GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Orn_DAP_Arg_deC - Pyridoxal-dependent decarboxylase C-terminal sheet domain
Pfam: PF00278 (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: 116
Sequences: 3443
Seq/Len: 29.68
HH_delta: 0.081 (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
47_L92_E0.972523.076
11_R23_R0.883432.794
59_P78_M0.792262.506
2_L29_D0.760772.406
4_T27_V0.758472.399
5_R88_W0.702232.221
25_Y60_S0.692742.191
27_V62_I0.687672.175
25_Y83_L0.687152.174
23_R58_Y0.674722.134
9_V25_Y0.646382.045
3_V88_W0.579981.835
24_W63_W0.577721.827
57_C78_M0.545241.725
22_R76_D0.539291.706
104_N110_R0.525051.661
32_Y66_T0.516771.635
3_V90_V0.512881.622
23_R60_S0.492151.557
45_P92_E0.489891.550
72_V75_R0.486611.539
4_T89_L0.467591.479
61_T75_R0.457111.446
58_Y82_E0.453781.435
99_I113_E0.453741.435
4_T29_D0.435211.377
64_G71_D0.433781.372
9_V23_R0.421971.335
99_I111_P0.412131.304
30_G65_P0.410491.298
60_S79_L0.407171.288
22_R61_T0.401021.268
59_P76_D0.397141.256
61_T72_V0.390451.235
46_I74_A0.381411.206
6_V83_L0.376661.191
35_F98_T0.376021.189
26_Y63_W0.374281.184
51_R54_E0.372411.178
36_D42_H0.366361.159
68_D105_F0.365531.156
8_G26_Y0.36481.154
67_C106_N0.355061.123
34_S94_M0.354371.121
9_V85_V0.349981.107
10_K24_W0.339911.075
36_D40_Y0.339611.074
36_D101_L0.335691.062
11_R58_Y0.333311.054
5_R28_D0.319811.012
9_V60_S0.316821.002
31_V39_L0.314030.993
99_I110_R0.310680.983
32_Y108_F0.308990.977
66_T108_F0.307850.974
29_D33_G0.300330.950
74_A77_V0.299660.948
62_I89_L0.295760.936
37_P44_F0.295550.935
9_V84_E0.293860.930
2_L98_T0.293790.929
69_S106_N0.29250.925
96_A102_S0.291570.922
51_R84_E0.28830.912
68_D106_N0.286890.907
6_V25_Y0.285870.904
65_P108_F0.285630.903
73_I91_F0.279740.885
56_P82_E0.275350.871
61_T74_A0.274450.868
8_G85_V0.273070.864
84_E87_D0.271040.857
62_I79_L0.269520.853
54_E82_E0.269170.851
53_D84_E0.269030.851
37_P101_L0.265340.839
2_L94_M0.264230.836
57_C82_E0.262260.830
31_V40_Y0.260630.824
53_D57_C0.260050.823
36_D41_D0.256750.812
56_P80_P0.25560.808
40_Y68_D0.254190.804
45_P93_N0.254070.804
52_P56_P0.252560.799
47_L52_P0.252280.798
80_P87_D0.252280.798
5_R86_G0.251750.796
54_E57_C0.251260.795
40_Y101_L0.251040.794
9_V82_E0.250770.793
37_P42_H0.248670.787
36_D39_L0.248240.785
30_G33_G0.247580.783
48_P83_L0.246080.778
53_D59_P0.245640.777
38_W70_G0.243780.771
27_V89_L0.240410.760
46_I62_I0.239050.756
31_V73_I0.237970.753
103_S106_N0.232670.736
61_T76_D0.231060.731
6_V9_V0.228790.724
77_V87_D0.227840.721
31_V68_D0.227760.720
37_P73_I0.227490.720
104_N109_P0.225070.712
38_W41_D0.223930.708
51_R55_E0.222870.705
80_P83_L0.222710.704
34_S44_F0.221190.700
57_C84_E0.221060.699
37_P40_Y0.218190.690
49_L88_W0.216820.686
24_W61_T0.213850.676
9_V83_L0.213780.676
10_K67_C0.213770.676
32_Y69_S0.209980.664
49_L90_V0.209140.662
32_Y68_D0.208520.660
76_D90_V0.207920.658
68_D101_L0.206320.653
38_W101_L0.206090.652
36_D105_F0.205190.649
35_F39_L0.201830.638
53_D58_Y0.200830.635
63_W72_V0.199380.631
94_M98_T0.19930.630
59_P82_E0.198950.629
27_V91_F0.198760.629
99_I112_A0.198610.628
38_W98_T0.198580.628
11_R82_E0.196740.622
54_E84_E0.195620.619
83_L89_L0.194680.616
37_P41_D0.19460.616
98_T107_G0.19090.604
33_G111_P0.188790.597
60_S82_E0.187630.593
97_Y106_N0.187160.592
40_Y44_F0.186430.590
98_T113_E0.185890.588
30_G66_T0.184870.585
37_P98_T0.184010.582
65_P98_T0.183390.580
63_W89_L0.182380.577
43_Q77_V0.182210.576
58_Y83_L0.182090.576
38_W42_H0.182080.576
13_R58_Y0.181680.575
51_R56_P0.181020.573
42_H101_L0.180780.572
75_R78_M0.178930.566
30_G111_P0.177880.563
36_D106_N0.177860.563
51_R58_Y0.177680.562
75_R91_F0.177140.560
97_Y105_F0.177050.560
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
3vabA0.93199.90.081
7odcA0.991499.90.086
3n2bA0.913899.90.121
3n29A0.913899.90.148
3mt1A0.887999.90.155
2o0tA0.982899.90.172
1knwA0.93199.90.19
2oo0A0.991499.90.196
3btnA0.991499.90.199
2j66A0.93199.80.211

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