GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF433 - Protein of unknown function (DUF433)
Pfam: PF04255 (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: 56
Sequences: 867
Seq/Len: 15.48
HH_delta: -0.055 (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_E46_L0.62392.303
8_L20_P0.622182.297
25_L28_L0.591332.183
34_P46_L0.582862.152
46_L50_R0.510631.885
20_P23_D0.507841.875
19_I43_S0.50631.869
4_D7_I0.482611.782
34_P50_R0.402391.486
34_P49_I0.392041.447
38_A42_P0.38961.438
32_E40_D0.38761.431
27_L41_Y0.379511.401
8_L23_D0.371011.370
38_A46_L0.369431.364
50_R54_A0.354111.307
45_T48_D0.352021.300
11_Q22_R0.349741.291
38_A49_I0.346291.278
2_V15_R0.338961.251
32_E36_E0.327431.209
8_L18_R0.318881.177
2_V13_V0.293471.083
13_V17_T0.288461.065
27_L37_I0.283851.048
22_R26_D0.282491.043
19_I42_P0.278411.028
33_S36_E0.277581.025
24_I37_I0.27651.021
1_I12_P0.275941.019
40_D43_S0.265260.979
17_T45_T0.264780.978
17_T43_S0.259760.959
36_E40_D0.256150.946
15_R45_T0.250110.923
19_I23_D0.247550.914
14_I52_A0.24680.911
8_L13_V0.240290.887
3_I12_P0.240250.887
26_D30_A0.237890.878
5_P56_A0.228640.844
9_G20_P0.228170.842
23_D27_L0.226840.837
11_Q51_A0.221430.817
17_T48_D0.21920.809
27_L30_A0.217330.802
27_L40_D0.215450.795
23_D41_Y0.213440.788
51_A54_A0.213020.786
25_L52_A0.210640.778
30_A39_E0.210470.777
25_L56_A0.209880.775
13_V43_S0.204310.754
4_D13_V0.202460.747
12_P55_Y0.202370.747
47_E51_A0.20150.744
2_V17_T0.197640.730
1_I6_D0.195730.723
26_D54_A0.194670.719
12_P30_A0.193420.714
39_E42_P0.19330.714
31_G42_P0.192280.710
25_L51_A0.191240.706
7_I17_T0.189390.699
18_R28_L0.188570.696
29_A56_A0.188370.695
6_D9_G0.183990.679
37_I44_L0.183020.676
44_L49_I0.182980.676
19_I41_Y0.179940.664
25_L30_A0.179590.663
39_E54_A0.177870.657
9_G27_L0.177050.654
41_Y48_D0.176910.653
27_L43_S0.17670.652
13_V26_D0.17270.638
27_L32_E0.171870.635
25_L29_A0.170020.628
2_V7_I0.169940.627
15_R21_V0.168670.623
15_R48_D0.166790.616
9_G23_D0.165340.610
7_I18_R0.163780.605
7_I41_Y0.163570.604
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
2ga1A199.7-0.055
4admA0.982155.40.803
2lvsA0.7551.30.808
3r6qA0.982139.40.82
1yfmA0.982136.90.823
1vdkA0.982134.20.826
3i71A0.7532.80.828
3uj3X0.964332.20.828
4hgvA0.982129.50.831
2di0A0.696429.20.832

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