GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LRR_8 - Leucine rich repeat
Pfam: PF13855 (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: CL0022
Length: 61
Sequences: 47901
Seq/Len: 785.26
HH_delta: -0.221 (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
10_N34_N2.240442.583
34_N58_N2.210242.549
36_N59_N2.059772.375
5_S29_T2.0432.356
29_T53_Y2.02012.329
12_K35_N1.877872.165
4_E28_E1.697671.958
28_E52_R1.687321.946
7_D31_D1.585981.829
35_N59_N1.519631.752
9_S31_D1.465011.689
26_N50_N1.407941.624
33_S55_D1.400351.615
2_N26_N1.373091.583
22_S47_N1.350911.558
31_D55_D1.344281.550
41_P44_A1.300291.499
32_L56_L1.254341.446
8_L32_L1.198311.382
17_P20_S1.192031.375
33_S57_S1.080411.246
36_N60_N1.056661.218
9_S33_S1.033161.191
25_P49_P0.960021.107
12_K36_N0.917611.058
21_F24_L0.888231.024
15_E39_S0.877321.012
55_D58_N0.870821.004
11_N35_N0.851070.981
22_S44_A0.835520.963
7_D29_T0.822440.948
38_T60_N0.817980.943
13_L37_L0.808730.933
4_E26_N0.803780.927
5_S31_D0.79940.922
19_D44_A0.79520.917
37_L41_P0.772370.891
45_F48_L0.736830.850
14_T36_N0.735680.848
11_N59_N0.723830.835
37_L59_N0.718980.829
52_R55_D0.7160.826
15_E41_P0.709890.819
14_T38_T0.701880.809
16_I40_I0.699230.806
37_L61_L0.695920.802
28_E50_N0.69120.797
51_L54_L0.688140.794
3_L11_N0.674230.777
4_E7_D0.665170.767
28_E31_D0.664670.766
39_S42_P0.646540.746
17_P41_P0.638920.737
49_P52_R0.628050.724
24_L48_L0.621920.717
3_L6_L0.61110.705
27_L30_L0.609780.703
18_P43_D0.608790.702
7_D10_N0.604680.697
44_A48_L0.603160.696
21_F45_F0.599470.691
19_D22_S0.598040.690
29_T55_D0.595830.687
20_S24_L0.58180.671
13_L17_P0.575480.664
23_N47_N0.569030.656
43_D46_S0.553490.638
18_P41_P0.543660.627
24_L27_L0.543370.627
18_P42_P0.537050.619
13_L35_N0.533330.615
30_L54_L0.532870.614
3_L24_L0.523990.604
19_D43_D0.52360.604
23_N26_N0.519020.598
4_E52_R0.518730.598
25_P47_N0.513730.592
46_S49_P0.503630.581
16_I32_L0.498690.575
33_S58_N0.495190.571
56_L59_N0.491730.567
8_L11_N0.481870.556
17_P21_F0.475130.548
15_E18_P0.473430.546
53_Y57_S0.466140.538
31_D34_N0.465290.537
15_E38_T0.442740.511
11_N37_L0.430790.497
7_D11_N0.424870.490
3_L27_L0.42320.488
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
4g8aA198.3-0.221
4g8aA198.2-0.208
4arnA198.1-0.174
2ifgA198.1-0.174
3g39A198-0.145
2r9uA197.9-0.134
2wfhA197.9-0.133
4arnA0.983697.9-0.133
2xotA197.9-0.126
3g39A197.9-0.126

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