GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cyclin_N - Cyclin N-terminal domain
Pfam: PF00134 (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: 127
Sequences: 2595
Seq/Len: 20.43
HH_delta: -0.011 (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
80_C118_I0.865393.813
57_Y61_R0.727983.207
31_R60_D0.645132.842
62_F117_E0.610722.691
42_C52_L0.505082.225
119_L126_L0.458272.019
83_L118_I0.454632.003
58_L126_L0.453982.000
51_T89_E0.4471.969
58_L80_C0.445581.963
35_I56_I0.445161.961
86_K115_E0.412721.818
34_I77_A0.390681.721
59_F80_C0.37331.645
99_I111_I0.342351.508
115_E119_L0.324841.431
63_L73_L0.299811.321
65_K123_N0.29621.305
108_K112_L0.292921.291
93_P98_L0.291431.284
75_L106_F0.289511.275
115_E124_F0.289481.275
81_L98_L0.284611.254
58_L118_I0.279651.232
37_W41_L0.276761.219
78_L111_I0.276511.218
79_A114_M0.273661.206
85_S93_P0.27031.191
34_I59_F0.268831.184
76_I114_M0.267261.177
66_R117_E0.266181.173
62_F66_R0.26461.166
107_T110_D0.263061.159
106_F114_M0.261261.151
30_M70_R0.260991.150
38_I81_L0.259621.144
75_L114_M0.256291.129
39_I52_L0.253151.115
113_E117_E0.25231.112
91_N94_S0.249371.099
95_I112_L0.247091.089
66_R121_A0.241131.062
79_A118_I0.239491.055
82_F95_I0.237541.047
99_I108_K0.236991.044
61_R122_L0.233251.028
62_F121_A0.232081.022
31_R35_I0.23051.016
69_N80_C0.230321.015
108_K124_F0.227831.004
29_E33_I0.227091.000
65_K121_A0.225790.995
27_T30_M0.224920.991
40_E101_I0.220650.972
42_C49_P0.213150.939
117_E121_A0.212730.937
45_L98_L0.20990.925
102_S105_T0.209020.921
99_I102_S0.208830.920
31_R77_A0.205390.905
120_S123_N0.204480.901
66_R69_N0.201360.887
110_D113_E0.200480.883
56_I60_D0.19830.874
75_L110_D0.196340.865
29_E65_K0.196110.864
114_M117_E0.194510.857
69_N72_K0.192750.849
84_A89_E0.192090.846
102_S106_F0.191580.844
92_P98_L0.190880.841
33_I37_W0.189670.836
85_S89_E0.189490.835
49_P61_R0.188170.829
35_I59_F0.18710.824
30_M34_I0.184710.814
82_F111_I0.18450.813
54_L88_E0.184040.811
48_S51_T0.1840.811
75_L111_I0.183160.807
116_R123_N0.18230.803
74_Q106_F0.181740.801
35_I60_D0.180970.797
60_D63_L0.180560.795
72_K110_D0.179710.792
42_C81_L0.17870.787
119_L124_F0.177740.783
28_P65_K0.17740.782
53_H57_Y0.175810.775
72_K120_S0.175460.773
40_E44_R0.173880.766
54_L84_A0.173810.766
94_S97_D0.17320.763
86_K119_L0.171420.755
75_L79_A0.170920.753
51_T88_E0.170170.750
96_S99_I0.170050.749
109_K112_L0.169440.747
52_L56_I0.169120.745
47_L85_S0.169110.745
94_S106_F0.168840.744
38_I55_A0.167710.739
97_D101_I0.167390.737
110_D120_S0.167190.737
84_A88_E0.166810.735
79_A88_E0.165760.730
40_E56_I0.165630.730
116_R125_D0.164680.726
91_N111_I0.164530.725
78_L102_S0.164270.724
38_I59_F0.164260.724
57_Y62_F0.164050.723
27_T108_K0.162820.717
91_N96_S0.162440.716
83_L119_L0.162430.716
53_H90_D0.161970.714
26_I30_M0.16170.712
92_P97_D0.161340.711
32_Q36_D0.16130.711
116_R124_F0.161250.710
96_S108_K0.161160.710
31_R37_W0.160990.709
62_F82_F0.160820.709
59_F77_A0.15940.702
117_E120_S0.159130.701
55_A59_F0.158950.700
45_L97_D0.15860.699
93_P97_D0.157780.695
92_P124_F0.157470.694
45_L89_E0.15710.692
33_I74_Q0.156890.691
33_I103_D0.15630.689
37_W74_Q0.155990.687
96_S110_D0.155850.687
87_M126_L0.154930.683
37_W78_L0.154730.682
40_E103_D0.152880.674
30_M36_D0.152290.671
42_C53_H0.152280.671
76_I83_L0.150650.664
74_Q105_T0.150030.661
30_M33_I0.149970.661
51_T90_D0.14990.660
43_Q48_S0.149620.659
114_M122_L0.149230.657
39_I56_I0.148970.656
59_F73_L0.148940.656
41_L50_E0.148250.653
76_I87_M0.148170.653
36_D70_R0.147610.650
30_M73_L0.147450.650
109_K113_E0.146550.646
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
3g33B199.9-0.011
4eojB199.9-0.009
2cchB199.90.003
2f2cA0.992199.90.006
1g3nC0.992199.90.01
2b9rA0.992199.90.013
1w98B199.90.013
1f5qB0.968599.90.02
2w96A199.90.032
2pk2A0.992199.80.213

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