GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPP_enzyme_M - Thiamine pyrophosphate enzyme central domain
Pfam: PF00205 (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: CL0085
Length: 137
Sequences: 6472
Seq/Len: 47.24
HH_delta: 0.07 (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
36_E56_H1.470463.328
30_E135_R1.376263.115
30_E131_K1.305892.956
128_G133_F1.257752.847
109_I133_F1.246492.821
4_A107_I1.191022.696
18_A31_L1.148142.599
84_I130_I1.033732.340
7_L105_K0.976172.209
78_A81_V0.969882.195
32_R36_E0.907522.054
6_D10_S0.892522.020
83_A86_T0.890552.016
39_G58_L0.782771.772
7_L80_L0.775831.756
16_I35_A0.773951.752
35_A42_V0.767841.738
16_I82_L0.737821.670
11_A14_P0.736081.666
8_L82_L0.723611.638
7_L124_V0.711131.610
49_K54_E0.705191.596
29_E33_E0.699441.583
69_P73_E0.697081.578
33_E37_K0.69691.577
80_L107_I0.691621.565
16_I40_I0.680821.541
3_E6_D0.680431.540
116_I127_V0.67861.536
44_T59_F0.676481.531
5_A137_L0.660851.496
5_A9_S0.657151.487
34_L38_L0.654911.482
117_G122_P0.651241.474
42_V52_I0.642341.454
132_A135_R0.624821.414
84_I109_I0.620671.405
16_I34_L0.609081.379
15_V78_A0.595411.348
122_P125_A0.588561.332
73_E77_Q0.586131.327
18_A22_A0.569921.290
54_E59_F0.55691.260
3_E7_L0.555761.258
4_A126_I0.552431.250
60_L74_A0.55241.250
8_L80_L0.547591.239
14_P79_D0.547591.239
30_E33_E0.542991.229
101_N104_A0.528161.195
32_R53_P0.527731.194
22_A31_L0.520611.178
83_A88_L0.514831.165
131_K135_R0.514051.163
11_A80_L0.513531.162
28_A32_R0.512681.160
35_A52_I0.511451.158
91_F94_Y0.502011.136
15_V43_A0.498441.128
43_A60_L0.493491.117
34_L134_L0.491921.113
4_A124_V0.486091.100
105_K123_D0.483231.094
33_E135_R0.481881.091
84_I134_L0.476061.077
33_E36_E0.472461.069
14_P40_I0.468111.059
36_E58_L0.467031.057
52_I56_H0.458531.038
13_R77_Q0.455471.031
44_T54_E0.455341.031
132_A136_A0.452571.024
15_V81_V0.447051.012
22_A51_V0.443451.004
126_I133_F0.443391.004
2_D6_D0.432870.980
63_L75_L0.432770.980
20_R47_M0.428110.969
32_R56_H0.424360.960
11_A79_D0.423010.957
29_E32_R0.422640.957
133_F136_A0.419940.950
10_S105_K0.416160.942
90_D93_T0.410390.929
35_A58_L0.404660.916
1_I136_A0.400520.907
3_E124_V0.396910.898
129_D132_A0.393360.890
23_R51_V0.392620.889
31_L134_L0.38980.882
18_A42_V0.389080.881
16_I84_I0.386750.875
60_L71_A0.386280.874
52_I59_F0.384620.871
16_I31_L0.382790.866
17_L86_T0.382620.866
12_K79_D0.37570.850
7_L107_I0.368580.834
109_I126_I0.368160.833
113_P127_V0.367760.832
13_R79_D0.366620.830
6_D9_S0.359940.815
17_L45_T0.359870.815
27_A30_E0.357790.810
20_R87_R0.35350.800
21_G110_D0.352810.799
110_D115_E0.352440.798
64_G67_G0.352190.797
17_L83_A0.351860.796
45_T48_G0.345630.782
15_V75_L0.342260.775
73_E76_E0.339050.767
115_E118_K0.338550.766
76_E102_P0.337690.764
50_G54_E0.333530.755
15_V74_A0.332980.754
106_I120_Y0.331040.749
32_R52_I0.325290.736
4_A7_L0.32440.734
9_S37_K0.324280.734
112_D115_E0.324090.734
30_E34_L0.323170.731
18_A44_T0.322770.731
9_S38_L0.322670.730
130_I135_R0.320930.726
9_S12_K0.320610.726
87_R90_D0.310050.702
23_R28_A0.307370.696
70_A73_E0.305590.692
44_T49_K0.305360.691
22_A84_I0.305210.691
109_I137_L0.303990.688
7_L10_S0.302690.685
39_G57_P0.302660.685
108_Q122_P0.298490.676
20_R89_S0.294140.666
53_P56_H0.293840.665
10_S80_L0.292420.662
35_A39_G0.29230.662
2_D136_A0.282640.640
38_L58_L0.280750.635
49_K89_S0.279940.634
116_I125_A0.279840.633
30_E37_K0.279620.633
83_A106_I0.279190.632
44_T51_V0.278290.630
31_L35_A0.276640.626
14_P80_L0.274220.621
68_S71_A0.273940.620
17_L81_V0.26710.605
35_A38_L0.266080.602
45_T50_G0.264970.600
88_L108_Q0.264770.599
63_L66_F0.264540.599
23_R50_G0.260440.589
25_S29_E0.258360.585
83_A92_N0.257940.584
21_G111_P0.255260.578
25_S129_D0.254670.576
18_A51_V0.253270.573
107_I126_I0.252480.571
81_V106_I0.252070.571
4_A137_L0.252050.570
1_I126_I0.251250.569
30_E134_L0.249620.565
83_A108_Q0.249050.564
43_A75_L0.24780.561
27_A131_K0.247540.560
40_I58_L0.245160.555
117_G125_A0.244960.554
99_A102_P0.243990.552
71_A74_A0.241550.547
75_L78_A0.24130.546
107_I124_V0.239980.543
49_K59_F0.239690.543
90_D94_Y0.237640.538
8_L14_P0.237510.538
8_L38_L0.236990.536
89_S92_N0.234730.531
67_G71_A0.234580.531
1_I133_F0.234270.530
22_A27_A0.234060.530
109_I130_I0.232970.527
82_L109_I0.232650.527
42_V59_F0.232390.526
87_R115_E0.230540.522
72_N77_Q0.228520.517
132_A137_L0.227640.515
66_F89_S0.22670.513
67_G72_N0.226620.513
66_F91_F0.226380.512
22_A25_S0.225070.509
47_M86_T0.223920.507
10_S98_P0.223780.506
8_L40_I0.222360.503
32_R58_L0.221960.502
87_R92_N0.220450.499
94_Y98_P0.219530.497
66_F90_D0.21930.496
89_S93_T0.218750.495
52_I55_D0.217560.492
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
2pgnA0.985499.90.07
4kgdA0.963599.90.08
4fegA0.963599.90.08
1ybhA0.978199.90.089
2ihtA0.985499.90.09
2uz1A0.978199.90.092
2panA0.992799.80.099
1t9bA0.992799.80.102
1q6zA0.985499.80.104
1ozhA0.978199.80.106

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