GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Polysacc_synt_2 - Polysaccharide biosynthesis protein
Pfam: PF02719 (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: CL0063
Length: 293
Sequences: 20231
Seq/Len: 69.05
HH_delta: 0.176 (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
6_A28_L2.370773.578
70_N117_E2.08533.147
61_G68_R1.81712.742
17_Q211_Q1.808842.730
102_K106_L1.634942.467
65_D68_R1.594632.406
237_L241_E1.526982.304
3_V15_V1.50722.275
29_F61_G1.483772.239
212_L228_L1.472972.223
122_R162_K1.461452.206
80_I217_A1.453582.194
96_N99_E1.430232.158
235_K238_D1.399192.112
17_Q21_Y1.384452.089
27_I78_P1.32842.005
2_L78_P1.305811.971
66_K113_E1.281641.934
64_R102_K1.248651.884
21_Y218_A1.247521.883
14_L84_A1.245721.880
70_N114_A1.2261.850
14_L82_F1.22481.848
184_K188_N1.209491.825
17_Q214_L1.206191.820
83_H125_F1.185251.789
27_I59_V1.170631.767
211_Q215_Q1.16711.761
17_Q20_R1.160511.751
238_D241_E1.153981.741
168_F213_V1.146271.730
166_V216_A1.140791.722
66_K70_N1.13011.705
242_A246_L1.119451.689
79_D121_E1.116051.684
109_Q113_E1.108481.673
242_A245_E1.105651.669
15_V28_L1.102341.664
4_T83_H1.095491.653
98_F102_K1.021381.541
82_F217_A1.018761.537
108_T145_A1.016611.534
126_I213_V1.016071.533
68_R71_R1.009891.524
70_N118_H1.001141.511
109_Q148_L0.99611.503
14_L210_V0.989341.493
66_K110_N0.987141.490
6_A15_V0.97831.476
149_V163_F0.957551.445
104_N141_T0.943161.423
113_E116_I0.934691.411
143_R147_K0.92991.403
32_D58_P0.928951.402
115_A123_F0.909491.373
73_F81_V0.907731.370
122_R164_S0.902791.362
81_V115_A0.889831.343
185_Q190_G0.888921.341
70_N74_E0.886311.338
125_F145_A0.880051.328
214_L218_A0.877281.324
83_H108_T0.862491.302
215_Q219_L0.846351.277
198_D235_K0.843171.272
111_V123_F0.837361.264
166_V213_V0.83371.258
1_V80_I0.830061.253
200_T233_P0.82521.245
205_T208_E0.823321.242
106_L109_Q0.819841.237
10_I171_V0.818821.236
112_A152_A0.818711.236
16_R175_R0.818461.235
66_K117_E0.817941.234
116_I156_S0.817891.234
153_N163_F0.817211.233
241_E244_I0.814331.229
32_D35_K0.810761.224
74_E118_H0.809821.222
71_R74_E0.809521.222
63_V107_G0.793021.197
16_R20_R0.789931.192
67_E71_R0.778721.175
147_K150_Q0.77621.171
113_E117_E0.770891.163
37_Y40_E0.764961.154
114_A118_H0.76451.154
21_Y214_L0.763441.152
68_R72_I0.759741.147
1_V18_L0.75781.144
123_F149_V0.754731.139
67_E70_N0.754291.138
2_L29_F0.754181.138
69_L114_A0.751971.135
84_A126_I0.750661.133
17_Q207_E0.740211.117
17_Q210_V0.737421.113
29_F69_L0.733561.107
63_V85_A0.731551.104
82_F213_V0.730341.102
202_F231_G0.729631.101
29_F68_R0.726551.096
206_I210_V0.72521.094
126_I168_F0.724951.094
105_V144_L0.724161.093
31_R62_D0.718831.085
168_F209_A0.717091.082
