GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thymidylate_kin - Thymidylate kinase
Pfam: PF02223 (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: CL0023
Length: 186
Sequences: 12642
Seq/Len: 67.97
HH_delta: 0.045 (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
131_E134_K1.820973.777
125_L175_A1.267382.629
126_D172_I1.221882.534
157_R161_L1.195472.480
15_L18_E1.150242.386
128_D176_S1.122682.329
43_R47_R1.050182.178
41_L44_E1.006322.087
133_L137_A0.995692.065
124_F172_I0.974352.021
127_V132_A0.950411.971
150_L154_R0.932371.934
10_T86_D0.910251.888
26_K81_K0.782231.622
17_A21_K0.772651.603
127_V175_A0.764111.585
3_G7_S0.757931.572
121_L171_V0.756751.570
14_R18_E0.753991.564
12_Q15_L0.742951.541
149_D153_L0.728111.510
15_L19_A0.720391.494
72_V75_P0.715811.485
42_I45_L0.711441.476
74_R78_K0.703051.458
131_E176_S0.685081.421
134_K138_K0.673021.396
158_E162_E0.664491.378
156_V160_Y0.664351.378
13_I17_A0.661731.372
7_S127_V0.655631.360
126_D174_D0.645061.338
127_V131_E0.639381.326
108_W167_P0.639341.326
70_A74_R0.639291.326
128_D131_E0.638391.324
109_R112_K0.636061.319
71_R75_P0.62651.299
4_I132_A0.625571.297
6_G136_I0.625151.297
13_I24_G0.624771.296
40_E44_E0.617351.280
14_R17_A0.613211.272
165_K172_I0.605021.255
72_V76_A0.603091.251
131_E135_R0.598821.242
129_P154_R0.594491.233
105_D109_R0.593881.232
144_D147_E0.588941.222
151_E154_R0.577811.198
75_P79_R0.575591.194
109_R113_D0.572531.187
152_Y156_V0.556981.155
44_E47_R0.555871.153
136_I139_R0.554841.151
64_D68_H0.553511.148
67_W71_R0.551811.145
27_V30_T0.55021.141
133_L153_L0.539571.119
138_K141_E0.538191.116
126_D161_L0.537961.116
153_L157_R0.534831.109
105_D108_W0.532161.104
148_E151_E0.530241.100
106_W110_L0.52471.088
174_D177_R0.519011.076
149_D152_Y0.51741.073
154_R158_E0.516861.072
124_F170_W0.511651.061
129_P133_L0.507461.053
132_A136_I0.507251.052
122_T170_W0.504211.046
130_E134_K0.500211.037
64_D67_W0.496531.030
126_D157_R0.494881.026
40_E43_R0.491071.019
76_A79_R0.487381.011
76_A81_K0.485211.006
37_P41_L0.484141.004
151_E155_R0.482061.000
30_T68_H0.479320.994
4_I153_L0.475070.985
106_W109_R0.474350.984
123_F171_V0.4720.979
41_L45_L0.466640.968
37_P40_E0.466440.967
108_W112_K0.466080.967
159_A162_E0.465090.965
25_Y82_I0.459290.953
154_R157_R0.457960.950
17_A24_G0.454740.943
5_D132_A0.45230.938
36_T39_G0.451060.936
30_T34_G0.450340.934
127_V135_R0.450230.934
31_F34_G0.446190.925
129_P161_L0.443280.919
12_Q16_L0.442040.917
43_R46_L0.440770.914
3_G8_G0.435230.903
8_G135_R0.43520.903
155_R158_E0.434460.901
12_Q125_L0.43440.901
144_D148_E0.430670.893
148_E152_Y0.424650.881
137_A149_D0.422410.876
135_R175_A0.41820.867
75_P78_K0.417050.865
32_P46_L0.41540.862
42_I46_L0.407980.846
31_F64_D0.406770.844
11_T15_L0.406450.843
112_K115_F0.40520.840
21_K24_G0.404980.840
39_G42_I0.395640.821
17_A84_I0.395170.820
4_I7_S0.394630.819
18_E21_K0.391650.812
133_L150_L0.384340.797
73_I83_V0.383170.795
155_R159_A0.382470.793
35_S40_E0.376970.782
145_E148_E0.374780.777
13_I86_D0.374250.776
28_I81_K0.372640.773
29_I32_P0.371570.771
16_L20_L0.369020.765
20_L23_K0.366620.760
111_N114_I0.36640.760
12_Q175_A0.365460.758
4_I124_F0.363540.754
124_F161_L0.361690.750
3_G10_T0.357390.741
73_I77_L0.357330.741
5_D87_R0.356150.739
74_R77_L0.351550.729
27_V31_F0.351270.729
71_R74_R0.346880.719
107_I110_L0.343670.713
46_L51_E0.343210.712
107_I111_N0.343090.712
38_I41_L0.342460.710
153_L156_V0.34120.708
3_G9_K0.33940.704
8_G11_T0.33780.701
129_P157_R0.337350.700
6_G139_R0.337060.699
10_T14_R0.336530.698
130_E133_L0.334920.695
129_P150_L0.334910.695
7_S132_A0.333850.692
65_R68_H0.333820.692
28_I72_V0.333650.692
111_N115_F0.333140.691
147_E151_E0.331810.688
110_L114_I0.325950.676
13_I29_I0.325410.675
2_E160_Y0.32450.673
2_E5_D0.323760.672
30_T33_P0.323340.671
2_E168_N0.320760.665
132_A157_R0.319890.663
152_Y155_R0.318950.662
163_L170_W0.318890.661
28_I31_F0.317670.659
161_L172_I0.317030.658
114_I118_K0.315990.655
7_S124_F0.31530.654
67_W70_A0.314710.653
13_I26_K0.313050.649
112_K118_K0.310520.644
5_D152_Y0.31020.643
64_D69_L0.310130.643
141_E147_E0.309630.642
123_F173_I0.309530.642
5_D136_I0.308210.639
10_T13_I0.30810.639
40_E45_L0.307630.638
161_L165_K0.305560.634
19_A23_K0.304430.631
124_F157_R0.302230.627
65_R69_L0.301260.625
133_L136_I0.300140.623
158_E161_L0.299520.621
2_E163_L0.297920.618
108_W111_N0.297580.617
2_E124_F0.296130.614
106_W111_N0.29560.613
29_I36_T0.294690.611
33_P43_R0.294540.611
32_P35_S0.294490.611
13_I84_I0.293590.609
6_G152_Y0.291940.606
159_A163_L0.289470.600
164_A172_I0.286690.595
144_D149_D0.285970.593
23_K82_I0.281880.585
146_E149_D0.281010.583
39_G64_D0.28060.582
5_D153_L0.279930.581
17_A20_L0.27280.566
20_L25_Y0.271780.564
134_K137_A0.271750.564
164_A167_P0.271060.562
17_A23_K0.26980.560
17_A22_E0.269650.559
4_I129_P0.268780.557
2_E87_R0.264340.548
162_E165_K0.263440.546
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
4tmkA199.90.045
4hlcA0.994699.90.049
3v9pA0.994699.90.05
3lv8A199.90.061
4edhA199.90.061
3ld9A0.973199.90.088
3hjnA0.962499.90.115
3tmkA0.946299.90.142
4eaqA0.983999.90.145
2z0hA0.962499.80.231

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