GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3436 - Domain of unknown function (DUF3436)
Pfam: PF11918 (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: 55
Sequences: 267
Seq/Len: 4.85
HH_delta: 0.544 (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
5_T13_N0.311722.206
10_S13_N0.291742.064
46_M52_K0.23461.660
36_P50_S0.227751.612
29_P35_L0.224991.592
26_V39_T0.20651.461
50_S54_E0.203531.440
15_P47_L0.188081.331
45_A49_K0.18731.325
40_P47_L0.182111.289
31_Q54_E0.181721.286
36_P52_K0.181451.284
9_Q17_L0.180041.274
26_V34_A0.177531.256
40_P51_I0.174981.238
18_V49_K0.169631.200
7_G33_P0.166361.177
44_L51_I0.165031.168
26_V32_P0.162121.147
45_A55_V0.161581.143
7_G16_R0.161311.141
18_V45_A0.15531.099
34_A52_K0.152771.081
3_V38_L0.149681.059
47_L50_S0.14831.049
19_I31_Q0.148121.048
18_V50_S0.146911.040
6_A35_L0.144931.026
10_S51_I0.144371.022
29_P51_I0.143651.016
25_Y48_Q0.143421.015
13_N49_K0.13970.989
29_P54_E0.139440.987
41_E50_S0.134580.952
45_A48_Q0.130360.922
29_P33_P0.130220.921
15_P20_S0.129280.915
5_T10_S0.128670.910
32_P36_P0.127850.905
16_R22_E0.127660.903
25_Y45_A0.12680.897
3_V15_P0.126750.897
5_T44_L0.126680.896
20_S38_L0.124410.880
10_S17_L0.12440.880
9_Q13_N0.124150.878
40_P46_M0.124120.878
8_V21_Y0.122470.867
24_S36_P0.121220.858
1_A5_T0.120050.849
34_A54_E0.119490.846
31_Q41_E0.118630.839
6_A34_A0.116760.826
18_V55_V0.116360.823
33_P54_E0.116010.821
26_V50_S0.11580.819
6_A24_S0.1150.814
6_A10_S0.11480.812
8_V46_M0.113860.806
6_A39_T0.113080.800
5_T8_V0.112520.796
1_A4_L0.11210.793
52_K55_V0.112010.793
12_L25_Y0.11080.784
39_T53_H0.110710.783
9_Q15_P0.109630.776
48_Q55_V0.106510.754
33_P55_V0.106510.754
18_V40_P0.105110.744
30_Q33_P0.104280.738
15_P44_L0.103680.734
24_S37_N0.102420.725
33_P38_L0.101750.720
30_Q39_T0.10140.718
35_L44_L0.101090.715
43_L50_S0.100450.711
11_S42_Q0.100320.710
18_V24_S0.100230.709
20_S48_Q0.099580.705
4_L14_D0.098670.698
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
1j7xA198.90.544
3izxA0.927330.10.885
4e2vA0.945524.80.89
2lr2A0.818222.70.891
4itqA0.4182200.894
2ashA0.927317.60.896
2e0wA0.854516.60.897
3bldA0.945515.40.899
3d9wA0.8727150.9
2dg5B0.854514.50.9
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