GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3991 - Protein of unknown function (DUF3991)
Pfam: PF13154 (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: 77
Sequences: 365
Seq/Len: 4.74
HH_delta: 0.624 (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_T14_V0.31242.526
26_D30_N0.291182.355
47_L57_F0.268352.170
44_G60_I0.265532.147
30_N57_F0.250792.028
32_V45_A0.205971.665
22_L36_Y0.205491.662
25_Q29_G0.201531.630
48_R58_K0.194861.576
10_D13_I0.189871.535
34_V42_P0.188911.528
24_Y34_V0.183291.482
1_A5_E0.168841.365
26_D57_F0.161091.303
24_Y32_V0.160861.301
4_T11_P0.158321.280
60_I67_K0.156861.268
44_G67_K0.148691.202
37_D43_V0.148331.199
48_R63_G0.147221.190
1_A23_I0.14171.146
43_V69_F0.137661.113
26_D50_T0.135531.096
32_V47_L0.134781.090
33_F45_A0.133881.083
6_E9_I0.133841.082
42_P46_E0.133571.080
34_V65_S0.132131.068
40_G66_D0.130561.056
66_D71_F0.129161.044
19_N41_K0.125841.018
29_G54_R0.125131.012
9_I30_N0.123751.001
23_I31_V0.123520.999
46_E60_I0.12340.998
68_W72_N0.122870.994
12_E41_K0.121850.985
67_K71_F0.120990.978
49_G55_K0.119530.967
48_R54_R0.11930.965
1_A55_K0.116780.944
5_E11_P0.116650.943
5_E15_D0.116510.942
32_V40_G0.11640.941
10_D17_F0.114450.925
6_E13_I0.114380.925
35_G60_I0.109830.888
23_I69_F0.109690.887
36_Y42_P0.109580.886
6_E18_I0.108870.880
9_I13_I0.108630.878
46_E61_A0.107250.867
8_G23_I0.105230.851
5_E28_Y0.103810.839
14_V31_V0.103790.839
17_F47_L0.103510.837
11_P15_D0.102740.831
49_G58_K0.102450.828
26_D32_V0.101560.821
66_D70_G0.10070.814
10_D38_E0.100690.814
4_T62_A0.100650.814
28_Y41_K0.100620.814
5_E33_F0.100170.810
35_G46_E0.099130.802
5_E10_D0.099120.801
8_G38_E0.098610.797
19_N43_V0.098540.797
15_D38_E0.098280.795
67_K72_N0.098030.793
19_N39_N0.097780.791
1_A6_E0.097750.790
58_K73_I0.097350.787
24_Y35_G0.097080.785
39_N56_P0.096480.780
3_L37_D0.096350.779
14_V73_I0.096320.779
17_F32_V0.096230.778
1_A28_Y0.095980.776
37_D65_S0.095630.773
22_L42_P0.095270.770
32_V48_R0.095080.769
54_R58_K0.094890.767
15_D18_I0.094810.767
9_I22_L0.09430.763
34_V45_A0.093580.757
45_A50_T0.093180.753
25_Q35_G0.093150.753
33_F57_F0.092350.747
63_G67_K0.088840.718
28_Y38_E0.088620.717
2_Y37_D0.088370.715
6_E21_G0.087860.710
50_T56_P0.087590.708
12_E39_N0.087410.707
29_G59_G0.087380.707
37_D41_K0.087380.707
16_A23_I0.087370.706
1_A19_N0.086070.696
41_K49_G0.086010.695
44_G68_W0.085870.694
13_I31_V0.085410.691
23_I47_L0.085110.688
9_I38_E0.08470.685
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
1q57A0.909198.10.624
1nuiA0.909197.80.655
2au3A0.961970.709
1dd9A0.96195.30.761
4edgA0.96194.40.772
1p32A0.545528.30.875
1yqfA0.519523.80.88
3jv1A0.519516.80.887
3qv0A0.5195160.888
3b0cT0.376612.90.892
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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