GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4258 - Domain of unknown function (DUF4258)
Pfam: PF14076 (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: 73
Sequences: 1226
Seq/Len: 16.79
HH_delta: 0.482 (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
9_R13_R0.777863.766
6_A10_M0.618532.994
9_R12_E0.546842.647
42_R47_G0.541052.619
24_L70_V0.374791.814
19_D22_D0.365311.769
6_A16_S0.361991.752
9_R69_T0.343421.663
30_I43_L0.336441.629
8_E12_E0.336311.628
42_R46_G0.327041.583
61_D64_P0.314171.521
15_I70_V0.311391.507
45_I58_I0.269551.305
22_D48_G0.247281.197
41_C46_G0.246411.193
19_D50_E0.24631.192
59_A68_I0.246081.191
29_I49_K0.242781.175
40_P47_G0.242551.174
35_D38_R0.242451.174
23_A28_E0.24031.163
9_R17_E0.233621.131
13_R69_T0.231271.120
22_D25_E0.224921.089
58_I65_I0.221341.072
36_D41_C0.216681.049
17_E20_I0.215791.045
61_D66_V0.212711.030
8_E64_P0.212461.029
49_K54_L0.21211.027
55_H69_T0.211281.023
38_R41_C0.203720.986
23_A70_V0.2030.983
7_R10_M0.202020.978
57_V68_I0.200550.971
20_I67_V0.19560.947
16_S19_D0.191620.928
54_L70_V0.190990.925
24_L54_L0.187020.905
11_Q64_P0.186620.903
18_E51_G0.185620.899
32_D35_D0.184430.893
10_M16_S0.184250.892
43_L46_G0.181040.876
44_Y57_V0.17590.852
44_Y55_H0.175090.848
20_I42_R0.173570.840
60_P65_I0.172640.836
14_G51_G0.172110.833
31_E45_I0.169610.821
19_D49_K0.168310.815
48_G53_P0.167520.811
33_Y41_C0.166670.807
26_N29_I0.164310.795
9_R66_V0.163480.791
7_R63_D0.161950.784
56_V70_V0.158080.765
44_Y49_K0.15630.757
34_S44_Y0.156190.756
32_D43_L0.152880.740
33_Y36_D0.151880.735
49_K52_R0.150130.727
7_R64_P0.149860.725
20_I70_V0.149790.725
31_E55_H0.149770.725
39_G42_R0.148060.717
57_V69_T0.147350.713
6_A17_E0.146690.710
6_A13_R0.145350.704
23_A56_V0.145260.703
33_Y38_R0.143310.694
31_E44_Y0.142270.689
7_R18_E0.142110.688
8_E52_R0.140860.682
40_P44_Y0.140240.679
22_D51_G0.139610.676
11_Q50_E0.138280.669
7_R27_G0.13810.669
26_N30_I0.137620.666
10_M55_H0.137490.666
39_G47_G0.137470.666
57_V65_I0.137370.665
30_I45_I0.13660.661
51_G63_D0.135350.655
11_Q38_R0.135330.655
53_P56_V0.135220.655
8_E13_R0.134530.651
20_I69_T0.134070.649
11_Q25_E0.131690.638
21_E25_E0.131320.636
34_S55_H0.128510.622
42_R57_V0.127770.619
40_P66_V0.126480.612
26_N66_V0.126360.612
8_E51_G0.126340.612
21_E60_P0.126230.611
33_Y55_H0.126230.611
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
3u97A0.931597.80.482
3tn4A0.452136.20.803
2hx6A0.945223.20.82
2fhzB0.931520.70.824
2vjqA0.397318.20.828
2pxgA0.931516.10.831
1xk7A0.452114.90.834
4f78A0.986314.60.835
3ubmA0.424714.10.836
3sxxA113.40.837

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