GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Polysacc_synt_3 - Polysaccharide biosynthesis protein
Pfam: PF13440 (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: CL0222
Length: 251
Sequences: 15027
Seq/Len: 59.87
HH_delta: 0.3 (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
52_D55_D1.571834.193
119_R122_A1.508894.025
24_A223_S1.359033.625
103_F160_L1.314763.507
91_F95_L1.110562.962
92_W149_W1.06232.834
184_R187_K0.902822.408
121_R125_L0.886582.365
126_I165_I0.808752.157
16_G19_D0.781872.086
206_D222_Y0.766072.043
96_L149_W0.738331.969
215_G218_A0.730981.950
99_L102_F0.72251.927
100_A156_I0.710761.896
126_I166_S0.705011.881
147_N150_S0.695031.854
58_S179_K0.671091.790
75_A79_I0.667891.781
8_L227_R0.657041.753
210_I214_L0.655871.749
149_W153_L0.651621.738
130_R162_A0.647371.727
133_L161_L0.645011.720
83_Y91_F0.639441.706
106_L163_L0.636761.698
103_F163_L0.624751.666
55_D58_S0.593891.584
125_L129_V0.582421.554
210_I222_Y0.578631.543
53_K57_R0.577091.539
110_F166_S0.568411.516
164_L168_Y0.56451.506
150_S154_A0.5611.496
179_K182_W0.557291.486
214_L218_A0.556591.485
79_I95_L0.546541.458
113_I117_R0.543841.451
180_F184_R0.542411.447
77_L80_L0.541321.444
82_A95_L0.539291.438
11_L151_I0.53571.429
96_L152_L0.533371.423
96_L153_L0.530521.415
134_R155_F0.529431.412
9_I13_R0.521121.390
137_L154_A0.511051.363
54_Q58_S0.508831.357
44_S47_R0.505891.349
96_L156_I0.502721.341
138_L142_L0.502471.340
25_L211_G0.496841.325
69_L73_I0.49591.323
82_A91_F0.494741.320
60_L113_I0.4891.304
190_L194_L0.484391.292
26_I94_L0.472851.261
146_L150_S0.46761.247
23_Y27_F0.466961.246
107_S162_A0.466021.243
139_V143_Y0.463431.236
22_I89_E0.461641.231
211_G219_V0.459941.227
134_R158_S0.459611.226
79_I83_Y0.458811.224
17_P217_E0.453351.209
197_L201_L0.453091.209
23_Y148_L0.449221.198
44_S188_Y0.448511.196
9_I12_A0.445141.187
146_L153_L0.444621.186
149_W152_L0.442521.180
95_L99_L0.441081.177
218_A221_I0.440291.174
80_L83_Y0.435351.161
67_S109_L0.435191.161
138_L154_A0.434511.159
17_P220_G0.425951.136
102_F105_A0.425231.134
62_F66_V0.421831.125
99_L156_I0.421511.124
10_L138_L0.41481.106
165_I168_Y0.414451.105
122_A169_L0.406921.085
41_L63_S0.406751.085
129_V165_I0.404321.078
118_G247_K0.403671.077
179_K183_R0.397551.060
41_L44_S0.397141.059
154_A158_S0.396871.059
58_S62_F0.396521.058
186_L190_L0.395551.055
57_R61_R0.39351.050
188_Y192_F0.392361.047
181_S184_R0.391691.045
110_F163_L0.391671.045
217_E221_I0.39081.042
120_F243_V0.390471.042
204_Q207_R0.388081.035
129_V132_L0.387781.034
137_L141_L0.387711.034
210_I219_V0.386411.031
139_V142_L0.386041.030
46_V116_A0.385771.029
98_A101_I0.384291.025
239_A243_V0.384031.024
208_L212_Y0.383151.022
110_F167_F0.382891.021
138_L141_L0.381541.018
140_L144_L0.381191.017
115_R123_Y0.379231.012
158_S162_A0.378461.009
12_A20_F0.378131.009
17_P221_I0.377761.008
65_L69_L0.376541.004
