GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPR_16 - Tetratricopeptide repeat
Pfam: PF13432 (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: 65
Sequences: 67318
Seq/Len: 1035.66
HH_delta: -0.228 (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
34_W53_Y4.447272.152
46_R49_E4.405542.132
12_D15_E4.380882.120
21_E37_L4.244682.054
38_G54_Y4.094761.981
37_L53_Y4.09391.981
4_A20_F4.047951.959
3_L19_A4.03981.955
41_L53_Y3.775481.827
41_L49_E3.555451.720
7_L19_A3.528551.707
20_F36_L3.513351.700
7_L15_E3.506641.697
17_I44_Q3.113491.507
17_I21_E2.900891.404
6_A10_Q2.868891.388
17_I41_L2.838631.374
24_L34_W2.763941.337
5_R36_L2.647311.281
51_L55_E2.635211.275
34_W56_R2.58431.251
41_L46_R2.52561.222
23_A33_A2.501771.211
7_L12_D2.469351.195
30_N33_A2.263711.095
3_L7_L2.255861.092
31_P61_D2.226431.077
35_Y39_R2.218681.074
13_Y40_I2.168341.049
56_R60_L2.156631.044
14_D44_Q2.135141.033
13_Y43_Q2.085491.009
27_D30_N2.007330.971
37_L41_L1.998370.967
22_Q26_Q1.979520.958
17_I37_L1.954690.946
19_A22_Q1.892470.916
8_Y40_I1.87920.909
42_Y50_A1.869120.904
17_I40_I1.862650.901
31_P57_A1.860230.900
3_L6_A1.850740.896
24_L33_A1.844470.893
8_Y36_L1.828130.885
8_Y16_A1.825640.883
34_W60_L1.822070.882
42_Y47_Y1.818540.880
39_R42_Y1.786280.864
8_Y43_Q1.773470.858
4_A23_A1.753880.849
53_Y56_R1.74270.843
56_R59_E1.693560.820
5_R9_Q1.670240.808
24_L37_L1.647830.797
34_W57_A1.632670.790
49_E52_A1.628470.788
5_R8_Y1.627190.787
36_L39_R1.616180.782
42_Y54_Y1.616130.782
23_A26_Q1.577450.763
15_E18_A1.553890.752
35_Y57_A1.534540.743
13_Y44_Q1.533720.742
39_R43_Q1.517820.734
16_A40_I1.50450.728
55_E58_L1.482650.717
17_I46_R1.446990.700
8_Y13_Y1.427690.691
40_I44_Q1.40170.678
22_Q25_K1.369990.663
20_F40_I1.34390.650
32_E36_L1.338660.648
7_L10_Q1.323830.641
49_E53_Y1.295690.627
21_E41_L1.294330.626
50_A54_Y1.278190.619
15_E19_A1.273770.616
57_A60_L1.262220.611
38_G50_A1.211250.586
55_E59_E1.184530.573
18_A21_E1.162870.563
8_Y20_F1.161890.562
18_A22_Q1.158680.561
39_R54_Y1.15410.558
4_A16_A1.142040.553
8_Y39_R1.139750.552
14_D17_I1.108070.536
16_A20_F1.099940.532
48_D52_A1.093040.529
48_D51_L1.090890.528
52_A56_R1.09010.527
57_A61_D1.087920.526
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
4i2zA198.3-0.228
4gywA198.2-0.213
3gyzA198.2-0.202
4ga2A198.2-0.199
4gywA198.2-0.198
3gyzA198.1-0.183
3vtxA198.1-0.17
4gcnA198.1-0.166
1kt0A198.1-0.166
2pziA198-0.154

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