GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cyclin_C - Cyclin C-terminal domain
Pfam: PF02984 (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: CL0065
Length: 118
Sequences: 1353
Seq/Len: 11.47
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
40_Y81_C0.386172.608
3_P28_L0.292961.979
74_D77_D0.288581.949
51_L82_I0.276461.867
26_Y73_Y0.256181.730
66_S70_L0.255431.725
9_R13_I0.239671.619
102_K105_S0.23391.580
28_L45_I0.22591.526
44_V81_C0.217921.472
51_L75_K0.214361.448
31_S85_I0.212321.434
79_K83_E0.210731.423
75_K82_I0.206191.393
6_F43_S0.203931.377
48_A81_C0.202591.368
52_L82_I0.202161.365
13_I70_L0.194231.312
20_V57_L0.193531.307
37_F88_L0.192751.302
36_E87_E0.192591.301
1_P29_E0.189321.279
11_L14_S0.186741.261
63_W73_Y0.18591.256
54_R63_W0.181781.228
100_I104_Y0.181381.225
63_W71_T0.17851.206
66_S69_K0.176911.195
28_L32_L0.176271.191
9_R70_L0.175471.185
17_D59_K0.17491.181
54_R67_L0.174271.177
8_R25_R0.172891.168
92_A95_S0.170961.155
55_K75_K0.170531.152
26_Y29_E0.170051.149
10_F47_A0.167881.134
53_A56_I0.167111.129
47_A63_W0.163991.108
7_L24_A0.163671.105
8_R21_R0.160431.084
34_D43_S0.16041.083
72_G79_K0.160131.082
49_A85_I0.159261.076
3_P12_K0.157411.063
20_V24_A0.155051.047
40_Y45_I0.15421.042
17_D53_A0.154041.040
11_L16_A0.152771.032
21_R25_R0.152631.031
98_Q101_R0.151241.022
55_K89_L0.150971.020
11_L25_R0.149711.011
51_L78_L0.149531.010
4_Y25_R0.148531.003
54_R61_P0.148211.001
56_I106_S0.147470.996
82_I86_Q0.146570.990
16_A54_R0.146550.990
43_S73_Y0.145180.981
73_Y78_L0.144890.979
21_R57_L0.144280.975
65_E68_E0.144140.974
2_T5_D0.143860.972
27_L58_G0.143830.971
29_E104_Y0.142780.964
20_V23_L0.141860.958
91_K99_A0.141710.957
19_E69_K0.141160.953
101_R105_S0.141130.953
96_K107_Q0.14090.952
98_Q102_K0.140850.951
22_N34_D0.14040.948
96_K106_S0.140140.947
34_D100_I0.139510.942
52_L100_I0.139420.942
9_R69_K0.138740.937
56_I89_L0.138710.937
31_S37_F0.138630.936
52_L56_I0.138340.934
88_L101_R0.13830.934
43_S103_K0.13740.928
64_P67_L0.136290.921
98_Q107_Q0.135910.918
56_I86_Q0.13450.908
21_R78_L0.133020.898
58_G91_K0.132910.898
30_L51_L0.132410.894
69_K78_L0.131840.890
43_S47_A0.131820.890
9_R43_S0.131070.885
99_A103_K0.130130.879
33_L100_I0.12990.877
40_Y84_L0.129880.877
22_N25_R0.128760.870
87_E90_S0.128490.868
12_K70_L0.128150.866
10_F73_Y0.127810.863
27_L30_L0.12670.856
98_Q106_S0.125430.847
22_N31_S0.125180.846
30_L100_I0.124510.841
9_R66_S0.124150.839
75_K102_K0.123680.835
37_F68_E0.123440.834
2_T81_C0.122840.830
2_T42_P0.122620.828
65_E80_E0.12260.828
89_L92_A0.122520.828
44_V73_Y0.121920.823
103_K106_S0.119530.807
95_S98_Q0.119530.807
95_S105_S0.119150.805
41_P91_K0.118550.801
14_S21_R0.117960.797
23_L29_E0.117230.792
100_I105_S0.11520.778
1_P6_F0.115140.778
4_Y8_R0.114850.776
1_P26_Y0.114320.772
15_N68_E0.11420.771
18_Q107_Q0.1140.770
44_V48_A0.11340.766
10_F16_A0.113340.766
3_P31_S0.113260.765
91_K98_Q0.113060.764
78_L82_I0.112860.762
97_L105_S0.112160.758
92_A98_Q0.111650.754
13_I47_A0.111630.754
37_F92_A0.111150.751
5_D87_E0.11110.750
31_S67_L0.110920.749
55_K86_Q0.110870.749
26_Y68_E0.110450.746
53_A57_L0.110340.745
65_E79_K0.11030.745
37_F41_P0.110260.745
54_R71_T0.109980.743
31_S77_D0.10950.740
88_L97_L0.109070.737
88_L102_K0.109050.737
4_Y53_A0.108780.735
11_L22_N0.108590.733
51_L76_E0.108350.732
83_E91_K0.108350.732
59_K62_P0.107870.729
21_R28_L0.107770.728
65_E85_I0.107720.728
38_L75_K0.107610.727
5_D80_E0.107320.725
81_C86_Q0.107290.725
11_L31_S0.10720.724
32_L56_I0.106640.720
54_R59_K0.106010.716
48_A58_G0.105940.716
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
2cchB0.991599.90.168
4eojB0.991599.90.171
2b9rA0.991599.90.177
1g3nC0.847599.60.367
1w98B0.923799.60.381
2f2cA0.82299.60.394
3g33B199.60.404
2w96A0.889899.50.423
3rgfB0.940799.50.426
4f6uB0.940799.50.43

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