GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Chromo - Chromo (CHRromatin Organisation MOdifier) domain
Pfam: PF00385 (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: CL0049
Length: 55
Sequences: 2409
Seq/Len: 43.8
HH_delta: -0.062 (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
10_R20_E1.517673.487
9_H52_F1.409463.238
24_K33_N1.365623.137
9_H53_E1.139612.618
30_Y33_N1.101572.531
4_E24_K1.053532.420
25_W34_T0.823181.891
36_E40_N0.777911.787
24_K30_Y0.771351.772
12_V20_E0.740481.701
37_P40_N0.700151.609
2_E26_K0.665471.529
21_Y53_E0.650481.494
22_L33_N0.579251.331
6_I23_V0.55671.279
22_L35_W0.511361.175
8_D22_L0.504391.159
21_Y38_E0.491751.130
29_P32_E0.467541.074
46_P50_E0.464141.066
28_Y32_E0.460531.058
5_R30_Y0.45971.056
43_N46_P0.457491.051
40_N44_C0.446161.025
38_E53_E0.431970.992
9_H21_Y0.41780.960
11_V16_N0.387620.891
49_I52_F0.359360.826
20_E37_P0.356920.820
12_V15_G0.356310.819
11_V39_E0.352280.809
13_K16_N0.330880.760
6_I9_H0.330620.760
8_D11_V0.32710.751
47_E51_E0.314980.724
40_N43_N0.298090.685
7_L33_N0.296910.682
4_E26_K0.29330.674
10_R35_W0.292460.672
2_E8_D0.280680.645
12_V16_N0.274780.631
16_N38_E0.274190.630
48_L51_E0.267240.614
16_N43_N0.265520.610
4_E7_L0.262330.603
36_E41_L0.257640.592
21_Y41_L0.256390.589
2_E12_V0.255720.587
9_H38_E0.255460.587
38_E42_K0.254680.585
42_K47_E0.252810.581
37_P42_K0.250630.576
3_V36_E0.250240.575
25_W36_E0.250030.574
28_Y31_S0.247270.568
14_G46_P0.246910.567
40_N47_E0.245630.564
7_L30_Y0.244650.562
6_I21_Y0.242870.558
11_V15_G0.241690.555
26_K51_E0.237590.546
20_E35_W0.237380.545
3_V21_Y0.23380.537
28_Y41_L0.230680.530
7_L49_I0.228380.525
28_Y33_N0.224790.516
5_R24_K0.223480.513
21_Y28_Y0.221940.510
23_V34_T0.21930.504
2_E42_K0.215830.496
9_H16_N0.21410.492
37_P43_N0.213330.490
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
4haeA0.945599.1-0.062
2rsnA0.945599.1-0.055
2rsoA0.963699.1-0.041
3lweA0.927399-0.02
1q3lA0.909199-0.014
2dntA0.945599-0.011
1g6zA0.927399-0.011
2k1bA0.909199-0.008
1pdqA0.909199-0.007
3f2uA0.909199-0.004

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