GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Transket_pyr - Transketolase pyrimidine binding domain
Pfam: PF02779 (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: CL0254
Length: 178
Sequences: 6594
Seq/Len: 37.04
HH_delta: 0.158 (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
142_V153_L1.264713.070
64_A78_E1.197042.906
18_E42_A1.088982.644
18_E44_P1.016262.467
140_K162_S0.936072.272
14_A44_P0.924072.243
75_P106_P0.91442.220
24_V67_L0.859512.087
14_A45_F0.846242.054
16_L155_R0.832742.022
3_I11_E0.828072.010
61_V100_M0.750581.822
15_E151_K0.739251.795
16_L159_R0.725931.762
157_A166_V0.721611.752
67_L74_R0.706051.714
108_P157_A0.673821.636
139_M167_Y0.66061.604
140_K164_G0.659151.600
129_D169_R0.657411.596
104_Q138_G0.650871.580
15_E155_R0.645641.567
16_L19_E0.628191.525
133_L167_Y0.614521.492
7_D35_F0.60841.477
25_V30_L0.594051.442
155_R159_R0.591711.436
131_A135_S0.58691.425
106_P163_D0.585011.420
12_A151_K0.576861.400
17_A39_F0.575821.398
94_D109_V0.572351.389
15_E18_E0.572131.389
38_T41_L0.570241.384
8_A147_P0.569191.382
18_E43_F0.567511.378
142_V166_V0.564511.370
7_D11_E0.563911.369
106_P164_G0.5611.362
140_K166_V0.550371.336
26_I53_T0.540911.313
61_V111_T0.527191.280
11_E151_K0.526041.277
15_E19_E0.525461.276
152_G156_A0.524261.273
3_I8_A0.52381.272
16_L23_V0.519941.262
22_R74_R0.518961.260
136_I139_M0.51361.247
12_A155_R0.511621.242
26_I51_I0.502571.220
20_D75_P0.501241.217
68_A107_V0.500121.214
77_V158_I0.499061.212
31_G52_N0.497781.208
26_I64_A0.495641.203
93_F132_I0.488771.187
83_D129_D0.487741.184
110_G167_Y0.487151.183
11_E15_E0.486881.182
148_A152_G0.486411.181
9_F154_L0.484071.175
74_R163_D0.476971.158
61_V78_E0.476431.157
65_A100_M0.471781.145
64_A107_V0.470371.142
25_V38_T0.470041.141
20_D23_V0.466981.134
20_D158_I0.465681.130
17_A23_V0.465211.129
75_P108_P0.460121.117
152_G155_R0.458481.113
14_A18_E0.456831.109
13_L76_P0.455961.107
82_A169_R0.452951.100
96_I139_M0.448651.089
3_I7_D0.4481.088
85_L113_A0.440821.070
122_G125_H0.439021.066
24_V74_R0.43861.065
7_D174_L0.436771.060
16_L158_I0.435961.058
12_A15_E0.435191.056
108_P166_V0.433181.052
25_V50_F0.431731.048
28_A34_T0.431041.046
139_M165_P0.429151.042
38_T42_A0.427171.037
19_E155_R0.425541.033
8_A12_A0.421571.023
34_T79_S0.421561.023
82_A133_L0.419881.019
100_M107_V0.415931.010
61_V92_A0.415031.008
130_E141_V0.414521.006
11_E38_T0.413191.003
65_A94_D0.413171.003
150_A170_E0.411460.999
7_D10_G0.410490.996
12_A16_L0.410050.995
69_L105_L0.409620.994
12_A154_L0.408560.992
148_A151_K0.406650.987
58_Q95_Q0.404110.981
68_A76_P0.404020.981
102_Y122_G0.400740.973
130_E169_R0.400380.972
157_A168_I0.399940.971
19_E159_R0.399920.971
112_R170_E0.399490.970
142_V157_A0.39870.968
171_P175_Y0.398090.966
85_L132_I0.386120.937
24_V51_I0.383960.932
32_G37_V0.38330.930
132_I136_I0.381210.925
25_V77_V0.379720.922
145_S149_E0.379570.921
142_V156_A0.3790.920
85_L133_L0.377640.917
14_A38_T0.375630.912
26_I60_M0.374280.909