45_L63_S0.375961.003
160_L164_L0.371140.990
30_V97_L0.370160.987
141_L146_L0.369680.986
140_L143_Y0.369260.985
186_L189_G0.369050.984
112_S115_R0.367580.980
180_F183_R0.365020.974
141_L144_L0.364940.973
183_R187_K0.364230.972
187_K191_P0.364110.971
31_S35_I0.364020.971
72_V76_I0.362450.967
111_R115_R0.361930.965
10_L142_L0.361590.964
63_S185_L0.358970.957
94_L98_A0.358880.957
78_A81_I0.358060.955
87_D216_P0.35770.954
23_Y151_I0.357690.954
73_I77_L0.356150.950
89_E92_W0.355660.949
19_D22_I0.354430.945
75_A102_F0.354010.944
96_L99_L0.353390.943
38_S42_R0.352170.939
46_V249_A0.351720.938
24_A220_G0.351640.938
103_F156_I0.351240.937
56_I117_R0.349070.931
153_L156_I0.348790.930
114_L122_A0.347160.926
100_A159_A0.346410.924
27_F31_S0.34360.917
10_L139_V0.342540.914
245_F249_A0.341430.911
139_V144_L0.341080.910
58_S182_W0.340640.909
136_L139_V0.340480.908
40_G189_G0.339890.907
153_L157_I0.338420.903
129_V133_L0.336980.899
62_F65_L0.336850.898
12_A224_V0.334760.893
95_L98_A0.334020.891
112_S116_A0.333630.890
67_S105_A0.332770.888
58_S61_R0.331460.884
92_W96_L0.331040.883
78_A98_A0.33060.882
42_R46_V0.330250.881
82_A94_L0.329450.879
25_L28_S0.329250.878
156_I159_A0.329010.878
222_Y226_Q0.328620.877
68_L106_L0.328560.876
227_R231_L0.328550.876
202_L205_I0.327370.873
45_L59_L0.326790.872
62_F183_R0.326610.871
8_L20_F0.326040.870
92_W95_L0.32560.868
190_L193_S0.325080.867
137_L157_I0.324820.866
130_R134_R0.324740.866
76_I80_L0.32420.865
8_L12_A0.322870.861
207_R211_G0.32220.859
133_L137_L0.322020.859
82_A98_A0.319510.852
55_D182_W0.319250.852
79_I82_A0.319140.851
25_L219_V0.31910.851
207_R219_V0.318660.850
43_Q47_R0.317780.848
98_A102_F0.317340.846
126_I162_A0.317260.846
17_P20_F0.317040.846
111_R127_D0.316360.844
68_L72_V0.316210.843
138_L151_I0.315120.841
206_D226_Q0.314780.840
21_G220_G0.313350.836
67_S70_L0.312440.833
125_L128_I0.311830.832
115_R120_F0.311780.832
192_F195_S0.309420.825
15_L19_D0.309360.825
128_I132_L0.308730.823
133_L158_S0.308390.823
99_L103_F0.308340.822
11_L23_Y0.308290.822
134_R154_A0.308270.822
20_F224_V0.307680.821
204_Q208_L0.306980.819
18_E216_P0.305740.816
48_S188_Y0.305620.815
132_L136_L0.30470.813
226_Q229_A0.304410.812
126_I130_R0.304380.812
223_S227_R0.304350.812
219_V223_S0.30350.810
71_A75_A0.303390.809
206_D209_L0.303320.809
205_I209_L0.302950.808
156_I160_L0.302150.806
76_I79_I0.30160.804
31_S34_S0.301460.804
59_L182_W0.30090.803
107_S163_L0.30010.800
39_L42_R0.29890.797
21_G219_V0.298650.797
22_I216_P0.298290.796
155_F159_A0.297620.794
55_D59_L0.297140.793
114_L166_S0.296930.792
168_Y171_R0.296890.792
46_V112_S0.296330.790
54_Q57_R0.296090.790
200_W204_Q0.295750.789
56_I60_L0.295740.789
179_K184_R0.295660.789
74_L78_A0.295530.788
44_S185_L0.295390.788
91_F94_L0.294340.785
226_Q230_S0.293120.782
199_S203_S0.292220.779
237_S241_S0.290170.774
187_K190_L0.289770.773
