GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LRR_5 - Leucine rich repeats (6 copies)
Pfam: PF13306 (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: 129
Sequences: 43588
Seq/Len: 337.89
HH_delta: 0.087 (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
16_S39_S2.000622.577
62_S85_N1.99432.569
39_S62_S1.993622.568
85_N107_E1.946882.508
90_S112_S1.885132.428
44_N67_N1.870742.410
67_N90_S1.83782.367
61_E84_K1.596322.056
68_N91_N1.546341.992
66_P87_D1.504821.938
84_K106_K1.500051.932
100_F103_C1.485011.913
38_K61_E1.470021.893
73_G76_A1.46361.885
89_P109_N1.425541.836
13_N36_S1.423561.834
15_E38_K1.423461.833
43_P64_T1.397681.800
59_S82_N1.379151.776
82_N104_N1.341431.728
36_S59_S1.335631.720
96_G99_S1.331831.715
87_D109_N1.313791.692
18_T41_N1.283641.653
64_T87_D1.27921.648
41_N64_T1.272621.639
22_T45_N1.26841.634
27_G30_A1.224231.577
20_P41_N1.220851.573
45_N91_N1.171181.509
50_G53_A1.113621.434
42_F65_F1.076541.387
65_F88_I1.063941.370
19_F42_F1.057141.362
88_I110_I0.997551.285
66_P89_P0.969251.248
58_K81_T0.947651.221
84_K104_N0.893351.151
54_F57_C0.874061.126
93_T115_T0.869041.119
55_S79_N0.859811.107
12_S35_T0.843151.086
61_E82_N0.8371.078
11_C14_L0.824931.063
51_D75_N0.814531.049
32_S56_N0.805791.038
35_T58_K0.794691.024
24_K47_T0.785121.011
33_N56_N0.768630.990
31_F34_C0.761210.980
25_K50_G0.753260.970
61_E64_T0.739720.953
89_P111_P0.737960.951
20_P43_P0.731830.943
78_S102_N0.731750.943
71_S94_E0.726920.936
38_K59_S0.726020.935
70_K93_T0.722730.931
21_N45_N0.722080.930
99_S103_C0.708860.913
43_P66_P0.708770.913
69_L73_G0.698250.899
15_E36_S0.696790.898
10_N33_N0.690370.889
38_K41_N0.679990.876
99_S102_N0.672870.867
23_I46_L0.672540.866
94_E116_K0.67170.865
74_D98_S0.670150.863
114_I118_E0.661290.852
21_N44_N0.655830.845
28_E50_G0.654240.843
23_I27_G0.653390.842
47_T70_K0.647450.834
47_T68_N0.64520.831
93_T96_G0.63870.823
80_C83_L0.637990.822
19_F23_I0.636890.820
29_N32_S0.630670.812
93_T113_N0.630030.812
52_N75_N0.627610.808
105_L108_I0.622640.802
95_I99_S0.619830.798
42_F46_L0.617420.795
71_S96_G0.614870.792
25_K48_S0.613710.790
90_S111_P0.606460.781
51_D73_G0.606450.781
48_S71_S0.590830.761
92_I114_I0.58550.754
98_S101_S0.582360.750
15_E18_T0.579630.747
75_N78_S0.575710.742
75_N98_S0.573290.738
87_D90_S0.572770.738
83_L105_L0.572680.738
55_S76_A0.57260.738
12_S33_N0.571090.736
116_K119_E0.563750.726
83_L86_I0.563230.725
41_N44_N0.559270.720
23_I45_N0.556680.717
84_K87_D0.555560.716
29_N52_N0.555450.715
65_F69_L0.554520.714
89_P112_S0.553950.714
77_F80_C0.549910.708
109_N112_S0.549340.708
49_I53_A0.546010.703
64_T67_N0.540990.697
62_S87_D0.540490.696
106_K109_N0.532440.686
55_S58_K0.527530.679
32_S53_A0.527280.679
56_N79_N0.523360.674
60_L63_I0.520510.670
28_E51_D0.520450.670
25_K28_E0.51850.668
37_L40_I0.518360.668
52_N55_S0.517210.666
71_S74_D0.5140.662
79_N102_N0.513030.661
14_L17_I0.510060.657
87_D107_E0.509340.656
16_S41_N0.508320.655
26_I30_A0.506680.653
72_I77_F0.505570.651
74_D96_G0.504880.650
72_I76_A0.503620.649
48_S51_D0.503060.648
44_N90_S0.502440.647
76_A99_S0.501770.646
95_I100_F0.49810.642
60_L83_L0.497330.641
34_C57_C0.495560.638
64_T85_N0.494410.637
49_I72_I0.491870.634
37_L60_L0.491590.633
34_C37_L0.49060.632
88_I91_N0.490530.632
47_T50_G0.486920.627
18_T39_S0.48380.623
30_A76_A0.483590.623
58_K79_N0.482550.622
110_I114_I0.482290.621
29_N53_A0.481660.620
92_I95_I0.48130.620
48_S73_G0.480480.619
97_S119_E0.480180.618
32_S55_S0.479940.618
84_K105_L0.473280.610
69_L72_I0.472440.609
67_N112_S0.472390.608
32_S35_T0.469230.604
57_C103_C0.469190.604
92_I96_G0.466150.600
46_L69_L0.465290.599
40_I63_I0.463410.597
16_S20_P0.458750.591
97_S118_E0.458470.591
41_N62_S0.458260.590
55_S78_S0.455070.586
111_P114_I0.455010.586
66_P111_P0.45480.586
51_D74_D0.454480.585
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
4fdwA0.984599.50.087
4fdwA0.984599.50.091
3sb4A199.50.099
4h09A199.50.107
4gt6A0.984599.50.11
4fs7A199.50.116
4gt6A199.40.142
4h09A0.984599.40.144
4fs7A0.992299.40.169
3sb4A199.20.241

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