14_A43_F0.371930.903
10_G14_A0.365360.887
149_E153_L0.365090.886
28_A60_M0.364620.885
4_S7_D0.363030.881
32_G52_N0.362860.881
86_T129_D0.360080.874
40_G50_F0.360020.874
104_Q164_G0.358430.870
59_N63_M0.358110.869
151_K155_R0.353540.858
134_R141_V0.348620.846
9_F79_S0.347060.843
23_V76_P0.344260.836
156_A159_R0.343810.835
37_V41_L0.343360.834
56_A59_N0.340920.828
92_A111_T0.340260.826
63_M67_L0.335990.816
96_I133_L0.334440.812
27_G31_G0.332690.808
69_L103_G0.332170.806
7_D38_T0.330950.803
11_E39_F0.330370.802
82_A129_D0.32880.798
68_A105_L0.328140.797
154_L168_I0.325770.791
31_G50_F0.325460.790
108_P154_L0.322770.784
43_F49_R0.322040.782
22_R75_P0.320610.778
140_K156_A0.320260.777
64_A79_S0.317830.772
14_A50_F0.317380.770
101_A136_I0.314470.763
153_L156_A0.314460.763
121_G172_R0.313210.760
43_F52_N0.311240.756
85_L110_G0.308670.749
17_A38_T0.307810.747
67_L76_P0.30730.746
51_I63_M0.305850.742
162_S166_V0.304020.738
21_P158_I0.303810.738
141_V167_Y0.300060.728
26_I63_M0.299470.727
92_A96_I0.297990.723
31_G37_V0.297880.723
106_P162_S0.296960.721
96_I110_G0.296460.720
133_L139_M0.296180.719
121_G124_H0.295950.718
86_T93_F0.295880.718
5_M175_Y0.295430.717
53_T63_M0.292970.711
61_V110_G0.28820.700
79_S111_T0.285020.692
10_G13_L0.284310.690
13_L36_G0.282480.686
39_F43_F0.282050.685
57_E84_F0.281820.684
53_T59_N0.280190.680
144_P153_L0.27870.677
64_A77_V0.278590.676
119_G173_G0.277560.674
14_A39_F0.276740.672
3_I174_L0.275870.670
141_V169_R0.27580.670
132_I135_S0.274930.667
81_F120_D0.273840.665
144_P149_E0.2720.660
104_Q163_D0.269710.655
31_G40_G0.268650.652
10_G37_V0.268530.652
101_A139_M0.267740.650
7_D39_F0.26750.649
9_F168_I0.265560.645
77_V108_P0.264240.641
14_A42_A0.26380.640
111_T170_E0.262810.638
108_P168_I0.262610.638
8_A150_A0.262380.637
60_M78_E0.262020.636
40_G43_F0.261970.636
82_A113_A0.26110.634
77_V109_V0.25860.628
52_N116_G0.258490.628
18_E45_F0.258340.627
97_R128_E0.258190.627
23_V75_P0.257880.626
6_R35_F0.257340.625
113_A169_R0.256960.624
58_Q94_D0.256760.623
86_T132_I0.25570.621
39_F50_F0.255430.620
81_F117_Y0.255190.619
5_M145_S0.255070.619
101_A138_G0.255050.619
58_Q91_R0.254610.618
156_A162_S0.254590.618
91_R136_I0.254440.618
9_F150_A0.25410.617
9_F109_V0.253570.616
153_L166_V0.252150.612
77_V154_L0.251670.611
75_P163_D0.251330.610
83_D127_I0.251290.610
93_F124_H0.250.607
21_P49_R0.249750.606
45_F49_R0.247690.601
10_G35_F0.247040.600
9_F37_V0.24670.599
38_T50_F0.246390.598
75_P158_I0.246140.598
93_F135_S0.244640.594
30_L81_F0.244230.593
20_D159_R0.244180.593
97_R139_M0.242330.588
81_F172_R0.242020.588
84_F124_H0.241770.587
14_A17_A0.241350.586
22_R49_R0.238470.579
108_P158_I0.237760.577
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
3uk1A0.94941000.158
3rimA0.96071000.165
3komA0.93821000.167
3m49A0.95511000.169
1gpuA0.93821000.173
3l84A0.92131000.174
3mosA0.93821000.19
1r9jA0.94381000.191
2r8oA0.93821000.193
2e6kA0.93821000.195

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