138_M142_K0.713111.076
125_F165_S0.70361.062
18_L214_L0.701281.058
103_T107_G0.698341.054
146_E167_R0.697391.052
59_V72_I0.693971.047
29_F72_I0.68791.038
150_Q165_S0.687741.038
115_A120_V0.686911.037
234_V239_L0.683621.032
215_Q218_A0.683431.031
7_G30_D0.680111.026
156_S160_D0.67551.019
125_F149_V0.674761.018
73_F115_A0.674531.018
13_E207_E0.672121.014
167_R225_I0.671821.014
198_D237_L0.671671.014
132_V143_R0.665961.005
73_F78_P0.665041.004
4_T85_A0.664561.003
34_N38_E0.661980.999
121_E162_K0.660550.997
204_M209_A0.650310.981
167_R227_V0.648670.979
140_A144_L0.646310.975
162_K222_G0.64580.975
106_L110_N0.642320.969
101_V105_V0.636940.961
238_D242_A0.633060.955
101_V144_L0.631790.953
14_L18_L0.627570.947
35_K39_L0.62740.947
112_A123_F0.620720.937
140_A147_K0.620380.936
116_I161_T0.618740.934
234_V238_D0.618630.934
27_I77_K0.615570.929
87_L103_T0.613960.927
9_S173_G0.611880.923
127_S146_E0.60830.918
81_V111_V0.607460.917
1_V82_F0.606830.916
4_T111_V0.605160.913
36_L40_E0.60240.909
151_A155_Y0.597690.902
148_L151_A0.597540.902
13_E16_R0.593830.896
241_E245_E0.586430.885
150_Q154_Q0.584890.883
9_S206_I0.583550.881
19_L26_L0.580120.875
183_K187_K0.578450.873
181_L185_Q0.577870.872
15_V26_L0.575830.869
65_D69_L0.574390.867
114_A117_E0.574110.866
244_I247_S0.570580.861
84_A213_V0.569030.859
124_V166_V0.568520.858
110_N114_A0.567420.856
186_I243_M0.56560.854
63_V103_T0.559810.845
34_N37_Y0.559090.844
240_A244_I0.551380.832
94_E137_V0.549270.829
13_E17_Q0.54280.819
81_V123_F0.541460.817
36_L39_L0.540340.815
113_E152_A0.539930.815
93_M100_A0.539380.814
164_S216_A0.534640.807
172_L205_T0.533490.805
33_E60_I0.529740.799
197_P237_L0.525740.793
74_E77_K0.524110.791
169_G229_D0.522340.788
73_F114_A0.521880.788
83_H111_V0.521860.788
73_F118_H0.517090.780
101_V140_A0.516930.780
108_T149_V0.516170.779
234_V242_A0.514660.777
178_V182_F0.512830.774
112_A148_L0.511640.772
92_L96_N0.508020.767
61_G65_D0.505750.763
101_V141_T0.505230.762
61_G72_I0.504720.762
145_A149_V0.503830.760
152_A156_S0.503250.759
3_V18_L0.502970.759
184_K187_K0.500780.756
140_A151_A0.500190.755
13_E206_I0.499940.754
18_L22_G0.498390.752
181_L184_K0.496620.749
59_V68_R0.495760.748
110_N113_E0.494540.746
99_E102_K0.494290.746
1_V217_A0.494170.746
200_T235_K0.491280.741
72_I78_P0.48920.738
69_L110_N0.483360.729
150_Q163_F0.482010.727
171_V209_A0.480750.726
64_R103_T0.479530.724
183_K243_M0.479490.724
87_L99_E0.478520.722
101_V106_L0.47830.722
150_Q225_I0.478280.722
32_D60_I0.475720.718
168_F171_V0.473220.714
179_I239_L0.47110.711
216_A226_F0.471070.711
12_S16_R0.46930.708
15_V22_G0.467530.706
112_A149_V0.467080.705
212_L216_A0.466310.704
2_L72_I0.466150.703
153_N162_K0.462260.698
