GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Toprim_3 - Toprim domain
Pfam: PF13362 (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: 3787
Seq/Len: 39.45
HH_delta: 0.129 (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
84_K88_D1.234823.553
13_S87_N0.915752.635
5_A11_A0.844562.430
43_R73_A0.844542.430
52_K58_K0.823492.369
5_A14_I0.800822.304
84_K92_A0.793912.284
26_A48_A0.769252.213
89_L93_R0.759452.185
8_I27_L0.747632.151
43_R75_S0.719962.071
3_I47_A0.700932.017
87_N91_Q0.649581.869
45_I77_V0.524411.509
13_S90_L0.523741.507
5_A23_V0.509131.465
87_N90_L0.487551.403
35_V38_P0.485421.397
58_K62_K0.469391.351
42_R72_I0.468911.349
49_D56_G0.468021.347
53_A56_G0.4631.332
51_D56_G0.457121.315
61_E65_E0.45521.310
47_A79_P0.448081.289
25_A28_G0.424211.221
9_E13_S0.416371.198
44_V67_L0.412081.186
6_E49_D0.406311.169
83_G92_A0.401621.156
11_A25_A0.398381.146
57_Q78_E0.3861.111
3_I45_I0.385421.109
3_I14_I0.384881.107
48_A59_A0.383281.103
14_I23_V0.383181.102
86_W89_L0.378411.089
50_N84_K0.376631.084
10_T85_D0.373221.074
34_N38_P0.368811.061
46_I60_A0.367451.057
56_G60_A0.359711.035
84_K93_R0.356651.026
56_G85_D0.35341.017
46_I63_A0.350221.008
66_R69_A0.345650.995
2_L41_G0.339810.978
60_A64_A0.33530.965
48_A63_A0.328790.946
61_E64_A0.327320.942
14_I86_W0.326250.939
7_G49_D0.324760.934
68_E71_G0.324440.933
13_S91_Q0.315490.908
11_A23_V0.31480.906
3_I20_G0.308450.887
16_Q21_V0.30790.886
16_Q19_T0.306780.883
26_A63_A0.306660.882
60_A76_I0.306580.882
4_I44_V0.301270.867
16_Q20_G0.30020.864
29_A59_A0.298240.858
9_E87_N0.293810.845
50_N81_P0.291870.840
26_A29_A0.286680.825
29_A56_G0.279840.805
9_E90_L0.278350.801
50_N83_G0.277870.799
62_K65_E0.271260.780
5_A10_T0.270730.779
57_Q61_E0.270650.779
71_G74_V0.270160.777
82_E92_A0.268520.773
2_L24_V0.267240.769
10_T87_N0.26510.763
29_A48_A0.264930.762
10_T56_G0.262330.755
43_R92_A0.259710.747
31_N63_A0.253930.731
75_S78_E0.253680.730
7_G14_I0.251750.724
53_A59_A0.251730.724
17_Q22_P0.251340.723
33_K37_I0.250970.722
45_I75_S0.249840.719
47_A86_W0.245940.708
65_E69_A0.245920.708
16_Q23_V0.245230.706
46_I67_L0.242640.698
34_N37_I0.241720.695
10_T27_L0.240010.691
33_K36_A0.239930.690
22_P41_G0.239230.688
3_I77_V0.238080.685
8_I12_L0.236910.682
73_A78_E0.236560.681
79_P86_W0.234650.675
52_K57_Q0.233810.673
10_T84_K0.232630.669
9_E27_L0.227880.656
5_A47_A0.227620.655
5_A86_W0.226530.652
7_G10_T0.225630.649
79_P82_E0.225070.648
65_E68_E0.221460.637
9_E12_L0.220730.635
33_K66_R0.217390.625
20_G23_V0.216310.622
53_A58_K0.216270.622
36_A70_A0.212920.613
17_Q23_V0.211860.610
36_A66_R0.211320.608
10_T48_A0.210620.606
50_N57_Q0.207780.598
63_A67_L0.203990.587
52_K93_R0.203250.585
77_V89_L0.203210.585
72_I75_S0.200640.577
5_A8_I0.199390.574
68_E76_I0.198720.572
70_A73_A0.197420.568
59_A62_K0.19740.568
44_V74_V0.197380.568
32_L69_A0.195490.562
9_E47_A0.195320.562
57_Q76_I0.195150.561
14_I90_L0.193590.557
16_Q22_P0.193570.557
48_A60_A0.193340.556
40_P64_A0.193190.556
39_E68_E0.192280.553
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
2au3A0.958399.60.129
4edgA0.958399.60.134
1dd9A0.958399.60.152
1nuiA0.927199.60.188
1q57A0.927199.50.235
1t6t10.947998.40.533
2fcjA0.927197.70.613
3lfjA0.87587.70.784
1vsqC0.864684.80.793
1bleA0.864682.70.798

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