GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2493 - Protein of unknown function (DUF2493)
Pfam: PF10686 (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: 71
Sequences: 2421
Seq/Len: 34.1
HH_delta: 0.32 (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
5_R37_V1.308312.722
24_L28_H1.204452.506
40_G62_R0.970122.018
14_W19_L0.945791.968
11_G14_W0.910531.894
50_A60_V0.899491.872
48_I52_W0.869991.810
36_L49_A0.826231.719
14_W45_A0.812821.691
17_H23_A0.793051.650
35_V61_I0.755731.572
8_I49_A0.704391.466
25_D55_E0.691461.439
52_W56_R0.662181.378
15_T18_E0.661641.377
26_K30_R0.658231.370
35_V59_P0.642161.336
28_H52_W0.636431.324
41_A46_D0.635781.323
12_R41_A0.588661.225
19_L48_I0.586681.221
38_H50_A0.586091.219
12_R46_D0.584291.216
24_L52_W0.57841.203
5_R35_V0.5571.159
16_D22_A0.55311.151
36_L53_A0.537511.118
23_A26_K0.530591.104
50_A62_R0.527941.098
13_D43_K0.525431.093
9_T38_H0.506831.055
14_W48_I0.490511.021
47_R51_R0.480541.000
25_D51_R0.478830.996
9_T41_A0.477750.994
18_E45_A0.476220.991
19_L51_R0.469820.978
48_I51_R0.458430.954
29_A55_E0.454620.946
4_M34_M0.442320.920
7_L38_H0.441590.919
10_G44_G0.415910.865
25_D48_I0.41420.862
6_V36_L0.410390.854
8_I28_H0.410190.853
29_A56_R0.407170.847
38_H46_D0.405530.844
16_D19_L0.394990.822
38_H41_A0.377780.786
51_R55_E0.370270.770
9_T45_A0.369370.769
24_L45_A0.353990.737
22_A25_D0.34580.719
43_K47_R0.331510.690
50_A54_R0.325650.678
16_D55_E0.316270.658
46_D50_A0.310370.646
4_M43_K0.309840.645
17_H53_A0.30620.637
12_R39_G0.29870.621
27_V31_H0.298360.621
25_D52_W0.298220.620
24_L29_A0.296980.618
24_L27_V0.294360.612
22_A26_K0.29390.611
9_T50_A0.288990.601
19_L47_R0.288010.599
11_G17_H0.28130.585
46_D62_R0.280480.584
9_T46_D0.278410.579
19_L25_D0.275330.573
17_H51_R0.274520.571
12_R45_A0.271670.565
41_A50_A0.270820.563
9_T12_R0.269040.560
12_R54_R0.264790.551
53_A60_V0.261610.544
27_V30_R0.260370.542
32_P43_K0.258860.539
25_D56_R0.257180.535
28_H36_L0.255450.531
10_G46_D0.253920.528
40_G54_R0.252290.525
31_H45_A0.251420.523
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
3uqzA0.957799.20.32
3majA0.929699.10.352
2iz6A0.971898.50.491
2a33A0.971898.40.496
1rcuA0.943798.30.511
1wehA0.957798.30.515
1wekA0.985998.20.527
1t35A0.929698.20.531
3quaA0.9718980.566
1ydhA0.971897.80.583

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