GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thr_synth_N - Threonine synthase N terminus
Pfam: PF14821 (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: 79
Sequences: 1252
Seq/Len: 15.85
HH_delta: -0.019 (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
55_F72_K0.791692.787
59_S68_E0.77282.721
67_P70_E0.689662.428
55_F75_I0.682412.403
49_S52_E0.645452.272
14_F62_L0.580242.043
73_E77_K0.578842.038
48_L56_E0.510911.799
13_S16_E0.491471.730
9_S29_Y0.4761.676
1_K32_E0.436421.537
4_S25_D0.432971.524
6_R26_G0.423091.490
12_V17_A0.417831.471
20_Q29_Y0.417541.470
50_Y79_Y0.413021.454
45_L48_L0.400021.408
39_K43_E0.395541.393
48_L53_L0.395261.392
45_L53_L0.392241.381
11_P32_E0.390491.375
51_A76_E0.387761.365
55_F68_E0.383751.351
51_A75_I0.373721.316
31_P61_F0.371971.310
44_E56_E0.360571.269
66_I70_E0.353331.244
7_G10_P0.337551.188
31_P35_P0.335681.182
2_Y61_F0.323671.140
74_I77_K0.322571.136
5_T30_V0.321321.131
40_E44_E0.317941.119
12_V20_Q0.316861.116
14_F66_I0.313521.104
55_F59_S0.312871.102
52_E76_E0.308171.085
72_K76_E0.306051.078
71_L75_I0.299761.055
37_L45_L0.295211.039
12_V29_Y0.293341.033
8_K11_P0.290911.024
13_S65_D0.286621.009
12_V24_P0.28040.987
55_F71_L0.277920.978
37_L60_P0.273830.964
53_L57_I0.269390.948
68_E72_K0.266260.937
43_E46_K0.264570.931
70_E73_E0.263980.929
3_I7_G0.262450.924
66_I71_L0.261870.922
56_E68_E0.260280.916
1_K13_S0.258720.911
52_E72_K0.2460.866
53_L75_I0.244510.861
50_Y78_A0.243960.859
20_Q24_P0.242210.853
1_K8_K0.240750.848
15_K65_D0.237970.838
3_I6_R0.234410.825
75_I78_A0.229270.807
60_P64_D0.226510.797
66_I74_I0.226370.797
46_K53_L0.221750.781
3_I32_E0.220870.778
9_S24_P0.215910.760
58_L71_L0.215420.758
1_K11_P0.209740.738
24_P29_Y0.203290.716
54_A79_Y0.199620.703
7_G32_E0.19910.701
17_A29_Y0.199060.701
9_S20_Q0.198670.699
16_E20_Q0.197850.697
6_R30_V0.197740.696
30_V34_I0.196940.693
2_Y6_R0.196110.690
56_E60_P0.195660.689
5_T50_Y0.194240.684
50_Y54_A0.194220.684
52_E56_E0.193260.680
33_E39_K0.193230.680
8_K36_K0.193080.680
73_E76_E0.192910.679
18_I66_I0.19210.676
14_F64_D0.192020.676
33_E38_S0.191010.672
3_I10_P0.188210.663
35_P61_F0.187260.659
26_G30_V0.186690.657
15_K34_I0.185810.654
17_A37_L0.185040.651
15_K58_L0.183520.646
50_Y65_D0.181220.638
5_T26_G0.180910.637
14_F65_D0.178790.629
6_R23_A0.178490.628
4_S23_A0.175030.616
43_E47_N0.173790.612
36_K39_K0.172930.609
55_F76_E0.172740.608
43_E49_S0.172040.606
7_G26_G0.172010.606
35_P60_P0.17140.603
7_G25_D0.171240.603
3_I8_K0.171160.603
25_D54_A0.169750.598
18_I65_D0.168570.593
43_E72_K0.168190.592
29_Y51_A0.168010.592
69_E73_E0.166160.585
51_A69_E0.165560.583
39_K69_E0.164170.578
37_L42_L0.163330.575
48_L52_E0.16310.574
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
4f4fA199.9-0.019
3v7nA0.987399.90.001
1vb3A199.80.134
1kl7A199.70.233
1e5xA0.924198.10.654
1v8zA0.5949970.737
2o2eA0.797592.90.806
1x1qA0.784891.30.815
3iauA0.784890.60.819
3zf7u0.924172.90.852

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