GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OKR_DC_1_N - OrnLysArg decarboxylase N-terminal domain
Pfam: PF03709 (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: CL0304
Length: 115
Sequences: 76098
Seq/Len: 661.72
HH_delta: -0.124 (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
10_A22_D3.744722.508
21_V39_I3.672632.460
27_D49_E3.273052.192
47_D76_R3.206132.147
30_L60_K3.18092.130
52_D60_K3.030412.030
26_T52_D2.929141.962
23_A32_I2.921091.956
25_S49_E2.908221.948
44_I57_L2.866051.920
72_L90_V2.761921.850
21_V32_I2.652011.776
24_D28_D2.618621.754
12_A100_T2.615071.752
92_G107_R2.563121.717
58_L70_V2.474091.657
34_E64_R2.404291.610
16_R104_I2.376121.591
62_R91_D2.332281.562
10_A14_E2.192221.468
25_S28_D2.184021.463
36_F39_I2.174661.457
52_D56_E2.148511.439
59_D88_G2.134211.429
21_V36_F2.129451.426
46_W55_Q2.071721.388
53_E56_E2.027041.358
32_I35_S1.973221.322
42_V68_I1.960511.313
76_R81_D1.933961.295
23_A29_A1.927321.291
26_T57_L1.922911.288
60_K63_E1.89261.268
32_I36_F1.873441.255
27_D52_D1.871531.254
60_K64_R1.865371.249
83_P87_L1.845721.236
32_I39_I1.836041.230
33_I61_I1.826861.224
30_L57_L1.799211.205
73_L98_E1.73451.162
79_T83_P1.725051.155
78_T81_D1.701631.140
107_R110_A1.695911.136
84_A88_G1.695511.136
72_L85_E1.664331.115
55_Q84_A1.655721.109
27_D31_A1.604171.074
58_L72_L1.597641.070
91_D111_A1.594071.068
55_Q85_E1.569431.051
56_E59_D1.53151.026
28_D32_I1.527431.023
29_A57_L1.517411.016
30_L52_D1.496131.002
49_E52_D1.480960.992
44_I70_V1.476640.989
102_E107_R1.460560.978
46_W72_L1.446090.969
33_I65_N1.423360.953
23_A28_D1.422540.953
46_W53_E1.41270.946
31_A35_S1.408380.943
92_G110_A1.404650.941
44_I58_L1.398640.937
13_L108_I1.396130.935
18_R109_E1.386550.929
99_D102_E1.370410.918
58_L90_V1.322660.886
43_V73_L1.316730.882
28_D31_A1.31480.881
80_E84_A1.313630.880
42_V70_V1.292650.866
58_L88_G1.289830.864
11_E15_Q1.280250.857
104_I109_E1.278280.856
7_R10_A1.275370.854
81_D84_A1.271760.852
42_V61_I1.267150.849
84_A87_L1.266170.848
41_A108_I1.252370.839
7_R11_E1.23240.825
10_A20_V1.23060.824
30_L34_E1.227810.822
77_D95_W1.226790.822
56_E60_K1.225650.821
85_E89_E1.217240.815
100_T104_I1.204970.807
102_E105_A1.199390.803
74_A96_L1.19510.800
31_A34_E1.187840.796
79_T82_L1.175780.788
79_T99_D1.166770.781
65_N68_I1.165810.781
105_A110_A1.162630.779
48_G52_D1.156510.775
82_L95_W1.153820.773
82_L102_E1.152330.772
29_A33_I1.148890.769
8_E12_A1.139670.763
9_L73_L1.129360.756
26_T30_L1.128340.756
85_E93_F1.121210.751
47_D75_E1.112520.745
45_S96_L1.11230.745
71_F107_R1.08870.729
8_E11_E1.075330.720
69_P91_D1.06970.716
46_W81_D1.06910.716
59_D84_A1.048620.702
57_L61_I1.047130.701
82_L86_V1.042850.698
33_I68_I1.023610.686
52_D57_L1.010070.677
71_F111_A0.984850.660
41_A112_A0.984440.659
43_V71_F0.982390.658
38_D65_N0.98210.658
23_A26_T0.981410.657
12_A16_R0.972820.652
98_E103_F0.959680.643
26_T49_E0.957360.641
46_W76_R0.952040.638
107_R111_A0.942620.631
28_D49_E0.939880.630
45_S75_E0.937160.628
14_E20_V0.936550.627
47_D78_T0.933330.625
44_I72_L0.932470.625
43_V103_F0.93230.624
101_A105_A0.93120.624
85_E90_V0.909710.609
44_I61_I0.909090.609
62_R68_I0.907910.608
75_E97_F0.898510.602
16_R109_E0.895750.600
59_D63_E0.89460.599
34_E60_K0.886920.594
30_L33_I0.877890.588
71_F92_G0.875540.586
9_L98_E0.866360.580
18_R104_I0.860550.576
70_V90_V0.855740.573
62_R69_P0.840420.563
55_Q88_G0.834780.559
46_W85_E0.834330.559
55_Q59_D0.832450.558
55_Q81_D0.826430.554
11_E14_E0.820410.549
46_W90_V0.820110.549
13_L18_R0.813750.545
92_G111_A0.811710.544
94_I98_E0.810470.543
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
3to5A0.973999.3-0.124
3dzdA0.973999.2-0.106
2vycA0.991399.2-0.087
3n0rA0.947899.2-0.08
3rqiA0.973999.2-0.079
3r0jA0.973999.1-0.074
3eq2A0.973999.1-0.073
1ny5A0.973999.1-0.071
4eukA0.956599.1-0.067
2ayxA0.973999.1-0.061

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