GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CBFD_NFYB_HMF - Histone-like transcription factor (CBFNF-Y) and archaeal histone
Pfam: PF00808 (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: CL0012
Length: 65
Sequences: 2745
Seq/Len: 42.23
HH_delta: -0.026 (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
53_R60_D0.767692.930
35_E39_Y0.606322.314
58_Y62_A0.568592.170
45_N56_I0.531112.027
48_A56_I0.452291.726
16_P19_M0.417021.592
12_M21_V0.400381.528
44_A56_I0.390241.489
31_K38_Q0.383991.465
44_A61_V0.377061.439
59_E63_K0.37031.413
37_I41_A0.369631.411
9_K13_K0.324781.239
51_D63_K0.322741.232
15_D18_V0.319971.221
43_E46_E0.317341.211
5_L12_M0.307571.174
47_I50_R0.306851.171
50_R63_K0.306611.170
42_K46_E0.30541.166
31_K35_E0.2991.141
23_K26_V0.292331.116
47_I63_K0.282051.076
15_D22_S0.279671.067
44_A64_A0.277311.058
39_Y43_E0.275241.050
60_D64_A0.273791.045
43_E47_I0.273611.044
29_I43_E0.2671.019
8_V12_M0.266161.016
15_D21_V0.265581.014
27_E30_A0.26080.995
46_E50_R0.260720.995
40_L61_V0.258730.987
33_A36_F0.2570.981
60_D63_K0.255230.974
21_V39_Y0.2550.973
30_A34_E0.252850.965
18_V29_I0.250950.958
49_Q57_T0.245110.935
13_K21_V0.244340.932
19_M54_K0.241140.920
40_L64_A0.237940.908
36_F39_Y0.237620.907
40_L44_A0.237250.905
9_K26_V0.235050.897
49_Q53_R0.233510.891
6_A13_K0.231520.884
47_I51_D0.229260.875
6_A21_V0.227820.869
3_L41_A0.227550.868
37_I43_E0.226410.864
24_E53_R0.225120.859
24_E27_E0.221480.845
53_R57_T0.217630.831
59_E62_A0.211990.809
38_Q42_K0.209430.799
9_K16_P0.209010.798
56_I64_A0.207380.791
42_K45_N0.206240.787
8_V11_I0.205050.783
38_Q41_A0.204910.782
10_R13_K0.201220.768
11_I16_P0.199730.762
21_V25_A0.198680.758
52_K58_Y0.197720.755
20_R37_I0.197690.754
12_M26_V0.19730.753
38_Q46_E0.197130.752
7_R52_K0.196910.751
8_V33_A0.196740.751
30_A41_A0.19640.750
40_L43_E0.195930.748
24_E52_K0.19520.745
33_A37_I0.195090.745
6_A14_S0.194520.742
3_L7_R0.193350.738
6_A10_R0.193060.737
32_A35_E0.192480.735
45_N49_Q0.191330.730
11_I14_S0.189950.725
28_A31_K0.189480.723
14_S19_M0.188080.718
3_L6_A0.187950.717
41_A45_N0.187460.715
42_K52_K0.18690.713
14_S17_D0.185950.710
9_K12_M0.185540.708
23_K27_E0.185310.707
15_D19_M0.18410.703
5_L30_A0.183940.702
15_D32_A0.182210.695
12_M36_F0.179580.685
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
4g92C199.3-0.026
2bykA199.3-0.014
1n1jB199.3-0.002
1jfiA199.30.007
2bykB199.20.037
1n1jA199.20.039
1b67A0.984699.20.065
3b0cW199.10.074
1jfiB199.10.087
1f1eA0.984699.10.108

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