GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Toprim_2 - Toprim-like
Pfam: PF13155 (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: CL0413
Length: 96
Sequences: 3121
Seq/Len: 32.51
HH_delta: 0.161 (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
90_K94_D1.194313.873
49_K80_K0.908762.947
58_E62_K0.847692.749
3_F12_Y0.827462.684
11_S93_N0.765812.484
49_K82_R0.670482.174
29_G54_F0.630762.046
6_P30_G0.62472.026
3_F9_A0.533411.730
62_K66_K0.511241.658
7_I11_S0.50911.651
56_N90_K0.508261.648
1_V53_A0.497461.613
51_V84_E0.47991.556
61_R85_D0.423211.373
35_E38_Q0.411311.334
48_K79_I0.409581.328
65_E69_K0.403391.308
50_I71_L0.396081.285
39_I70_E0.393881.277
54_F67_L0.380041.233
52_L64_A0.377951.226
54_F63_A0.36761.192
53_A86_P0.365011.184
59_A63_A0.363691.180
8_D55_D0.361931.174
26_S29_G0.360831.170
52_L67_L0.356131.155
65_E68_Q0.35491.151
1_V51_V0.348661.131
64_A83_I0.337931.096
3_F26_S0.335741.089
60_G91_D0.328321.065
64_A68_Q0.324641.053
13_Y18_E0.321121.041
19_N26_S0.302570.981
12_Y17_K0.300150.973
58_E61_R0.29050.942
66_K69_K0.286670.930
41_F45_N0.286520.929
57_D60_G0.285630.926
11_S14_Q0.2840.921
7_I93_N0.281920.914
7_I10_L0.280440.910
55_D60_G0.275860.895
28_A31_G0.275230.893
3_F6_P0.271670.881
1_V12_Y0.269780.875
2_V54_F0.268640.871
26_S31_G0.268140.870
56_N89_G0.265590.861
12_Y16_G0.265530.861
67_L71_L0.265180.860
1_V84_E0.262660.852
69_K74_E0.261160.847
32_T59_A0.257950.837
36_K69_K0.257380.835
8_D90_K0.25630.831
11_S15_L0.254130.824
74_E80_K0.25240.819
38_Q41_F0.252220.818
70_E73_E0.252180.818
92_W95_Y0.248460.806
28_A32_T0.248280.805
27_L31_G0.247890.804
36_K73_E0.246910.801
34_S67_L0.246720.800
34_S54_F0.246660.800
18_E65_E0.245360.796
10_L13_Y0.245140.795
18_E40_K0.244980.795
12_Y92_W0.244410.793
86_P92_W0.242940.788
3_F53_A0.241980.785
67_L70_E0.240460.780
61_R65_E0.239450.777
51_V82_R0.238190.772
1_V17_K0.238160.772
60_G64_A0.237190.769
3_F17_K0.235870.765
8_D60_G0.235380.763
8_D54_F0.234180.759
56_N87_P0.234120.759
4_E55_D0.232990.756
37_Q41_F0.232080.753
50_I81_V0.230540.748
3_F8_D0.226790.736
8_D91_D0.226030.733
1_V19_N0.225590.732
38_Q42_L0.225570.732
33_L63_A0.224630.729
30_G33_L0.221870.720
31_G63_A0.221210.717
69_K72_K0.220620.716
36_K70_E0.217810.706
62_K72_K0.215030.697
46_P50_I0.214530.696
5_G12_Y0.21150.686
37_Q40_K0.210050.681
79_I82_R0.209240.679
27_L30_G0.208850.677
16_G19_N0.208510.676
56_N92_W0.20810.675
29_G67_L0.207130.672
64_A85_D0.203110.659
54_F92_W0.2030.658
53_A65_E0.202270.656
29_G33_L0.201750.654
73_E80_K0.199120.646
36_K40_K0.198330.643
29_G32_T0.19780.641
32_T66_K0.195130.633
40_K80_K0.193960.629
9_A66_K0.192980.626
6_P28_A0.192280.624
13_Y19_N0.191530.621
27_L92_W0.191050.620
34_S39_I0.188340.611
45_N79_I0.188290.611
27_L42_L0.187180.607
65_E81_V0.186320.604
9_A28_A0.18590.603
12_Y26_S0.184570.599
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
2au3A0.895899.70.161
4edgA0.895899.60.169
1dd9A0.895899.60.181
1nuiA0.885499.50.274
1q57A0.885499.40.308
1t6t10.9167980.601
2fcjA0.87597.60.649
3vdpA0.927192.20.773
1vddA0.947990.10.784
2h4aA0.979274.80.82

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