GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Linker_histone - linker histone H1 and H5 family
Pfam: PF00538 (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. )
Length: 77
Sequences: 785
Seq/Len: 10.19
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
16_L22_S0.604853.197
18_E22_S0.408662.160
51_A55_G0.369691.954
55_G61_L0.346311.830
2_H8_M0.344531.821
13_I27_I0.324321.714
11_E15_A0.322681.705
50_R54_R0.296731.568
55_G64_V0.291081.538
26_A29_K0.278641.473
56_V63_Q0.273841.447
65_K72_S0.272791.442
54_R58_K0.268281.418
5_Y8_M0.257931.363
30_Y34_K0.255421.350
60_K63_Q0.251551.330
11_E34_K0.23561.245
5_Y48_L0.226731.198
24_L28_K0.222211.174
28_K48_L0.220761.167
72_S76_S0.215891.141
4_P7_D0.2151.136
5_Y44_F0.207371.096
18_E32_K0.204691.082
17_K20_K0.20321.074
8_M31_I0.200971.062
13_I22_S0.199051.052
44_F55_G0.198521.049
28_K45_K0.198311.048
12_A30_Y0.196831.040
9_I48_L0.196171.037
19_R74_K0.191031.010
53_K56_V0.18910.999
11_E35_Y0.188580.997
20_K72_S0.185140.979
52_L73_F0.181710.960
43_N47_R0.181410.959
53_K63_Q0.180850.956
63_Q73_F0.180730.955
8_M36_K0.179790.950
6_S10_L0.179570.949
23_S72_S0.176240.931
47_R52_L0.174490.922
23_S29_K0.174460.922
14_K33_A0.174170.921
43_N50_R0.17320.915
24_L49_K0.171190.905
35_Y40_N0.170730.902
10_L14_K0.170130.899
14_K25_Q0.167560.886
47_R50_R0.167170.884
6_S75_L0.167160.884
2_H5_Y0.165130.873
71_G75_L0.163320.863
49_K63_Q0.160860.850
13_I61_L0.159770.844
13_I17_K0.15910.841
14_K32_K0.158780.839
16_L53_K0.158540.838
23_S26_A0.1570.830
19_R29_K0.156760.829
45_K56_V0.156690.828
54_R57_E0.155490.822
11_E30_Y0.154380.816
72_S75_L0.153430.811
63_Q71_G0.151880.803
26_A43_N0.151490.801
24_L31_I0.150730.797
6_S55_G0.15060.796
64_V73_F0.149630.791
43_N57_E0.148770.786
12_A22_S0.148530.785
30_Y76_S0.147590.780
19_R34_K0.147290.778
31_I48_L0.146950.777
10_L49_K0.145680.770
17_K60_K0.144940.766
15_A30_Y0.144790.765
46_S55_G0.144560.764
48_L73_F0.144140.762
10_L71_G0.142560.753
23_S65_K0.139390.737
26_A65_K0.138050.730
64_V72_S0.136910.724
59_G72_S0.136780.723
24_L63_Q0.135990.719
17_K22_S0.135730.717
27_I48_L0.135030.714
65_K71_G0.134370.710
20_K71_G0.133370.705
10_L51_A0.133270.704
33_A76_S0.132870.702
31_I35_Y0.132210.699
29_K65_K0.131940.697
11_E38_D0.130550.690
25_Q57_E0.129570.685
31_I47_R0.12930.683
3_P54_R0.128420.679
3_P52_L0.128060.677
39_L44_F0.127710.675
14_K62_V0.127490.674
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
2rqpA0.98799.80.044
1hstA0.96199.80.06
1uhmA0.97499.80.069
1ustA0.97499.80.074
1ussA0.97499.80.087
2lsoA0.97499.70.129
1ghcA0.948199.70.133
1vtnC0.909187.10.802
1qgpA0.844284.20.81
3lmmA0.818280.30.817

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