GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CENP-C_C - Mif2CENP-C like
Pfam: PF11699 (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: 85
Sequences: 16144
Seq/Len: 189.93
HH_delta: 0.044 (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
45_E52_S2.799613.184
45_E54_V2.565342.918
44_V79_A2.4372.772
41_K80_K2.184372.484
43_K56_T2.062442.346
45_E74_I2.062122.345
45_E72_K2.043552.324
16_M80_K1.970362.241
56_T59_G1.907892.170
47_T70_S1.885562.144
18_E80_K1.688221.920
43_K54_V1.609081.830
20_P78_E1.551361.764
38_Y60_S1.454141.654
41_K57_K1.406611.600
47_T52_S1.406141.599
18_E78_E1.308421.488
36_V60_S1.254391.427
24_E72_K1.220361.388
47_T72_K1.208691.375
34_T62_Q1.163811.324
41_K78_E1.151351.309
41_K77_E1.105091.257
34_T65_R1.102751.254
43_K75_G1.092091.242
29_N68_Y1.08971.239
48_I51_T1.059211.205
54_V74_I1.037191.180
27_P68_Y1.020661.161
37_F61_F0.972251.106
43_K74_I0.953591.085
40_I82_F0.922871.050
39_V79_A0.92111.048
49_H67_N0.894971.018
27_P70_S0.886141.008
19_L23_G0.835240.950
49_H68_Y0.830220.944
46_V61_F0.83020.944
37_F63_V0.813990.926
46_V55_V0.805680.916
39_V55_V0.796480.906
36_V62_Q0.791540.900
44_V55_V0.783950.892
24_E70_S0.779640.887
19_L81_L0.776180.883
34_T64_P0.770630.876
20_P23_G0.770540.876
73_N78_E0.764480.869
48_I67_N0.760910.865
22_G76_N0.758850.863
64_P67_N0.755920.860
52_S72_K0.749930.853
44_V71_I0.714220.812
48_I53_F0.714190.812
17_L81_L0.710450.808
16_M40_I0.709550.807
55_V61_F0.706360.803
35_M69_Y0.696920.793
14_S36_V0.692960.788
37_F81_L0.690840.786
30_S69_Y0.689160.784
39_V44_V0.687820.782
46_V71_I0.672060.764
21_P75_G0.667390.759
32_D66_G0.661460.752
44_V54_V0.642490.731
40_I80_K0.638150.726
21_P76_N0.637820.725
21_P73_N0.633730.721
35_M63_V0.598340.680
46_V63_V0.597910.680
55_V59_G0.593320.675
26_P70_S0.593120.675
11_F34_T0.586570.667
75_G79_A0.552040.628
16_M82_F0.550170.626
44_V59_G0.545450.620
11_F14_S0.537510.611
13_A33_N0.528680.601
14_S82_F0.518130.589
32_D65_R0.510180.580
21_P77_E0.50950.579
43_K77_E0.498980.567
15_G33_N0.482220.548
63_V69_Y0.474580.540
19_L71_I0.474340.539
13_A16_M0.472930.538
17_L25_K0.471130.536
12_F36_V0.460430.524
13_A25_K0.456060.519
31_R69_Y0.452080.514
52_S74_I0.448530.510
39_V59_G0.447690.509
25_K28_K0.445870.507
19_L73_N0.440010.500
39_V81_L0.438520.499
37_F46_V0.434290.494
36_V82_F0.424690.483
19_L44_V0.423960.482
47_T50_E0.421290.479
55_V79_A0.408910.465
22_G75_G0.408710.465
25_K37_F0.408090.464
28_K69_Y0.406530.462
17_L36_V0.404430.460
33_N71_I0.404360.460
39_V42_G0.400050.455
15_G37_F0.392740.447
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
2vpvA199.30.044
3l2hA1990.171
1sq4A1990.172
1rc6A1990.172
1sfnA1990.173
2fqpA0.9882990.174
3lagA198.90.182
1uijA0.988298.90.19
1sq4A198.90.191
2bnmA198.90.195

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