185_R269_L0.25940.591
21_L24_A0.2580.587
140_G144_E0.257280.586
153_P158_R0.256990.585
218_Q252_D0.256460.584
123_Q261_T0.256250.583
123_Q201_G0.255680.582
184_I187_L0.254940.580
91_R112_R0.254880.580
167_L171_F0.254780.580
256_S275_V0.254330.579
10_H32_F0.253150.576
17_R120_I0.25290.576
6_Y98_V0.252750.575
207_L211_L0.250840.571
180_I268_A0.250650.571
195_I198_Y0.250250.570
7_V10_H0.249430.568
208_I221_V0.248510.566
5_F21_L0.248450.566
189_P218_Q0.248070.565
224_P236_V0.247940.565
261_T265_E0.247810.564
49_R52_P0.24780.564
196_L219_F0.247070.563
187_L246_E0.247040.562
200_G262_T0.246710.562
194_K251_A0.246150.560
185_R245_A0.245850.560
12_L16_S0.245480.559
175_F178_P0.244860.558
152_F156_D0.243020.553
248_M251_A0.242530.552
28_H31_T0.241640.550
161_L178_P0.24140.550
125_W128_H0.240880.548
7_V35_S0.240850.548
87_I109_A0.23990.546
252_D271_K0.239530.545
121_S124_Y0.239190.545
49_R53_G0.239180.545
166_P170_F0.239120.544
235_H250_A0.238860.544
169_P173_V0.238530.543
258_G262_T0.238180.542
109_A112_R0.237750.541
48_V54_L0.237660.541
258_G265_E0.236930.539
179_I182_P0.236250.538
5_F8_Q0.235670.537
15_A19_L0.235670.537
100_S107_A0.234780.535
152_F158_R0.234180.533
111_R154_P0.23370.532
200_G223_G0.232740.530
180_I265_E0.23240.529
210_A276_I0.231840.528
80_A88_R0.231150.526
106_A110_A0.230890.526
160_A165_P0.230590.525
120_I262_T0.229550.523
15_A102_F0.22950.523
21_L120_I0.229050.522
225_N236_V0.228760.521
87_I90_L0.228730.521
103_Y121_S0.227940.519
157_R160_A0.227840.519
193_P250_A0.22680.516
146_Y150_Y0.226410.516
147_I150_Y0.226340.515
196_L217_Y0.226310.515
103_Y123_Q0.226040.515
51_I54_L0.225980.515
123_Q200_G0.225650.514
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
3froA0.95281000.324
2qzsA0.97171000.349
3okpA0.89311000.352
1rzuA0.97481000.354
2r60A0.94031000.354
1f0kA0.89941000.355
3c48A0.93711000.357
2gekA0.88991000.367
2iuyA0.79561000.372
2x6qA0.89311000.377

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