GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CM_2 - Chorismate mutase type II
Pfam: PF01817 (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: 81
Sequences: 1979
Seq/Len: 24.43
HH_delta: -0.007 (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
50_R64_E0.892812.623
3_E17_E0.74742.195
5_D41_R0.724182.127
3_E6_E0.680351.998
10_E13_D0.668451.964
10_E17_E0.645311.896
45_V49_L0.644461.893
43_E47_E0.632611.858
9_R52_L0.595031.748
7_I14_L0.579841.703
15_L70_I0.534061.569
7_I21_L0.528781.553
42_E75_R0.516011.516
47_E51_E0.510451.499
6_E10_E0.498161.463
20_D23_R0.469161.378
6_E17_E0.468751.377
22_V74_S0.453441.332
68_R72_E0.445081.307
36_I75_R0.433861.274
23_R77_I0.420891.236
10_E14_L0.419941.234
74_S78_Q0.415861.222
24_K27_E0.410961.207
9_R48_R0.403211.184
42_E71_I0.400681.177
3_E24_K0.396821.166
13_D17_E0.390711.148
17_E20_D0.387191.137
40_D43_E0.380951.119
22_V78_Q0.379681.115
37_F75_R0.373311.097
50_R60_P0.368091.081
53_A56_G0.360611.059
4_I22_V0.359861.057
50_R61_E0.358091.052
65_R69_A0.352431.035
53_A57_G0.349961.028
38_D42_E0.340861.001
28_Y32_N0.33650.988
40_D44_E0.335820.986
4_I25_I0.330580.971
16_A53_A0.327670.963
12_V49_L0.326830.960
59_D62_F0.32420.952
54_E60_P0.323330.950
62_F73_E0.322390.947
28_Y31_E0.315470.927
16_A56_G0.313780.922
64_E68_R0.313240.920
12_V56_G0.309940.910
45_V71_I0.309540.909
15_L66_I0.309120.908
3_E21_L0.303890.893
42_E78_Q0.300910.884
66_I70_I0.300460.883
45_V48_R0.298430.877
9_R13_D0.298420.877
69_A72_E0.297060.873
19_M74_S0.297030.873
63_I67_F0.293330.862
16_A57_G0.29290.860
53_A60_P0.28970.851
2_K51_E0.288520.848
25_I42_E0.287040.843
48_R52_L0.284310.835
1_R41_R0.284130.835
62_F66_I0.283070.831
46_L67_F0.277680.816
49_L67_F0.277140.814
28_Y34_L0.276370.812
4_I8_D0.276160.811
12_V63_I0.275470.809
69_A73_E0.274750.807
12_V16_A0.274370.806
2_K44_E0.273940.805
23_R27_E0.273490.803
34_L38_D0.272190.800
27_E31_E0.269040.790
2_K6_E0.268980.790
15_L63_I0.268520.789
53_A58_L0.26840.788
39_P43_E0.265670.780
12_V67_F0.265540.780
37_F78_Q0.261290.768
20_D24_K0.257920.758
37_F42_E0.251950.740
21_L25_I0.247960.728
8_D48_R0.247370.727
70_I73_E0.246890.725
46_L64_E0.246280.723
41_R44_E0.244910.719
5_D48_R0.244770.719
49_L63_I0.242930.714
27_E33_G0.242510.712
16_A20_D0.24020.706
72_E75_R0.237040.696
53_A63_I0.236040.693
27_E30_K0.235230.691
29_K78_Q0.231580.680
70_I74_S0.230950.678
13_D56_G0.229480.674
36_I78_Q0.228770.672
19_M71_I0.226470.665
25_I74_S0.226460.665
47_E50_R0.226090.664
15_L62_F0.222460.653
8_D67_F0.220760.648
15_L73_E0.220450.648
58_L62_F0.220220.647
12_V52_L0.214190.629
38_D71_I0.213830.628
57_G60_P0.212310.624
1_R29_K0.210570.619
2_K33_G0.208310.612
37_F71_I0.205910.605
49_L71_I0.205210.603
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
3nvtA0.987799.7-0.007
1ecmA199.7-0.003
3rmiA199.7-0
3retA0.987799.70.012
2d8dA0.987799.70.012
2gtvX199.70.028
1ybzA0.851999.50.169
2fp1A0.975399.50.173
2gbbA0.938399.50.18
2vklA0.901299.40.213

Page generated in 0.0344 seconds.