GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4113 - Domain of unknown function (DUF4113)
Pfam: PF13438 (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: 52
Sequences: 634
Seq/Len: 12.19
HH_delta: 0.835 (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
35_R38_L0.744733.720
9_D12_N0.440862.202
41_R48_E0.416882.082
41_R45_R0.366611.831
46_W49_L0.358651.791
22_L25_Q0.348751.742
45_R48_E0.304871.523
18_G25_Q0.299321.495
8_I20_I0.277691.387
29_R32_K0.272291.360
3_R7_A0.26791.338
11_I20_I0.255831.278
3_R10_A0.25541.276
38_L41_R0.252761.263
3_R6_Q0.244321.220
4_L7_A0.243681.217
10_A14_R0.239131.194
16_G19_T0.236551.182
30_S52_V0.230741.153
10_A27_F0.223281.115
24_S27_F0.221681.107
6_Q9_D0.218381.091
8_I23_A0.200571.002
14_R19_T0.198580.992
12_N23_A0.198470.991
13_R34_R0.198360.991
3_R8_I0.197730.988
6_Q13_R0.194560.972
10_A30_S0.191510.957
6_Q10_A0.188380.941
24_S28_R0.188110.940
13_R28_R0.18770.938
5_M12_N0.184290.921
21_R38_L0.183310.916
15_F30_S0.182770.913
26_G29_R0.182620.912
29_R35_R0.179690.898
15_F22_L0.177930.889
13_R49_L0.177160.885
30_S51_V0.177050.884
5_M9_D0.175680.878
28_R45_R0.175550.877
17_R24_S0.17260.862
5_M33_M0.167050.834
7_A29_R0.162310.811
13_R20_I0.161650.807
27_F32_K0.160710.803
39_S44_T0.159820.798
23_A42_Y0.155980.779
16_G31_W0.154180.770
3_R28_R0.150040.749
21_R25_Q0.149430.746
7_A37_M0.149210.745
11_I17_R0.14910.745
22_L51_V0.148320.741
46_W50_P0.147760.738
6_Q18_G0.14580.728
2_Q20_I0.144150.720
22_L40_P0.143270.716
17_R41_R0.142960.714
1_R9_D0.139940.699
48_E51_V0.139820.698
19_T29_R0.137680.688
1_R5_M0.134560.672
19_T25_Q0.134490.672
11_I46_W0.134360.671
15_F52_V0.133520.667
39_S50_P0.132820.663
21_R34_R0.132650.663
4_L10_A0.131940.659
5_M18_G0.13190.659
25_Q33_M0.131850.659
26_G40_P0.13170.658
14_R21_R0.130970.654
12_N26_G0.130210.650
33_M46_W0.129340.646
1_R8_I0.126760.633
10_A28_R0.126670.633
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
3hr8A0.8654410.835
1u94A0.846231.40.844
2zr9A0.846229.30.847
1s4kA0.961527.40.849
1zkeA0.442323.30.853
3cmuA0.846223.30.853
4alzA0.519.50.858
1xp8A0.846218.20.86
3cmwA0.846217.60.861
2pofA114.70.865
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0171 seconds.