GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Transketolase_C - Transketolase C-terminal domain
Pfam: PF02780 (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. )
Length: 124
Sequences: 8204
Seq/Len: 66.16
HH_delta: 0.093 (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
3_A53_A1.804522.832
51_E83_Y1.451482.278
28_A40_V1.4472.271
10_A37_K1.333542.093
11_D37_K1.307232.052
25_L40_V1.254441.969
13_T61_T1.184191.858
30_E33_E1.141241.791
12_I38_A1.132321.777
110_R114_L1.090181.711
72_K100_G1.06751.675
32_E37_K1.062071.667
55_L87_N1.018631.599
86_E98_R0.996631.564
51_E87_N0.992731.558
22_E26_E0.98741.550
55_L83_Y0.985991.547
39_G57_S0.979141.537
7_R29_E0.974241.529
81_A96_V0.968561.520
112_E115_E0.96841.520
16_A21_V0.959851.506
78_S82_E0.958191.504
24_A67_V0.937731.472
23_E26_E0.905031.420
41_I57_S0.876211.375
11_D62_G0.871841.368
13_T57_S0.871161.367
55_L88_G0.861771.352
26_E29_E0.843941.324
39_G61_T0.836751.313
16_A24_A0.831061.304
4_E42_D0.824851.294
7_R32_E0.824821.294
65_V99_L0.816071.281
39_G60_K0.809781.271
14_I38_A0.802051.259
81_A98_R0.801381.258
7_R37_K0.798291.253
14_I24_A0.785451.233
68_E77_G0.771461.211
50_D88_G0.770171.209
20_M23_E0.7681.205
29_E33_E0.762211.196
66_V77_G0.760271.193
83_Y87_N0.758261.190
15_I64_V0.756941.188
55_L59_K0.753061.182
104_E116_A0.745321.170
65_V97_K0.744181.168
64_V69_E0.737541.157
5_V39_G0.730881.147
30_E34_E0.726051.139
52_E56_E0.717951.127
41_I53_A0.708741.112
15_I43_L0.708491.112
109_G113_L0.705371.107
24_A40_V0.703821.105
107_P116_A0.700741.100
58_L84_L0.695191.091
113_L117_F0.694111.089
43_L76_L0.688561.081
7_R28_A0.679831.067
23_E114_L0.678221.064
13_T39_G0.669511.051
47_K103_D0.65671.031
85_A96_V0.650751.021
82_E98_R0.650521.021
5_V53_A0.636971.000
56_E59_K0.631530.991
13_T41_I0.617070.968
49_F54_L0.614280.964
12_I63_R0.611690.960
112_E116_A0.609090.956
17_Y46_I0.607140.953
29_E32_E0.602430.945
73_I103_D0.601970.945
49_F83_Y0.600440.942
56_E60_K0.593050.931
15_I41_I0.583320.915
51_E55_L0.581920.913
17_Y43_L0.580360.911
81_A85_A0.567250.890
16_A20_M0.565650.888
8_E39_G0.56450.886
21_V40_V0.554970.871
5_V28_A0.552840.868
19_S23_E0.549840.863
28_A32_E0.546320.857
60_K64_V0.536830.842
17_Y76_L0.536770.842
63_R95_P0.530740.833
6_L42_D0.529880.832
64_V84_L0.529720.831
79_A82_E0.520580.817
12_I65_V0.520020.816
4_E44_R0.519110.815
57_S60_K0.513770.806
3_A41_I0.512320.804
6_L21_V0.511290.802
3_A43_L0.507690.797
65_V68_E0.507120.796
67_V99_L0.503960.791
68_E75_G0.502870.789
107_P113_L0.499160.783
43_L46_I0.487980.766
5_V8_E0.484470.760
104_E107_P0.480660.754
5_V41_I0.479670.753
54_L84_L0.479320.752
79_A98_R0.477560.749
101_V106_I0.476060.747
58_L64_V0.468140.735
106_I117_F0.467730.734
20_M67_V0.466850.733
31_L38_A0.463420.727
101_V104_E0.460770.723
46_I50_D0.459410.721
111_A115_E0.455090.714
27_A99_L0.453380.712
11_D36_I0.451080.708
21_V42_D0.451030.708
89_F98_R0.445590.699
66_V98_R0.4430.695
26_E30_E0.44270.695
66_V70_H0.439430.690
66_V80_I0.428720.673
62_G94_A0.426810.670
109_G112_E0.420030.659
19_S22_E0.419010.658
86_E97_K0.417730.656
101_V113_L0.417060.655
31_L36_I0.413430.649
106_I116_A0.413020.648
13_T64_V0.411890.646
75_G78_S0.411080.645
27_A67_V0.409260.642
50_D54_L0.402270.631
8_E37_K0.398340.625
57_S61_T0.39780.624
16_A43_L0.395920.621
82_E86_E0.394530.619
90_N96_V0.39280.616
5_V56_E0.391130.614
10_A39_G0.391080.614
104_E117_F0.390130.612
27_A30_E0.388920.610
7_R25_L0.387960.609
8_E60_K0.384920.604
22_E25_L0.382960.601
99_L118_G0.38290.601
11_D39_G0.380730.598
90_N94_A0.378310.594
6_L25_L0.375570.589
69_E114_L0.371070.582
5_V57_S0.369170.579
72_K98_R0.367880.577
28_A38_A0.367290.576
32_E38_A0.365360.573
50_D53_A0.36470.572
8_E56_E0.3590.563
16_A42_D0.358080.562
66_V96_V0.351320.551
53_A61_T0.347050.545
107_P117_F0.34610.543
23_E67_V0.345720.543
46_I74_G0.344670.541
19_S114_L0.343330.539
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
3mosA0.959799.90.093
1w85B0.983999.90.093
1umdB0.975899.90.102
2ozlB0.991999.90.105
2bfdB0.975899.90.12
1ik6A0.959799.90.126
2o1xA0.943599.90.139
2o1sA0.935599.90.143
1qs0B0.951699.80.169
3l84A0.854899.70.252

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