GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Porphobil_deamC - Porphobilinogen deaminase C-terminal domain
Pfam: PF03900 (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: 74
Sequences: 1774
Seq/Len: 23.97
HH_delta: 0.022 (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
52_V68_L1.019232.648
13_E70_E0.986032.561
52_V71_E0.849912.208
42_S46_S0.848772.205
54_I71_E0.75431.959
32_E55_T0.752751.955
1_A5_E0.742371.928
37_R53_E0.705991.834
13_E66_K0.696881.810
56_G64_L0.688361.788
41_G49_I0.685051.779
27_K35_R0.679021.764
35_R55_T0.645881.678
3_E28_I0.642911.670
35_R53_E0.590231.533
23_G39_M0.588381.528
2_I58_I0.584841.519
10_F38_A0.565361.469
60_D63_E0.562121.460
17_G20_S0.525111.364
70_E74_A0.520231.351
5_E62_E0.510721.327
16_G20_S0.499481.297
67_K71_E0.499421.297
13_E73_L0.483291.255
54_I67_K0.481611.251
66_K70_E0.477241.240
54_I68_L0.46571.210
6_A36_L0.452841.176
71_E74_A0.443621.152
39_M51_R0.436831.135
15_G22_I0.419861.091
65_G69_A0.418731.088
19_H22_I0.401811.044
61_A65_G0.395561.027
63_E67_K0.391381.017
37_R51_R0.388051.008
67_K70_E0.384130.998
54_I64_L0.375480.975
14_L22_I0.37210.967
10_F68_L0.36830.957
27_K37_R0.36780.955
14_L38_A0.360260.936
10_F36_L0.358680.932
16_G22_I0.348720.906
10_F23_G0.347770.903
39_M49_I0.346120.899
67_K74_A0.331270.860
3_E26_A0.329220.855
10_F72_L0.326970.849
40_V72_L0.321070.834
6_A34_L0.319420.830
14_L40_V0.319080.829
62_E66_K0.316630.822
25_Y39_M0.31510.818
20_S40_V0.313950.816
10_F69_A0.310110.806
36_L68_L0.306870.797
57_P60_D0.299470.778
9_A13_E0.29670.771
28_I58_I0.296540.770
29_E35_R0.290920.756
63_E66_K0.288630.750
17_G40_V0.286580.744
69_A73_L0.284560.739
29_E32_E0.283180.736
42_S47_R0.282370.733
38_A68_L0.281540.731
16_G19_H0.280930.730
15_G20_S0.27640.718
24_A36_L0.275520.716
52_V72_L0.274130.712
6_A65_G0.273580.711
31_D58_I0.273180.710
9_A62_E0.271180.704
6_A61_A0.270810.703
8_R16_G0.261460.679
19_H41_G0.259070.673
4_V26_A0.259020.673
20_S23_G0.256990.668
17_G24_A0.256180.665
4_V24_A0.25530.663
11_L22_I0.254410.661
3_E27_K0.253350.658
56_G61_A0.247430.643
11_L41_G0.247120.642
61_A64_L0.246250.640
2_I59_E0.242440.630
9_A66_K0.240520.625
20_S50_I0.238690.620
1_A69_A0.23380.607
19_H38_A0.232090.603
29_E55_T0.231930.602
31_D59_E0.231270.601
40_V73_L0.230220.598
42_S45_G0.230160.598
41_G51_R0.229860.597
57_P67_K0.229860.597
43_P46_S0.224070.582
11_L15_G0.223280.580
56_G60_D0.2230.579
11_L73_L0.221560.576
10_F14_L0.220210.572
6_A23_G0.219410.570
10_F24_A0.217990.566
47_R50_I0.215630.560
34_L64_L0.210130.546
2_I61_A0.209450.544
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
1gtkA0.97399.70.022
3ecrA0.97399.70.041
4htgA0.986599.60.061
3ozbA0.932427.70.847
3vv4A0.770327.30.847
3la8A0.918927.30.847
3odgA0.932426.30.848
1vmkA0.932419.10.857
3phbE0.959518.60.858
3khsA0.959518.40.858

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