GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3284 - Domain of unknown function (DUF3284)
Pfam: PF11687 (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. )
Clan: CL0209
Length: 120
Sequences: 8216
Seq/Len: 68.47
HH_delta: 0.294 (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
62_E65_K1.905233.152
87_L93_E1.774942.936
6_T87_L1.685262.788
6_T93_E1.675822.772
85_E95_T1.563242.586
4_S93_E1.555742.574
10_S13_E1.469822.432
11_A86_P1.441712.385
84_I92_I1.41682.344
85_E93_E1.34962.233
9_V14_F1.298612.148
18_L84_I1.282782.122
60_E66_R1.259582.084
4_S95_T1.234672.043
66_R81_S1.22522.027
68_A81_S1.131791.872
66_R83_E1.13051.870
59_T70_T1.06011.754
12_E64_N1.050541.738
60_E68_A1.04811.734
83_E97_E0.975821.614
20_D23_L0.963531.594
43_S55_K0.927871.535
15_F61_Y0.91841.519
70_T79_T0.894381.480
57_K70_T0.874321.446
15_F64_N0.867211.435
62_E66_R0.858151.420
57_K72_S0.850711.407
18_L82_Y0.817211.352
11_A84_I0.816421.351
83_E95_T0.810651.341
12_E16_D0.808471.337
80_I96_Y0.804911.332
81_S97_E0.799441.323
17_Y23_L0.777771.287
68_A79_T0.757561.253
16_D63_P0.757121.253
9_V13_E0.751791.244
43_S57_K0.74391.231
11_A92_I0.714371.182
11_A65_K0.69381.148
19_I61_Y0.68371.131
45_Q53_E0.655791.085
44_Y56_V0.651961.079
7_L14_F0.650451.076
69_A80_I0.645381.068
78_F98_E0.643691.065
47_K53_E0.63971.058
16_D20_D0.638571.056
87_L90_G0.632831.047
7_L94_V0.631531.045
6_T90_G0.626831.037
81_S99_E0.61571.019
14_F84_I0.612571.013
69_A82_Y0.609941.009
67_Y82_Y0.602820.997
13_E16_D0.598680.990
11_A64_N0.59470.984
86_P89_D0.574210.950
59_T68_A0.572490.947
77_T101_E0.541070.895
40_K61_Y0.538210.890
82_Y96_Y0.533280.882
80_I98_E0.525070.869
59_T79_T0.521550.863
82_Y94_V0.510480.845
19_I63_P0.500070.827
8_N90_G0.491730.813
71_F78_F0.491590.813
56_V96_Y0.476580.788
11_A14_F0.469270.776
40_K60_E0.46720.773
70_T77_T0.46640.772
15_F84_I0.459120.760
54_A71_F0.452510.749
10_S14_F0.436550.722
56_V71_F0.42550.704
12_E86_P0.417720.691
56_V69_A0.416940.690
71_F98_E0.415920.688
61_Y67_Y0.409880.678
15_F63_P0.406990.673
12_E63_P0.406620.673
45_Q55_K0.405430.671
79_T99_E0.396490.656
71_F96_Y0.389920.645
16_D23_L0.380810.630
15_F67_Y0.378510.626
56_V100_Y0.370910.614
69_A96_Y0.370820.613
71_F80_I0.367810.608
65_K85_E0.367010.607
15_F19_I0.363230.601
46_K54_A0.358960.594
78_F100_Y0.345460.572
14_F92_I0.34510.571
41_G58_I0.343710.569
55_K72_S0.33980.562
86_P90_G0.335340.555
13_E17_Y0.328210.543
4_S85_E0.326830.541
24_Y46_K0.326740.541
10_S92_I0.324650.537
19_I67_Y0.321270.531
6_T89_D0.314550.520
65_K83_E0.312920.518
16_D19_I0.31090.514
26_I31_G0.310350.513
42_F58_I0.307880.509
26_I29_A0.307590.509
37_K58_I0.307390.509
9_V17_Y0.303910.503
10_S86_P0.303020.501
86_P92_I0.301830.499
21_S24_Y0.300360.497
16_D64_N0.299680.496
24_Y80_I0.297470.492
60_E81_S0.293770.486
28_Q31_G0.291520.482
5_K8_N0.291260.482
37_K42_F0.288430.477
6_T92_I0.286740.474
9_V92_I0.284070.470
54_A80_I0.282280.467
79_T97_E0.28160.466
69_A78_F0.280870.465
56_V80_I0.280030.463
14_F94_V0.279240.462
58_I61_Y0.273780.453
26_I52_R0.272840.451
11_A15_F0.272260.450
27_K30_T0.271510.449
42_F55_K0.271290.449
24_Y82_Y0.271190.449
37_K40_K0.27030.447
54_A76_G0.269710.446
44_Y54_A0.268190.444
35_P43_S0.266930.442
40_K57_K0.266550.441
24_Y48_F0.266450.441
24_Y96_Y0.264640.438
98_E101_E0.264060.437
58_I67_Y0.263890.437
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
3ggnA199.20.294
3ijtA199.20.315
2ns9A0.958399.10.338
2pcsA0.97599.10.34
2le1A0.991799.10.347
3f08A0.966799.10.351
2d4rA0.983399.10.354
3p9vA0.9917990.358
2m47A0.9667990.362
1t17A0.983398.80.412

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