GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cupin_1 - Cupin
Pfam: PF00190 (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: CL0029
Length: 144
Sequences: 1565
Seq/Len: 10.87
HH_delta: 0.168 (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
64_R89_K0.515753.640
42_E111_E0.367562.594
52_H102_H0.321132.267
133_A140_G0.298872.110
62_E90_A0.29342.071
60_V65_G0.277311.957
21_D24_D0.266751.883
52_H56_E0.266241.879
61_I115_L0.256561.811
68_G103_W0.25221.780
65_G112_A0.244211.724
66_R105_I0.238151.681
62_E113_L0.235281.661
20_A25_F0.233531.648
56_E102_H0.226291.597
62_E110_D0.219441.549
59_Y115_L0.205041.447
64_R107_D0.202421.429
50_H56_E0.199161.406
66_R83_S0.19361.367
132_L135_A0.192881.361
46_L71_G0.189441.337
67_V96_V0.188821.333
132_L136_F0.188631.331
28_L31_L0.187561.324
47_R104_I0.1831.292
46_L105_I0.178281.258
129_P140_G0.17661.247
133_A137_F0.172721.219
133_A141_E0.172371.217
66_R85_K0.168041.186
22_S122_N0.166871.178
58_V67_V0.164641.162
130_E140_G0.164631.162
54_A98_A0.163121.151
22_S35_A0.161551.140
56_E118_F0.161081.137
129_P133_A0.1611.136
67_V94_F0.159211.124
66_R107_D0.159071.123
55_D95_V0.156081.102
44_G128_P0.156031.101
60_V90_A0.155191.095
69_V82_F0.152881.079
133_A139_S0.151831.072
50_H102_H0.151181.067
65_G107_D0.149741.057
127_L132_L0.149311.054
16_R40_L0.148481.048
64_R110_D0.147271.040
129_P141_E0.145921.030
110_D129_P0.145371.026
45_G130_E0.145041.024
65_G113_L0.14431.019
29_L37_R0.143281.011
17_I47_R0.143051.010
52_H118_F0.142581.006
57_I93_V0.142481.006
126_Q133_A0.14231.004
40_L65_G0.141510.999
58_V96_V0.141460.999
14_G46_L0.13970.986
29_L32_N0.139470.984
19_E36_V0.138760.979
62_E111_E0.138450.977
35_A121_N0.13840.977
32_N121_N0.137190.968
16_R19_E0.137090.968
60_V63_G0.136170.961
132_L139_S0.135370.956
60_V88_L0.134480.949
21_D104_I0.134420.949
55_D138_L0.133730.944
69_V100_H0.133250.941
58_V114_V0.132790.937
31_L34_V0.132550.936
88_L92_D0.132080.932
30_G121_N0.13090.924
72_P122_N0.130650.922
48_A104_I0.129060.911
106_N112_A0.128770.909
26_P45_G0.12870.908
129_P136_F0.128250.905
130_E133_A0.127440.900
96_V102_H0.125640.887
34_V118_F0.125390.885
71_G80_R0.124630.880
101_P126_Q0.124320.878
119_D128_P0.123650.873
67_V102_H0.122990.868
23_E96_V0.122820.867
58_V94_F0.122490.865
23_E122_N0.122410.864
37_R40_L0.121680.859
89_K111_E0.121480.857
68_G117_I0.120750.852
47_R56_E0.120330.849
84_Q122_N0.120280.849
47_R50_H0.12020.848
100_H103_W0.118140.834
61_I113_L0.117970.833
130_E134_K0.117410.829
68_G106_N0.116930.825
59_Y116_I0.116730.824
53_N124_P0.116620.823
131_V135_A0.116620.823
60_V116_I0.116390.822
81_D125_N0.116350.821
64_R83_S0.116040.819
34_V37_R0.115840.818
31_L115_L0.114930.811
33_G118_F0.114570.809
138_L141_E0.114070.805
45_G106_N0.113780.803
72_P100_H0.113240.799
23_E26_P0.112850.797
24_D96_V0.112850.797
34_V103_W0.112210.792
46_L64_R0.111960.790
131_V134_K0.111770.789
117_I126_Q0.111470.787
43_P110_D0.111260.785
111_E130_E0.111180.785
25_F57_I0.110770.782
96_V124_P0.110750.782
99_G124_P0.11060.781
62_E114_V0.110570.780
13_E110_D0.110340.779
123_P135_A0.110020.777
28_L34_V0.10940.772
28_L32_N0.10910.770
49_P57_I0.108520.766
59_Y74_G0.108490.766
104_I114_V0.108330.765
70_V80_R0.108270.764
134_K138_L0.107920.762
64_R80_R0.107380.758
36_V125_N0.107030.755
33_G119_D0.10690.755
25_F82_F0.106650.753
50_H135_A0.106410.751
54_A123_P0.106030.748
50_H118_F0.105870.747
67_V104_I0.105710.746
36_V128_P0.105610.745
69_V103_W0.105560.745
56_E123_P0.105270.743
137_F140_G0.105140.742
72_P138_L0.10360.731
80_R140_G0.103530.731
35_A93_V0.103480.730
47_R52_H0.103390.730
73_G138_L0.103060.727
67_V88_L0.103010.727
81_D100_H0.102780.725
53_N98_A0.102570.724
49_P118_F0.102310.722
119_D122_N0.102290.722
48_A56_E0.10210.721
54_A99_G0.101930.719
21_D47_R0.101850.719
54_A120_T0.101780.718
88_L94_F0.101780.718
131_V137_F0.101690.718
128_P137_F0.101490.716
47_R102_H0.101270.715
71_G82_F0.100050.706
119_D124_P0.099950.706
126_Q139_S0.099730.704
71_G97_P0.099420.702
28_L70_V0.099070.699
29_L34_V0.099050.699
18_R29_L0.099040.699
30_G132_L0.098490.695
20_A131_V0.098460.695
90_A138_L0.098250.694
29_L69_V0.097740.690
92_D106_N0.09710.685
50_H96_V0.096750.683
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
3kglA0.944499.90.168
3kscA0.944499.90.188
3s7iA0.958399.90.21
3qacA0.944499.90.211
2cavA0.958399.90.212
3fz3A0.937599.90.221
2e9qA0.944499.90.236
1uijA0.958399.90.237
2ea7A0.958399.90.243
3kscA0.979299.90.252

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