GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glycos_transf_3 - Glycosyl transferase family ab domain
Pfam: PF00591 (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. )
Length: 252
Sequences: 2842
Seq/Len: 11.28
HH_delta: 0.019 (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
29_A245_A0.870774.078
215_R247_D0.75373.529
68_A72_E0.687533.219
204_A209_E0.644023.016
154_I160_T0.617692.892
70_L76_A0.600222.811
62_S65_E0.599162.806
244_E248_S0.583742.733
207_A252_L0.560012.622
192_G198_N0.557442.610
30_A245_A0.548132.567
178_E184_R0.544052.548
22_A202_L0.506922.374
129_E172_E0.468352.193
154_I224_A0.465332.179
66_A76_A0.462992.168
234_S237_E0.455022.131
219_L243_R0.448732.101
232_A238_G0.446772.092
128_A163_Y0.437332.048
164_E173_Y0.43442.034
104_N108_P0.425661.993
136_R165_L0.424571.988
223_A238_G0.42081.970
186_P189_E0.419741.966
58_P65_E0.41931.963
30_A226_L0.415851.947
65_E68_A0.408521.913
243_R247_D0.404221.893
200_R204_A0.398861.868
231_K241_K0.38991.826
32_V231_K0.386961.812
27_L225_A0.384531.801
27_L32_V0.384051.798
240_E243_R0.380571.782
61_L69_Q0.374731.755
233_S237_E0.371961.742
26_V218_V0.366141.715
23_A222_A0.365571.712
148_G153_E0.356381.669
215_R243_R0.356311.668
40_R50_D0.351651.647
125_P161_R0.346691.623
61_L65_E0.344671.614
162_V173_Y0.330671.548
54_A196_E0.313841.470
14_D151_S0.31371.469
143_A165_L0.312451.463
144_L228_V0.310121.452
244_E250_K0.309931.451
159_P174_E0.308391.444
129_E133_E0.307371.439
90_L93_V0.303661.422
32_V226_L0.31.405
188_E191_E0.299391.402
20_S77_F0.296291.387
69_Q73_T0.294871.381
142_R166_K0.293961.377
156_P185_A0.292881.371
144_L224_A0.291911.367
67_Q71_E0.291511.365
245_A248_S0.288381.350
135_L143_A0.287281.345
140_Y143_A0.284371.332
49_A59_I0.282651.324
176_D184_R0.281381.318
176_D179_D0.280241.312
223_A239_V0.279621.309
223_A227_Y0.279491.309
222_A242_A0.270861.268
203_R252_L0.270191.265
238_G242_A0.269611.262
163_Y170_I0.268951.259
87_L90_L0.267321.252
227_Y234_S0.265411.243
203_R207_A0.260661.221
40_R53_E0.254571.192
26_V222_A0.253161.185
133_E136_R0.252521.182
153_E156_P0.252241.181
155_S158_G0.249271.167
219_L239_V0.248471.164
196_E200_R0.248451.163
55_L199_A0.24461.145
32_V229_A0.244361.144
148_G152_D0.243561.141
241_K244_E0.24191.133
49_A79_F0.237841.114
51_V199_A0.237741.113
182_L220_L0.237631.113
227_Y232_A0.237351.111
245_A250_K0.236051.105
227_Y238_G0.235581.103
142_R164_E0.234231.097
154_I175_L0.233331.093
206_L251_A0.232781.090
219_L242_A0.2311.082
51_V202_L0.230811.081
6_I23_A0.229761.076
26_V246_I0.227181.064
148_G158_G0.225511.056
66_A83_F0.223691.047
26_V242_A0.222471.042
4_V225_A0.222261.041
159_P176_D0.222191.040
208_G247_D0.222081.040
33_P71_E0.221611.038
160_T177_P0.221111.035
236_E240_E0.220951.035
68_A71_E0.220181.031
159_P163_Y0.21981.029
