GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPR_12 - Tetratricopeptide repeat
Pfam: PF13424 (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: 78
Sequences: 59522
Seq/Len: 763.1
HH_delta: -0.186 (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
8_Y27_Y4.759272.443
49_L68_Y4.665542.395
12_A28_Y4.364872.241
61_D64_E4.35252.234
20_R23_E4.231122.172
29_E52_L3.988542.047
53_G69_Y3.84731.975
52_L68_Y3.821771.962
11_L27_Y3.66191.880
56_Y68_Y3.605481.851
56_Y64_E3.502951.798
15_Y27_Y3.409811.750
15_Y23_E3.347991.719
25_L29_E2.879681.478
28_Y51_N2.744661.409
25_L59_L2.595961.333
66_L70_Q2.531161.299
56_Y61_D2.527891.298
8_Y30_K2.510751.289
32_L49_L2.467241.267
14_V18_L2.456131.261
15_Y20_R2.433361.249
49_L71_K2.376151.220
25_L56_Y2.373441.218
13_R51_N2.33011.196
4_T7_A2.23921.149
50_N54_E2.126491.092
31_A48_T2.007871.031
35_E45_T1.966361.009
22_D59_L1.917340.984
16_R55_C1.911230.981
25_L52_L1.906120.978
11_L15_Y1.898070.974
21_Y58_R1.865370.958
16_R58_R1.812030.930
5_A31_A1.810190.929
46_A72_A1.808710.928
71_K75_I1.796780.922
57_Y62_Y1.782050.915
21_Y55_C1.777030.912
52_L56_Y1.735550.891
54_E57_Y1.696070.871
9_N51_N1.685680.865
25_L55_C1.670710.858
57_Y65_A1.669420.857
64_E67_E1.657450.851
30_K34_I1.647320.846
9_N13_R1.628980.836
45_T48_T1.628920.836
4_T45_T1.616150.830
57_Y69_Y1.597690.820
71_K74_D1.595520.819
68_Y71_K1.588850.816
28_Y55_C1.581960.812
16_R24_A1.575220.809
5_A35_E1.570050.806
13_R16_R1.563220.802
54_E58_R1.529260.785
30_K33_D1.50860.774
16_R51_N1.449350.744
12_A31_A1.445050.742
16_R21_Y1.440280.739
51_N54_E1.438660.739
27_Y30_K1.423280.731
23_E26_D1.41780.728
32_L48_T1.40450.721
8_Y34_I1.399060.718
55_C59_L1.39510.716
13_R17_E1.379630.708
6_N47_N1.376310.707
25_L61_D1.367070.702
64_E68_Y1.36430.700
50_N72_A1.344330.690
49_L72_A1.331430.683
21_Y59_L1.32880.682
53_G72_A1.328020.682
11_L14_V1.313530.674
32_L52_L1.269150.652
35_E43_P1.243130.638
62_Y66_L1.229350.631
10_N13_R1.210760.622
35_E44_D1.208590.620
9_N48_T1.204680.618
29_E68_Y1.198710.615
6_N10_N1.19650.614
26_D30_K1.194170.613
67_E71_K1.190330.611
8_Y31_A1.189710.611
15_Y18_L1.182140.607
29_E56_Y1.170020.601
49_L75_I1.163250.597
53_G65_A1.15710.594
16_R28_Y1.145960.588
26_D29_E1.142710.587
23_E27_Y1.13070.580
16_R54_E1.129920.580
24_A28_Y1.128490.579
56_Y59_L1.117670.574
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
4gywA0.910398.5-0.186
3qwwA198.4-0.169
3n71A198.3-0.154
4gywA0.910398.3-0.152
3gyzA0.910398.3-0.139
4i2zA0.910398.3-0.137
3qwpA198.3-0.135
4gcnA198.2-0.119
3gyzA0.910398.2-0.108
4houA0.85998.2-0.105

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