GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4040 - Domain of unknown function (DUF4040)
Pfam: PF13244 (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: 70
Sequences: 1938
Seq/Len: 27.69
HH_delta: 0.089 (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
4_L30_L0.793242.970
36_V44_A0.702972.632
14_S23_A0.590682.212
4_L27_F0.521871.954
9_L13_F0.483981.812
10_A23_A0.467431.750
10_A13_F0.462391.731
17_R66_L0.45831.716
35_F47_E0.453721.699
25_G56_T0.44421.663
17_R62_A0.369161.382
21_V59_F0.359631.346
35_F40_A0.356771.336
32_A47_E0.343871.287
7_A26_V0.342231.281
10_A14_S0.332061.243
58_L64_R0.32771.227
42_D46_T0.324961.217
4_L31_I0.315171.180
23_A26_V0.308791.156
60_L65_K0.307351.151
40_A43_V0.299951.123
59_F62_A0.299561.122
49_A59_F0.293251.098
3_L30_L0.281761.055
35_F46_T0.280881.052
34_L37_L0.278921.044
30_L33_L0.274771.029
20_A57_V0.267241.001
23_A31_I0.264180.989
8_A27_F0.262660.983
7_A27_F0.261550.979
28_G51_G0.259870.973
7_A23_A0.258780.969
10_A19_A0.249580.934
29_F52_T0.248970.932
61_L65_K0.248910.932
52_T56_T0.245130.918
28_G52_T0.244020.914
39_G46_T0.243650.912
54_L58_L0.2430.910
61_L64_R0.242160.907
36_V60_L0.241860.906
11_A64_R0.241210.903
28_G56_T0.234940.880
62_A66_L0.232990.872
49_A64_R0.230230.862
6_I10_A0.227080.850
43_V47_E0.226860.849
45_L49_A0.224670.841
32_A48_A0.221190.828
18_L60_L0.220020.824
11_A20_A0.218680.819
39_G45_L0.21710.813
33_L38_L0.215090.805
39_G49_A0.214930.805
6_I13_F0.214520.803
27_F30_L0.213540.800
6_I15_R0.21280.797
29_F49_A0.212710.796
22_I60_L0.211670.793
28_G54_L0.211610.792
36_V41_P0.210590.788
7_A10_A0.210350.788
45_L48_A0.206060.772
14_S19_A0.205710.770
46_T50_V0.205280.769
21_V56_T0.201330.754
42_D51_G0.201180.753
25_G42_D0.200820.752
51_G54_L0.199620.747
16_S25_G0.198570.743
16_S21_V0.198250.742
35_F43_V0.19780.741
28_G42_D0.197070.738
28_G41_P0.195470.732
47_E51_G0.194930.730
37_L59_F0.193580.725
63_L66_L0.193310.724
49_A55_T0.192190.720
5_V15_R0.190650.714
8_A12_V0.190140.712
6_I26_V0.190020.711
38_L52_T0.189580.710
42_D61_L0.189270.709
34_L43_V0.188420.705
18_L22_I0.187440.702
24_L51_G0.186170.697
48_A51_G0.184940.692
25_G67_P0.184030.689
26_V33_L0.183780.688
5_V24_L0.183770.688
16_S19_A0.182940.685
24_L35_F0.182940.685
36_V66_L0.182670.684
58_L65_K0.182420.683
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
4he8J199.30.089
3rkoJ199.30.108
4he8L114.20.84
3rkoL113.70.841
4he8M110.90.847
4he8N0.985790.853
3rkoM16.70.861
4he8K0.94293.20.879
1p58A0.55712.60.885
3rkoN12.40.886

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