156_P190_L0.219391.027
64_E68_A0.218081.021
216_D239_V0.216011.012
240_E244_E0.215861.011
6_I48_S0.215561.009
93_V96_E0.214431.004
161_R174_E0.213941.002
239_V243_R0.211760.992
154_I220_L0.211660.991
105_T127_Y0.211610.991
85_P90_L0.207560.972
219_L247_D0.207540.972
185_A190_L0.207180.970
14_D187_L0.205850.964
161_R172_E0.205650.963
92_P96_E0.205630.963
215_R219_L0.20530.961
164_E227_Y0.204950.960
87_L91_A0.203920.955
63_P67_Q0.202980.950
141_G167_N0.20280.950
27_L229_A0.201830.945
173_Y227_Y0.201760.945
133_E170_I0.199470.934
66_A78_L0.19810.928
22_A201_I0.197560.925
66_A70_L0.197230.924
232_A241_K0.196860.922
27_L30_A0.196260.919
209_E212_P0.195520.916
87_L110_L0.194890.913
199_A203_R0.192980.904
120_I131_M0.192620.902
148_G155_S0.192380.901
23_A27_L0.190360.891
20_S36_K0.189620.888
7_C48_S0.188580.883
57_V75_I0.188090.881
22_A205_V0.187530.878
237_E241_K0.185950.871
127_Y130_L0.185290.868
244_E247_D0.184930.866
6_I24_A0.184010.862
53_E59_I0.183430.859
27_L33_P0.182960.857
42_V81_P0.18290.856
226_L232_A0.182680.855
21_T52_L0.182260.853
33_P74_G0.180910.847
48_S51_V0.180420.845
241_K245_A0.179070.839
165_L170_I0.178720.837
185_A216_D0.177640.832
225_A228_V0.175690.823
4_V32_V0.175360.821
156_P217_A0.175240.821
69_Q75_I0.174990.819
208_G215_R0.174590.818
25_I75_I0.174280.816
224_A235_L0.174130.815
26_V251_A0.174080.815
180_F239_V0.173970.815
223_A242_A0.173870.814
13_G43_T0.172890.810
21_T192_G0.172880.810
27_L222_A0.170030.796
201_I204_A0.169350.793
227_Y235_L0.168760.790
60_D82_N0.16870.790
206_L252_L0.168490.789
136_R170_I0.168090.787
14_D191_E0.167760.786
215_R246_I0.167330.784
24_A75_I0.1670.782
69_Q76_A0.166890.781
65_E69_Q0.166710.781
182_L239_V0.166080.778
7_C23_A0.165640.776
205_V218_V0.165450.775
111_N160_T0.164850.772
15_K191_E0.164280.769
127_Y167_N0.164090.768
232_A237_E0.161850.758
13_G100_R0.161090.754
16_T151_S0.160940.754
3_V33_P0.160440.751
230_G238_G0.160330.751
37_H80_A0.160160.750
123_F127_Y0.15880.744
179_D236_E0.158420.742
58_P61_L0.158140.741
26_V245_A0.157890.739
144_L227_Y0.157530.738
111_N164_E0.157420.737
90_L202_L0.157330.737
183_K216_D0.156820.734
49_A77_F0.155840.730
53_E99_I0.155830.730
218_V221_N0.155020.726
64_E67_Q0.154430.723
166_K171_T0.154290.722
100_R124_H0.153020.717
163_Y172_E0.152970.716
157_L186_P0.152530.714
219_L223_A0.15150.709
198_N201_I0.151240.708
201_I205_V0.149140.698
248_S251_A0.149050.698
176_D220_L0.149050.698
27_L34_V0.149030.698
26_V127_Y0.148310.694
189_E196_E0.14830.694
22_A218_V0.148050.693
4_V23_A0.147730.692
185_A189_E0.145970.684
223_A235_L0.145630.682
200_R203_R0.145590.682
34_V225_A0.145540.682
87_L92_P0.144970.679
51_V55_L0.144870.678
165_L168_G0.144670.677
37_H112_P0.144420.676
30_A241_K0.144220.675
152_D155_S0.144110.675
91_A95_R0.143830.674
215_R218_V0.143590.672