217_E220_G0.28970.773
143_Y146_L0.289310.772
15_L148_L0.288620.770
47_R188_Y0.288370.769
122_A125_L0.288070.768
232_P237_S0.285870.763
78_A82_A0.285830.762
61_R65_L0.285510.762
79_I91_F0.284080.758
71_A98_A0.283230.755
107_S159_A0.282680.754
229_A232_P0.282650.754
119_R123_Y0.282110.752
158_S161_L0.280850.749
28_S223_S0.280660.749
45_L112_S0.280130.747
208_L211_G0.27940.745
28_S207_R0.278980.744
48_S55_D0.278060.742
63_S109_L0.277140.739
119_R125_L0.276940.739
19_D89_E0.276470.737
233_A237_S0.275980.736
88_P92_W0.275390.735
167_F171_R0.275160.734
93_L152_L0.273170.729
114_L117_R0.272810.728
88_P91_F0.272260.726
18_E21_G0.271650.725
151_I154_A0.270840.722
239_A242_S0.270410.721
205_I208_L0.269350.718
188_Y191_P0.269130.718
186_L191_P0.268010.715
161_L165_I0.267690.714
77_L81_I0.267630.714
43_Q46_V0.26740.713
71_A102_F0.267330.713
8_L11_L0.267080.712
109_L112_S0.266980.712
26_I97_L0.266650.711
26_I93_L0.266580.711
130_R158_S0.266250.710
18_E89_E0.265930.709
28_S35_I0.265850.709
121_R124_A0.26420.705
78_A95_L0.263890.704
15_L20_F0.263880.704
209_L212_Y0.263670.703
244_F248_L0.262970.701
194_L197_L0.262420.700
107_S166_S0.262310.700
75_A78_A0.261170.697
227_R230_S0.26060.695
220_G224_V0.259580.692
122_A165_I0.258210.689
120_F124_A0.257720.687
45_L116_A0.257690.687
60_L110_F0.256240.683
204_Q230_S0.255950.683
242_S245_F0.255670.682
178_F183_R0.255070.680
114_L123_Y0.254440.679
21_G24_A0.254160.678
20_F24_A0.254030.678
103_F107_S0.253640.677
162_A166_S0.253640.677
137_L140_L0.253610.676
108_Q111_R0.253550.676
230_S235_L0.253090.675
56_I59_L0.252420.673
100_A103_F0.25090.669
69_L72_V0.25060.668
35_I200_W0.250510.668
136_L140_L0.250070.667
75_A95_L0.250010.667
238_S242_S0.248870.664
59_L63_S0.248810.664
9_I20_F0.247590.660
10_L143_Y0.246280.657
57_R177_S0.246150.657
53_K56_I0.245140.654
116_A120_F0.243140.649
225_A229_A0.242570.647
166_S169_L0.24230.646
38_S239_A0.24220.646
73_I76_I0.240830.642
126_I169_L0.240770.642
97_L152_L0.240590.642
232_P244_F0.239250.638
203_S226_Q0.238020.635
75_A99_L0.237370.633
134_R138_L0.236940.632
140_L145_G0.236730.631
61_R176_L0.235990.629
159_A162_A0.235690.629
193_S198_L0.235440.628
102_F106_L0.235190.627
83_Y95_L0.235150.627
19_D148_L0.234820.626
27_F30_V0.233930.624
195_S199_S0.233160.622
66_V183_R0.232980.621
141_L151_I0.232710.621
96_L100_A0.232320.620
111_R126_I0.23190.619
111_R166_S0.231750.618
165_I169_L0.231720.618
24_A227_R0.231190.617
92_W153_L0.230730.615
177_S180_F0.23020.614
22_I93_L0.229140.611
68_L71_A0.228840.610
104_S159_A0.227990.608
223_S226_Q0.227590.607
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
3w4tA0.98899.80.3
3mktA0.984199.80.32
4humA0.984199.60.436
3w4tA0.74198.80.64
3mktA0.737198.60.662
4humA0.74198.10.711
1pw4A0.924337.50.9
3zuxA0.74126.20.908
2gfpA0.888410.90.922
3o7qA0.91637.60.927

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