GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF581 - Protein of unknown function (DUF581)
Pfam: PF04570 (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: CL0175
Length: 58
Sequences: 269
Seq/Len: 4.64
HH_delta: 0.851 (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
50_Q54_D0.48773.248
48_S52_L0.331962.211
26_L31_D0.296371.974
31_D43_S0.23641.574
9_P12_S0.235711.570
38_D44_E0.216581.442
21_L50_Q0.204681.363
17_S53_M0.198481.322
21_L57_K0.191141.273
13_E25_K0.183221.220
31_D35_Y0.180821.204
21_L37_G0.178361.188
27_D38_D0.177911.185
14_H38_D0.164271.094
38_D54_D0.161241.074
36_R39_K0.156431.042
48_S53_M0.154771.031
34_M50_Q0.154621.030
34_M43_S0.152251.014
19_C22_C0.151731.011
30_K55_E0.151691.010
18_F25_K0.15051.002
29_G40_A0.14780.984
25_K30_K0.146870.978
27_D49_Q0.144660.963
31_D34_M0.144250.961
14_H25_K0.14420.960
51_I55_E0.144050.959
29_G56_E0.142560.949
12_S56_E0.142490.949
30_K48_S0.142050.946
32_I39_K0.140860.938
33_Y40_A0.139620.930
25_K48_S0.138620.923
31_D36_R0.13850.922
28_P45_E0.136880.912
16_L51_I0.134780.898
34_M39_K0.132160.880
25_K49_Q0.130760.871
20_Y23_K0.130150.867
17_S44_E0.129620.863
29_G32_I0.129540.863
22_C26_L0.129480.862
18_F48_S0.128980.859
11_P48_S0.128980.859
27_D36_R0.128060.853
23_K49_Q0.127660.850
13_E33_Y0.12720.847
26_L35_Y0.125970.839
18_F30_K0.125430.835
13_E29_G0.125360.835
48_S56_E0.123630.823
44_E52_L0.123180.820
52_L56_E0.122450.816
37_G47_R0.121690.810
44_E53_M0.120940.805
15_F57_K0.120820.805
9_P23_K0.120290.801
29_G34_M0.119610.797
20_Y56_E0.11960.797
16_L19_C0.118740.791
22_C31_D0.118180.787
18_F27_D0.115540.770
26_L32_I0.114590.763
19_C26_L0.114220.761
12_S44_E0.113360.755
21_L34_M0.111730.744
43_S50_Q0.111140.740
20_Y49_Q0.111060.740
17_S39_K0.109590.730
17_S34_M0.109330.728
13_E48_S0.109320.728
36_R50_Q0.108970.726
37_G45_E0.108480.722
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
2iybE0.844859.50.851
1lv3A0.775954.90.855
2jtnA0.8448480.861
2l8eA0.810346.90.861
2xqnT0.8448360.87
1wigA0.93132.80.872
3j3bW0.775929.20.876
3u52A0.913828.10.877
3j39W0.775927.10.878
3izcZ0.775925.20.879
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