241_K250_K0.142620.668
144_L173_Y0.142360.667
135_L140_Y0.141750.664
4_V228_V0.141320.662
119_V146_V0.141060.661
226_L238_G0.14060.658
237_E240_E0.140530.658
125_P130_L0.140480.658
123_F165_L0.140460.658
226_L242_A0.140430.658
190_L217_A0.139590.654
12_D16_T0.139470.653
59_I79_F0.139030.651
128_A145_V0.138750.650
144_L162_V0.138610.649
166_K169_E0.138470.648
62_S82_N0.138470.648
165_L171_T0.137770.645
37_H84_H0.137680.645
230_G233_S0.137560.644
157_L187_L0.137080.642
126_E191_E0.136950.641
200_R209_E0.136710.640
176_D180_F0.136450.639
66_A69_Q0.135940.637
63_P83_F0.135490.634
4_V229_A0.135390.634
30_A242_A0.13520.633
192_G199_A0.135170.633
4_V133_E0.134910.632
197_E200_R0.133950.627
21_T25_I0.133320.624
52_L57_V0.133260.624
100_R122_V0.133230.624
200_R207_A0.13320.624
6_I119_V0.133110.623
185_A212_P0.132960.623
27_L226_L0.132760.622
220_L239_V0.132230.619
128_A161_R0.131730.617
86_A95_R0.131540.616
154_I180_F0.13140.615
10_G36_K0.130990.613
134_A137_D0.13080.612
165_L202_L0.130740.612
202_L206_L0.130630.612
14_D125_P0.130350.610
155_S159_P0.130320.610
140_Y175_L0.129890.608
22_A246_I0.12980.608
99_I103_F0.129120.605
86_A90_L0.128540.602
81_P95_R0.128510.602
228_V232_A0.128490.602
212_P215_R0.128150.600
5_D48_S0.12750.597
102_V109_L0.127070.595
239_V242_A0.126060.590
175_L182_L0.126030.590
148_G160_T0.126010.590
183_K186_P0.124930.585
128_A172_E0.124520.583
147_K153_E0.124270.582
207_A249_G0.124210.582
88_K92_P0.123920.580
20_S34_V0.123470.578
87_L95_R0.123310.577
88_K95_R0.123230.577
125_P191_E0.1230.576
49_A53_E0.122310.573
37_H131_M0.122220.572
141_G230_G0.121920.571
221_N228_V0.121140.567
119_V228_V0.120940.566
178_E183_K0.120730.565
80_A84_H0.120520.564
10_G20_S0.120420.564
246_I251_A0.119930.562
105_T124_H0.119860.561
43_T98_G0.11940.559
25_I57_V0.119310.559
12_D44_S0.119110.558
64_E241_K0.118360.554
51_V95_R0.118230.554
42_V48_S0.117920.552
109_L120_I0.117830.552
105_T110_L0.117560.550
151_S155_S0.117550.550
223_A226_L0.117510.550
93_V97_L0.117230.549
14_D42_V0.117140.549
35_A78_L0.117070.548
155_S217_A0.117040.548
69_Q72_E0.116790.547
122_V131_M0.116640.546
164_E171_T0.116390.545
156_P177_P0.116310.545
11_G108_P0.116220.544
204_A207_A0.116080.544
155_S160_T0.11590.543
175_L180_F0.115450.541
216_D243_R0.115410.540
42_V91_A0.115390.540
245_A251_A0.115190.539
70_L109_L0.115190.539
235_L238_G0.115170.539
120_I135_L0.114590.537
86_A92_P0.114390.536
158_G173_Y0.114290.535
58_P82_N0.113870.533
234_S240_E0.113750.533
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
1khdA0.9961000.019
1vquA0.9961000.032
4hkmA0.9961000.039
2elcA0.98021000.04
3r88A0.99211000.051
1o17A0.98411000.057
3h5qA0.84521000.316
2tptA0.8731000.327
1uouA0.90481000.329
2dsjA0.83731000.332

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