GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1707 - Domain of unknown function (DUF1707)
Pfam: PF08044 (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: 53
Sequences: 504
Seq/Len: 9.51
HH_delta: 0.812 (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
11_A49_F0.606132.690
36_A48_L0.539842.396
12_V37_Y0.480282.132
12_V33_L0.403661.792
3_A7_D0.394211.750
7_D42_R0.388881.726
23_R53_P0.375351.666
2_R51_D0.340431.511
24_L29_F0.331741.472
17_A20_A0.330231.466
16_R29_F0.32191.429
19_F29_F0.318271.413
48_L51_D0.314521.396
4_S23_R0.304781.353
33_L37_Y0.287351.275
10_R14_L0.286781.273
18_A49_F0.284361.262
3_A42_R0.272531.210
40_R44_E0.263591.170
9_E37_Y0.258061.145
18_A21_E0.255531.134
26_L30_D0.249531.108
25_S31_E0.244781.086
25_S28_E0.242731.077
4_S7_D0.232971.034
34_D38_A0.230791.024
30_D34_D0.229921.020
12_V36_A0.229771.020
2_R5_D0.222670.988
29_F33_L0.222040.986
14_L18_A0.219580.975
15_L29_F0.216150.959
21_E53_P0.214550.952
32_R51_D0.211750.940
1_L42_R0.204040.906
31_E40_R0.2030.901
18_A23_R0.20160.895
14_L49_F0.200930.892
19_F26_L0.199890.887
19_F34_D0.195720.869
16_R37_Y0.195120.866
39_A45_L0.193690.860
6_A47_A0.193340.858
13_D16_R0.191630.851
27_D30_D0.191520.850
12_V25_S0.188990.839
4_S53_P0.183340.814
6_A9_E0.181920.807
6_A24_L0.180410.801
30_D33_L0.179470.797
14_L46_D0.177940.790
19_F30_D0.176310.783
15_L51_D0.172960.768
2_R32_R0.171570.761
5_D22_G0.171550.761
27_D50_A0.16950.752
31_E35_A0.168830.749
1_L50_A0.167890.745
35_A50_A0.165590.735
27_D31_E0.16170.718
26_L38_A0.157140.697
6_A15_L0.154860.687
26_L35_A0.154130.684
2_R28_E0.1520.675
16_R34_D0.151470.672
35_A43_G0.151270.671
12_V16_R0.150070.666
9_E16_R0.148120.657
18_A29_F0.146690.651
46_D49_F0.14660.651
15_L41_T0.143610.637
17_A30_D0.143550.637
28_E41_T0.143060.635
2_R44_E0.142340.632
24_L31_E0.139640.620
14_L35_A0.138950.617
9_E35_A0.138490.615
30_D44_E0.136550.606
45_L50_A0.135960.603
26_L46_D0.135950.603
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
1ug3A0.905735.80.812
3l6aA0.905732.30.816
2p6vA123.90.827
3eiqC0.905722.40.829
3kioA0.981121.70.83
2ionA0.905720.50.832
2zu6B0.905719.90.833
2nszA0.905717.30.838
1uaxA0.981117.20.838
3a9fA0.3585170.838
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