207_E210_V0.462140.697
35_K38_E0.460490.695
194_V240_A0.460160.694
109_Q152_A0.459110.693
174_S205_T0.458650.692
116_I152_A0.457150.690
69_L73_F0.453470.684
165_S225_I0.452250.682
87_L100_A0.451210.681
151_A154_Q0.448340.677
166_V228_L0.448090.676
144_L148_L0.44430.671
80_I124_V0.443860.670
211_Q214_L0.442520.668
9_S13_E0.442270.667
15_V19_L0.441170.666
214_L217_A0.439540.663
27_I72_I0.438910.662
33_E37_Y0.437590.660
12_S175_R0.436910.659
147_K151_A0.435260.657
208_E230_M0.433360.654
186_I192_L0.43310.654
2_L81_V0.432870.653
83_H123_F0.431130.651
13_E210_V0.430590.650
148_L152_A0.43050.650
21_Y215_Q0.429110.648
21_Y211_Q0.429080.648
66_K114_A0.428060.646
7_G31_R0.427590.645
182_F192_L0.427490.645
149_V165_S0.424520.641
2_L73_F0.424120.640
86_A104_N0.423390.639
10_I209_A0.423030.638
194_V237_L0.419610.633
7_G32_D0.419420.633
115_A161_T0.416490.629
183_K247_S0.415210.627
29_F59_V0.414970.626
135_T154_Q0.414860.626
164_S220_A0.41410.625
100_A141_T0.413660.624
98_F109_Q0.41310.623
80_I122_R0.412390.622
150_Q153_N0.412230.622
99_E103_T0.411130.620
74_E117_E0.410710.620
177_S180_P0.409080.617
22_G26_L0.408030.616
213_V216_A0.40780.615
186_I244_I0.40770.615
207_E211_Q0.406420.613
73_F111_V0.403040.608
5_G8_G0.40280.608
129_D169_G0.401770.606
124_V213_V0.401330.606
14_L213_V0.398760.602
182_F240_A0.398740.602
212_L215_Q0.397140.599
210_V214_L0.393810.594
185_Q189_G0.390660.590
64_R99_E0.39060.589
80_I121_E0.389230.587
124_V164_S0.388580.586
178_V181_L0.387750.585
84_A168_F0.384950.581
16_R19_L0.381730.576
134_P143_R0.379360.572
35_K40_E0.378530.571
204_M208_E0.378520.571
140_A143_R0.378240.571
18_L217_A0.377760.570
138_M141_T0.377560.570
98_F110_N0.375810.567
14_L214_L0.374440.565
164_S224_E0.372850.563
107_G110_N0.372220.562
108_T112_A0.37070.559
184_K189_G0.370460.559
210_V213_V0.369290.557
73_F120_V0.36660.553
130_K139_G0.365910.552
121_E160_D0.365560.552
63_V111_V0.364820.551
3_V14_L0.364070.549
93_M137_V0.363410.548
208_E211_Q0.363350.548
7_G28_L0.362810.548
77_K118_H0.362770.547
169_G202_F0.3610.545
221_K224_E0.36070.544
32_D36_L0.35850.541
16_R207_E0.357860.540
136_N139_G0.357560.540
112_A116_I0.357140.539
105_V109_Q0.356920.539
163_F223_G0.356850.539
25_K79_D0.355370.536
144_L147_K0.353470.533
3_V6_A0.352360.532
170_N203_F0.351780.531
11_G15_V0.350410.529
185_Q193_T0.34960.528
104_N138_M0.34880.526
32_D37_Y0.347870.525
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
4j2oA0.94541000.176
3w1vA0.9421000.176
3nzoA0.96931000.209
2gn4A0.92831000.229
3rufA0.96931000.251
4egbA0.94881000.265
3m2pA0.88741000.284
3enkA0.94541000.285
3slgA0.93171000.287
2p5yA0.91131000.295

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