GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PSD2 - Protein of unknown function (DUF1585)
Pfam: PF07624 (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: 76
Sequences: 996
Seq/Len: 13.11
HH_delta: 0.773 (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
35_A66_I0.747443.005
54_A64_D0.581242.337
31_L65_L0.571562.298
58_N64_D0.566912.279
8_G11_E0.552762.222
54_A58_N0.536242.156
67_L71_T0.528662.125
54_A68_A0.506732.037
27_F62_L0.470781.892
25_R49_D0.47031.891
53_E57_A0.463791.864
61_R64_D0.449371.806
66_I70_V0.447791.800
19_R56_K0.434971.749
31_L62_L0.415081.669
11_E14_Q0.412411.658
35_A70_V0.360211.448
28_A55_F0.334431.344
28_A51_I0.332741.338
28_A65_L0.322831.298
27_F31_L0.311811.253
58_N61_R0.30851.240
31_L66_I0.307461.236
68_A71_T0.27731.115
35_A61_R0.27391.101
11_E34_Y0.273661.100
12_L16_L0.272221.094
19_R53_E0.264161.062
24_A60_Y0.263061.057
55_F62_L0.262971.057
10_A14_Q0.25851.039
54_A57_A0.25681.032
24_A56_K0.252441.015
50_R68_A0.244710.984
50_R54_A0.244010.981
16_L23_F0.242430.975
46_C49_D0.238770.960
8_G34_Y0.23780.956
35_A75_F0.226480.910
30_K39_P0.220740.887
53_E56_K0.211730.851
26_C60_Y0.207840.835
11_E15_Y0.206080.828
17_A56_K0.20550.826
47_E51_I0.20230.813
49_D52_V0.201750.811
73_D76_R0.2010.808
71_T76_R0.197380.793
64_D68_A0.19560.786
18_E69_I0.194910.784
48_I52_V0.19370.779
22_Q26_C0.193230.777
29_E48_I0.188030.756
21_D53_E0.186590.750
29_E39_P0.186020.748
19_R57_A0.18570.746
65_L69_I0.185350.745
28_A69_I0.185070.744
14_Q59_G0.185060.744
38_R44_D0.182010.732
53_E59_G0.179740.723
42_F47_E0.179640.722
58_N68_A0.17960.722
31_L69_I0.174810.703
21_D24_A0.174150.700
14_Q17_A0.174110.700
69_I72_S0.173840.699
70_V75_F0.171230.688
22_Q25_R0.171020.687
28_A32_L0.170570.686
26_C63_R0.17030.685
28_A52_V0.16950.681
62_L66_I0.167360.673
52_V56_K0.166610.670
55_F65_L0.165420.665
11_E17_A0.165380.665
56_K60_Y0.164320.661
52_V55_F0.163210.656
22_Q34_Y0.159640.642
8_G35_A0.15880.638
37_G71_T0.158790.638
22_Q49_D0.157150.632
23_F60_Y0.157060.631
8_G14_Q0.156830.630
26_C70_V0.156680.630
55_F61_R0.156290.628
14_Q18_E0.155080.623
36_L66_I0.154160.620
13_K17_A0.153090.615
25_R52_V0.152410.613
45_R49_D0.151510.609
32_L47_E0.150460.605
65_L68_A0.150210.604
16_L30_K0.150190.604
24_A52_V0.148750.598
13_K70_V0.14860.597
36_L47_E0.148340.596
42_F45_R0.147110.591
11_E71_T0.14640.589
31_L55_F0.145820.586
22_Q71_T0.145640.585
27_F55_F0.145090.583
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
3osjA0.960589.70.773
3pruC0.9079890.775
3gf3A0.9868850.789
3nphB0.868483.20.793
2ky4A0.881682.70.794
3iavA0.986881.60.797
3u9rB0.986879.60.801
3n6rB0.986876.30.806
2bzrA0.973774.30.809
3ohwB0.973770.30.814
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0532 seconds.