GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Clathrin - Region in Clathrin and VPS
Pfam: PF00637 (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: 143
Sequences: 1480
Seq/Len: 10.35
HH_delta: 0.387 (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
111_D114_E0.458553.618
31_E60_K0.354992.801
48_L52_Y0.341312.693
99_H118_Y0.340752.689
31_E52_Y0.303212.392
57_P60_K0.259542.048
46_T72_D0.234531.850
98_N101_E0.225711.781
15_S19_E0.225231.777
13_V29_Y0.210961.664
13_V17_F0.203121.603
22_Q25_E0.202851.601
46_T49_L0.19711.555
54_K83_H0.184541.456
53_I80_C0.183171.445
66_K91_Y0.178381.407
80_C89_A0.177491.400
27_I48_L0.173041.365
45_H68_S0.168121.326
80_C127_L0.167271.320
96_L108_K0.162561.283
103_L119_A0.16191.277
35_K63_E0.159671.260
64_F92_L0.154931.222
87_E114_E0.154521.219
51_L55_Y0.153821.214
89_A93_Y0.152361.202
52_Y60_K0.152171.201
11_S44_L0.150941.191
53_I61_L0.150161.185
25_E28_E0.14921.177
85_L88_E0.146391.155
50_E79_L0.14531.146
104_E108_K0.142051.121
62_L88_E0.141891.120
97_G106_L0.139871.104
34_V48_L0.13791.088
33_L37_N0.135561.070
86_Y108_K0.134721.063
67_T125_P0.134571.062
117_E120_K0.134251.059
31_E48_L0.133941.057
28_E60_K0.133461.053
93_Y99_H0.132321.044
77_L89_A0.131891.041
14_I47_L0.131271.036
39_E63_E0.130911.033
50_E75_K0.129691.023
59_E84_G0.129531.022
63_E67_T0.128951.017
34_V45_H0.128781.016
109_L115_A0.128441.013
19_E36_E0.127841.009
90_V102_A0.127611.007
78_R101_E0.127231.004
40_N70_N0.126360.997
76_A91_Y0.126340.997
22_Q88_E0.124960.986
32_A36_E0.124810.985
56_D59_E0.124680.984
28_E59_E0.123310.973
42_P74_D0.122590.967
87_E111_D0.121750.961
76_A92_L0.120590.951
50_E76_A0.120090.948
77_L96_L0.119830.945
53_I79_L0.119630.944
17_F115_A0.119340.942
65_L76_A0.118890.938
23_P54_K0.118270.933
101_E104_E0.117010.923
49_L116_I0.116810.922
106_L115_A0.116450.919
73_L96_L0.116220.917
46_T75_K0.115530.912
61_L119_A0.115410.911
11_S16_A0.115390.910
64_F106_L0.114940.907
10_I100_D0.114780.906
78_R93_Y0.114080.900
35_K110_K0.113960.899
27_I52_Y0.113340.894
50_E89_A0.112520.888
29_Y52_Y0.112450.887
77_L98_N0.112440.887
9_E14_I0.112230.886
13_V44_L0.112210.885
78_R100_D0.111930.883
9_E12_E0.111540.880
69_N124_D0.110570.872
74_D101_E0.110140.869
102_A105_I0.110050.868
49_L61_L0.109640.865
24_E63_E0.109450.864
42_P70_N0.109010.860
11_S15_S0.108910.859
77_L93_Y0.108710.858
9_E21_N0.108690.858
60_K123_D0.108280.854
47_L50_E0.107920.852
113_E117_E0.107790.850
69_N96_L0.107480.848
55_Y80_C0.107270.846
73_L92_L0.105760.834
80_C128_W0.105540.833
10_I33_L0.105390.832
42_P117_E0.105280.831
49_L55_Y0.105020.829
23_P85_L0.104670.826
19_E75_K0.10440.824
27_I31_E0.104320.823
98_N109_L0.103660.818
35_K69_N0.103520.817
42_P69_N0.102940.812
55_Y76_A0.102570.809
123_D128_W0.102520.809
112_Y120_K0.102480.809
51_L79_L0.102270.807
60_K86_Y0.102220.807
91_Y98_N0.102150.806
78_R82_K0.102140.806
69_N101_E0.101670.802
63_E66_K0.101570.801
19_E86_Y0.101440.800
67_T70_N0.1010.797
86_Y105_I0.100630.794
42_P72_D0.100550.793
102_A128_W0.100430.792
81_E105_I0.10030.791
80_C123_D0.099280.783
15_S67_T0.099130.782
68_S71_Y0.099040.781
61_L64_F0.098690.779
45_H70_N0.098520.777
21_N67_T0.098440.777
110_K126_E0.098380.776
76_A80_C0.0980.773
45_H77_L0.097690.771
10_I15_S0.097530.770
10_I18_E0.097470.769
88_E118_Y0.09710.766
15_S78_R0.097030.766
77_L119_A0.096590.762
33_L44_L0.095840.756
107_H112_Y0.095410.753
81_E89_A0.095070.750
96_L103_L0.0950.750
24_E120_K0.094950.749
63_E119_A0.094910.749
116_I120_K0.094790.748
113_E116_I0.09460.746
14_I26_L0.094320.744
45_H89_A0.094240.744
9_E103_L0.093780.740
16_A56_D0.093420.737
35_K59_E0.09340.737
83_H128_W0.093370.737
52_Y64_F0.092960.733
87_E117_E0.092920.733
51_L90_V0.092870.733
21_N84_G0.092790.732
30_L87_E0.092720.732
82_K121_K0.092640.731
32_A89_A0.092480.730
81_E107_H0.092250.728
14_I43_D0.091940.725
24_E40_N0.09180.724
120_K125_P0.091490.722
119_A127_L0.090990.718
50_E83_H0.090920.717
61_L73_L0.090780.716
104_E107_H0.090670.715
72_D100_D0.090610.715
91_Y118_Y0.090490.714
12_E104_E0.090450.714
52_Y55_Y0.089980.710
10_I29_Y0.089940.710
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
4g26A199.60.387
4g26A199.50.43
3spaA199.40.446
1b89A0.98699.40.45
3lvgA0.98699.30.475
1xi4A0.99399.10.525
1xi4A0.98699.10.533
3spaA1990.548
3lvgA0.97998.70.598
2xpiA0.98698.50.635

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