GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LRR_8 - Leucine rich repeat
Pfam: PF13855 (v26) Consensus Sequence
Clan: CL0022
Length: 61
Sequences: 32888
Seq/Len: 539.15
HH_delta: -0.179 (11Mar13)
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_N58_N2.122092.585
10_N34_N2.08772.543
12_R35_N2.043042.488
36_N59_N1.984412.417
29_S53_E1.919652.338
5_E29_S1.916682.334
28_E52_R1.558821.899
4_K28_E1.495991.822
41_P44_S1.38551.687
7_D31_D1.315951.603
26_N50_S1.30371.588
2_N26_N1.2981.581
33_S55_D1.288661.570
17_P20_S1.286811.567
35_N59_N1.264261.540
31_D55_D1.242051.513
32_L56_L1.221241.487
9_S31_D1.152741.404
22_S47_G1.144631.394
8_L32_L1.083021.319
25_P49_P1.067961.301
12_R36_N1.009211.229
36_N60_R0.995071.212
33_S57_S0.97391.186
9_S33_S0.935131.139
55_D58_N0.932461.136
14_T38_T0.880331.072
11_N59_N0.853451.039
21_F24_L0.828431.009
4_K7_D0.827241.008
19_G44_S0.820580.999
28_E31_D0.811330.988
4_K26_N0.789440.962
14_T36_N0.778820.949
11_N35_N0.770230.938
13_L37_L0.76910.937
45_F48_L0.762950.929
37_L41_P0.732150.892
15_E39_S0.731510.891
7_D10_N0.729880.889
3_L11_N0.726170.884
37_L59_N0.709710.864
22_S44_S0.687980.838
28_E50_S0.685180.835
52_R55_D0.664970.810
20_S24_L0.661930.806
38_T60_R0.654290.797
51_L54_L0.627620.764
37_L61_L0.622340.758
19_G22_S0.608560.741
46_S49_P0.602720.734
13_L17_P0.60260.734
3_L24_L0.602060.733
23_N47_G0.578760.705
17_P41_P0.578420.704
27_L30_L0.578080.704
16_I40_I0.573910.699
5_E31_D0.571530.696
3_L6_L0.549470.669
16_I32_L0.545010.664
33_S58_N0.542940.661
18_P41_P0.541430.659
21_F45_F0.537880.655
43_D46_S0.537260.654
44_S47_G0.533440.650
15_E18_P0.521560.635
24_L27_L0.521250.635
44_S48_L0.513880.626
15_E41_P0.511710.623
19_G43_D0.506040.616
31_D53_E0.505240.615
18_P42_P0.497690.606
31_D34_N0.490240.597
56_L61_L0.489230.596
40_I44_S0.481960.587
15_E38_T0.464250.565
29_S55_D0.461720.562
22_S46_S0.456680.556
24_L48_L0.451050.549
5_E9_S0.45040.549
37_L40_I0.445570.543
49_P52_R0.440520.537
8_L11_N0.439170.535
13_L35_N0.438680.534
20_S23_N0.436570.532
17_P21_F0.433560.528
20_S44_S0.433280.528
13_L20_S0.425040.518
25_P28_E0.421810.514
23_N26_N0.418550.510
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
4g8aA198.4-0.179
4g8aA198.3-0.16
2ifgA198.2-0.127
3g39A198.1-0.09
2wfhA198-0.083
2r9uA198-0.077
2xotA198-0.076
3a79B198-0.073
3g39A198-0.072
2xotA198-0.067

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