GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPR_11 - TPR repeat
Pfam: PF13414 (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: CL0020
Length: 69
Sequences: 66617
Seq/Len: 965.46
HH_delta: -0.277 (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
6_W25_Y4.660382.270
40_Y60_D4.585032.234
18_D21_E4.472562.179
53_D56_E4.219532.056
27_E43_L4.128892.012
10_G26_F4.081681.989
43_L60_D4.05791.977
9_L25_Y3.904281.902
44_G61_F3.716461.811
13_Y21_E3.571861.740
47_Y60_D3.45971.686
13_Y25_Y3.455761.684
47_Y56_E3.314011.615
26_F42_N3.13541.528
23_I27_E2.808991.368
23_I50_L2.762111.346
23_I47_Y2.74061.335
30_I40_Y2.662171.297
58_I62_E2.596361.265
51_G54_Y2.456841.197
12_I16_Q2.430751.184
13_Y18_D2.399941.169
47_Y53_D2.391341.165
11_Q42_N2.28631.114
40_Y63_K2.278571.110
36_N39_A2.255681.099
29_A39_A2.244321.093
6_W28_K2.233161.088
41_Y45_L2.2021.073
19_Y46_A2.194641.069
50_L53_D2.176851.061
33_D36_N2.140131.043
9_L13_Y2.094061.020
63_K67_L2.067661.007
20_E50_L2.029240.989
23_I43_L2.02240.985
19_Y49_K1.976440.963
43_L47_Y1.920250.936
23_I46_A1.913850.932
63_K66_K1.88670.919
48_M54_Y1.821160.887
48_M57_A1.814690.884
30_I39_A1.788370.871
7_Y42_N1.780070.867
14_F46_A1.774720.865
45_L48_M1.758540.857
28_K32_L1.757370.856
7_Y11_Q1.75640.856
14_F49_K1.697870.827
7_Y39_A1.684310.821
48_M61_F1.674130.816
9_L12_I1.654010.806
40_Y67_L1.643970.801
10_G29_A1.628290.793
14_F42_N1.597320.778
56_E59_E1.58530.772
45_L49_K1.583170.771
60_D63_K1.581610.771
6_W29_A1.5580.759
41_Y64_A1.555850.758
40_Y64_A1.555510.758
19_Y50_L1.554170.757
11_Q15_Q1.530590.746
37_A64_A1.529590.745
5_A9_L1.528370.745
28_K31_E1.527390.744
14_F22_A1.506280.734
25_Y28_K1.500710.731
21_E24_E1.496270.729
44_G64_A1.475630.719
5_A12_I1.466810.715
42_N45_L1.452650.708
46_A50_L1.438360.701
26_F46_A1.432320.698
11_Q14_F1.418930.691
6_W32_L1.418390.691
62_E65_L1.370350.668
30_I43_L1.364280.665
29_A32_L1.313560.640
64_A67_L1.303740.635
22_A46_A1.291970.629
23_I53_D1.29010.629
14_F26_F1.284630.626
14_F19_Y1.276920.622
8_N12_I1.270030.619
57_A61_F1.246340.607
27_E60_D1.22060.595
8_N11_Q1.194950.582
27_E47_Y1.177870.574
24_E28_K1.173760.572
7_Y36_N1.168940.569
56_E60_D1.162010.566
45_L61_F1.148880.560
62_E66_K1.146190.558
13_Y16_Q1.131980.551
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
4gywA0.985598.5-0.277
4i2zA0.985598.5-0.267
4gywA0.985598.4-0.252
3gyzA0.985598.4-0.249
4gcnA0.985598.4-0.236
3gyzA0.985598.4-0.233
4ga2A0.985598.3-0.23
4i2zA0.985598.3-0.211
3vtxA0.985598.3-0.208
2h6fA0.985598.2-0.204

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