GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Histone - Core histone H2AH2BH3H4
Pfam: PF00125 (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: 75
Sequences: 2592
Seq/Len: 34.56
HH_delta: -0.028 (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
60_R67_D0.709162.821
52_G63_I0.526112.093
42_Y46_E0.517892.060
65_P69_Q0.439141.747
51_A63_I0.396051.576
44_L48_L0.382381.521
51_A68_I0.36271.443
66_R70_L0.339741.352
57_H70_L0.338851.348
38_S42_Y0.337761.344
50_E53_N0.336661.339
55_A63_I0.330951.317
54_L57_H0.324851.292
9_F12_S0.324411.291
12_S28_I0.318871.269
70_L73_R0.311481.239
28_I32_A0.305211.214
10_P27_R0.304961.213
19_G28_I0.301981.201
51_A71_A0.299121.190
47_I51_A0.298361.187
10_P13_R0.296241.179
34_V37_Q0.287871.145
67_D70_L0.28671.141
29_S32_A0.28511.134
10_P17_E0.278831.109
47_I71_A0.276921.102
54_L70_L0.273591.088
28_I46_E0.269271.071
15_L68_I0.265841.058
54_L58_A0.264741.053
52_G56_R0.261721.041
46_E50_E0.257611.025
31_E34_V0.256791.022
47_I68_I0.253381.008
10_P41_E0.246920.982
15_L19_G0.24580.978
63_I71_A0.244780.974
47_I50_E0.242660.965
43_L46_E0.240960.959
69_Q73_R0.240860.958
38_S45_V0.236910.942
11_F15_L0.235550.937
58_A70_L0.235340.936
15_L33_L0.234680.934
34_V40_L0.227710.906
6_I11_F0.224220.892
16_R27_R0.223140.888
5_L37_Q0.220880.879
14_L17_E0.220750.878
58_A73_R0.220510.877
49_E53_N0.218060.867
10_P15_L0.217820.867
30_S33_L0.217750.866
9_F13_R0.216330.861
60_R64_T0.215160.856
9_F34_V0.214420.853
66_R69_Q0.214110.852
50_E71_A0.212770.846
54_L67_D0.212660.846
21_E31_E0.210350.837
52_G55_A0.205670.818
9_F19_G0.204590.814
33_L37_Q0.204110.812
13_R46_E0.202720.806
7_P16_R0.202640.806
31_E60_R0.20160.802
8_K61_K0.201210.800
39_V42_Y0.201020.800
13_R16_R0.196440.781
35_A38_S0.196080.780
37_Q41_E0.195110.776
43_L61_K0.194450.774
45_V49_E0.194370.773
50_E54_L0.191710.763
54_L64_T0.191360.761
31_E38_S0.190350.757
46_E71_A0.189550.754
8_K12_S0.189460.754
37_Q48_L0.188350.749
56_R59_K0.18810.748
7_P19_G0.188030.748
60_R63_I0.185340.737
15_L18_I0.18330.729
67_D71_A0.183210.729
58_A63_I0.182650.727
20_E69_Q0.180470.718
5_L8_K0.179610.715
15_L20_E0.179490.714
55_A58_A0.178390.710
35_A42_Y0.177120.705
14_L69_Q0.17640.702
17_E20_E0.175470.698
40_L56_R0.174490.694
38_S50_E0.173470.690
65_P68_I0.172650.687
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
3r45A199.4-0.028
1tzyC199.4-0.021
3nquA199.4-0.016
2yfvA199.4-0.012
2hueB0.973399.30.035
2l5aA199.30.036
3nqjA0.973399.20.064
4g92C0.986799.10.106
1n1jA0.9699.10.118
1jfiA0.986799.10.129

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