GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
R3H - R3H domain
Pfam: PF01424 (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: 63
Sequences: 1295
Seq/Len: 20.56
HH_delta: 0.147 (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
48_K61_S0.564742.168
49_S56_R0.553672.126
40_A47_S0.497741.911
24_E57_R0.466681.792
17_L44_G0.459611.765
14_E17_L0.447681.719
33_R37_H0.443581.703
37_H49_S0.424541.630
6_E10_E0.422231.621
20_G62_K0.414571.592
34_K38_E0.41081.577
28_M58_V0.377011.448
10_E14_E0.354351.361
38_E41_E0.331621.273
13_I16_F0.32071.231
16_F19_S0.313981.206
12_L15_F0.312571.200
40_A45_L0.311451.196
58_V61_S0.305071.171
12_L60_V0.303761.166
46_K61_S0.296681.139
22_S61_S0.290261.114
11_K26_P0.289471.111
25_F60_V0.284171.091
6_E39_L0.2841.090
25_F28_M0.273551.050
42_Y45_L0.27311.049
34_K41_E0.269431.035
44_G62_K0.26821.030
33_R49_S0.262961.010
17_L42_Y0.262121.006
10_E39_L0.258040.991
15_F23_L0.25740.988
34_K58_V0.251820.967
31_F35_L0.24960.958
7_K10_E0.249520.958
10_E42_Y0.247810.951
50_E57_R0.242110.930
14_E44_G0.240630.924
8_I25_F0.23690.910
29_N32_E0.236170.907
24_E50_E0.234050.899
7_K11_K0.233160.895
28_M36_I0.232390.892
26_P36_I0.231010.887
7_K26_P0.229820.882
56_R59_V0.22590.867
37_H56_R0.224480.862
15_F18_S0.222230.853
15_F26_P0.219160.841
22_S50_E0.218170.838
17_L45_L0.211220.811
24_E61_S0.210920.810
12_L24_E0.206510.793
8_I12_L0.198650.763
34_K47_S0.198640.763
41_E47_S0.19810.761
42_Y62_K0.195860.752
38_E44_G0.19470.748
31_F61_S0.192820.740
5_L36_I0.192550.739
11_K48_K0.192250.738
27_P58_V0.192140.738
51_G56_R0.191710.736
6_E14_E0.191550.735
18_S21_E0.191140.734
7_K14_E0.190690.732
28_M32_E0.19030.731
16_F21_E0.189630.728
25_F36_I0.189620.728
9_E40_A0.189490.728
32_E56_R0.189270.727
31_F41_E0.187090.718
14_E20_G0.18670.717
9_E30_S0.186660.717
17_L62_K0.186490.716
8_I11_K0.185860.714
39_L60_V0.184650.709
12_L25_F0.182510.701
33_R56_R0.181350.696
13_I47_S0.180190.692
13_I60_V0.180170.692
18_S22_S0.178980.687
12_L23_L0.177670.682
43_Y46_K0.177550.682
45_L57_R0.177270.681
10_E18_S0.177120.680
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
3gkuA199.30.147
1whrA0.968399.20.199
2cpmA199.20.202
1mszA199.20.218
2pt7G0.841397.40.565
1ug8A197.10.59
3d45A196.10.648
2a1rA194.70.681
2fphX122.10.835
1k3eA0.571412.70.851

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