GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4098 - Domain of unknown function (DUF4098)
Pfam: PF13345 (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: CL0059
Length: 76
Sequences: 1777
Seq/Len: 23.38
HH_delta: 0.412 (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
51_S70_S1.545253.848
32_S51_S1.266863.155
12_S31_G1.26483.150
50_S69_S1.224343.049
13_S51_S1.212133.018
13_S32_S1.191452.967
31_G50_S1.180082.939
32_S70_S1.168122.909
31_G69_S1.139342.837
12_S50_S1.051622.619
15_D53_D0.905682.255
13_S70_S0.776811.934
34_D53_D0.763211.901
49_T68_T0.750621.869
34_D72_D0.736241.833
12_S69_S0.71871.790
30_S49_T0.714331.779
53_D72_D0.66431.654
15_D34_D0.63811.589
30_S68_T0.585441.458
37_I40_V0.579371.443
11_T30_S0.506381.261
30_S35_I0.480451.196
15_D72_D0.444231.106
33_G52_G0.429551.070
20_N39_N0.395620.985
19_T38_Q0.394610.983
49_T54_I0.38880.968
23_A26_L0.385860.961
66_I73_I0.381550.950
14_G33_G0.365920.911
23_A42_S0.360610.898
58_G62_G0.352910.879
11_T16_I0.350140.872
54_I73_I0.338710.843
7_L23_A0.329150.820
18_L21_V0.315490.786
18_L37_I0.307690.766
18_L28_I0.300030.747
38_Q55_S0.297730.741
45_I61_A0.296810.739
29_S67_S0.292870.729
11_T68_T0.291110.725
17_K36_D0.277270.690
52_G71_G0.277180.690
56_L59_T0.274640.684
10_Q29_S0.274030.682
47_V54_I0.270570.674
37_I56_L0.266660.664
22_K41_E0.265930.662
8_N27_D0.261050.650
10_Q48_S0.25770.642
29_S46_K0.257150.640
28_I37_I0.250060.623
55_S74_S0.244440.609
24_D44_S0.242730.604
59_T62_G0.242720.604
6_N24_D0.237920.592
11_T49_T0.234550.584
58_G61_A0.23430.583
29_S44_S0.232420.579
39_N58_G0.230690.574
26_L45_I0.229320.571
47_V66_I0.224590.559
44_S63_N0.22240.554
57_E74_S0.219510.547
36_D74_S0.217740.542
24_D62_G0.212020.528
9_V16_I0.211480.527
61_A64_V0.210850.525
16_I35_I0.208460.519
35_I54_I0.207630.517
28_I66_I0.206620.515
58_G67_S0.205890.513
14_G52_G0.205770.512
56_L61_A0.202640.505
39_N59_T0.202110.503
17_K55_S0.201020.501
48_S67_S0.198740.495
8_N19_T0.198610.495
54_I66_I0.198590.495
7_L18_L0.19670.490
45_I66_I0.195050.486
10_Q27_D0.194730.485
24_D63_N0.193190.481
55_S67_S0.191080.476
58_G64_V0.190210.474
40_V60_E0.189760.473
40_V66_I0.185690.462
13_S30_S0.183230.456
7_L21_V0.182210.454
33_G71_G0.181460.452
35_I73_I0.179270.446
41_E65_D0.179040.446
20_N38_Q0.178310.444
22_K40_V0.177490.442
17_K20_N0.175190.436
48_S63_N0.173530.432
20_N37_I0.172270.429
22_K36_D0.171850.428
18_L60_E0.169610.422
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
3jx8A0.986897.60.412
3lycA0.986897.60.418
3ljyA197.40.443
3petA0.986897.40.448
3lycA0.960597.20.468
3jx8A0.960596.90.492
3petA0.960596.90.494
3ljyA0.973796.40.531
3syjA0.986817.50.796
4k3lA0.960516.10.8

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