GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1992 - Domain of unknown function (DUF1992)
Pfam: PF09350 (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: 427
Seq/Len: 6.01
HH_delta: 0.862 (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
7_R11_A0.33032.437
28_D43_R0.315532.328
51_L55_I0.292832.160
16_D21_A0.27362.019
1_W5_R0.259431.914
53_P56_E0.240781.776
8_E12_R0.212321.566
64_L68_L0.209731.547
2_A10_M0.209171.543
20_G24_P0.201441.486
38_E42_N0.195041.439
15_F21_A0.191421.412
10_M16_D0.183551.354
52_P55_I0.182111.344
3_E7_R0.178911.320
20_G25_L0.171541.266
32_P51_L0.165281.219
3_E6_I0.158281.168
41_A44_I0.156781.157
6_I53_P0.156621.155
48_A54_W0.156151.152
35_P39_R0.155781.149
56_E59_K0.152721.127
7_R10_M0.148871.098
41_A54_W0.147781.090
36_A48_A0.146691.082
56_E63_E0.145261.072
45_L56_E0.143831.061
2_A6_I0.143261.057
19_P27_L0.141291.042
30_D43_R0.137351.013
35_P46_K0.137031.011
39_R48_A0.135751.002
16_D67_A0.135581.000
11_A57_L0.135420.999
9_A18_L0.134640.993
51_L68_L0.134130.990
34_W37_E0.133530.985
5_R41_A0.131610.971
28_D46_K0.1310.966
9_A46_K0.129950.959
28_D32_P0.129470.955
21_A65_R0.128880.951
1_W4_R0.128650.949
17_N63_E0.127060.937
35_P38_E0.1250.922
35_P42_N0.124990.922
38_E60_E0.122040.900
37_E48_A0.120430.888
35_P41_A0.119030.878
37_E43_R0.118590.875
40_M43_R0.118550.875
12_R18_L0.116940.863
1_W51_L0.115080.849
8_E11_A0.114370.844
55_I62_E0.11430.843
56_E60_E0.113760.839
1_W53_P0.112510.830
62_E65_R0.112470.830
24_P57_L0.11120.820
16_D19_P0.110360.814
34_W58_R0.109310.806
57_L65_R0.108850.803
38_E54_W0.107410.792
10_M15_F0.106470.785
34_W52_P0.106220.784
4_R21_A0.106150.783
33_Y64_L0.106060.782
64_L67_A0.105920.781
55_I63_E0.105670.780
41_A47_N0.105230.776
17_N32_P0.105060.775
63_E66_E0.10430.769
44_I59_K0.104090.768
15_F26_P0.103850.766
58_R61_I0.103710.765
6_I15_F0.103310.762
39_R45_L0.103280.762
8_E14_E0.10320.761
61_I65_R0.102720.758
42_N67_A0.102190.754
19_P26_P0.101960.752
23_K26_P0.100730.743
8_E55_I0.100670.743
53_P58_R0.100510.742
5_R46_K0.099550.734
43_R47_N0.09940.733
7_R68_L0.099360.733
33_Y66_E0.099110.731
11_A67_A0.099090.731
4_R59_K0.098270.725
26_P66_E0.098210.725
10_M63_E0.097050.716
32_P63_E0.096550.712
2_A29_D0.09650.712
39_R42_N0.096320.711
30_D66_E0.096270.710
18_L24_P0.096050.709
4_R8_E0.095380.704
34_W62_E0.095360.704
39_R46_K0.094740.699
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
3l96A0.971854.20.862
3msuA0.971845.30.868
3hwkA0.943741.30.872
1vgmA0.957733.40.878
3o8jA0.943733.10.878
1a59A0.943731.10.879
3tqgA0.943729.50.881
3nl9A0.816928.20.882
1vgpA0.943726.20.884
1iomA0.943723.80.886
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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