GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1785 - Domain of unknown function (DUF1785)
Pfam: PF08699 (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: 615
Seq/Len: 11.83
HH_delta: 0.056 (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
34_T39_L0.291091.627
16_D20_G0.28961.618
4_G21_L0.266691.490
10_P14_P0.263121.470
43_D49_F0.243951.363
27_F46_H0.243721.362
34_T37_G0.243361.360
17_L20_G0.237291.326
21_L31_V0.235691.317
16_D22_E0.228411.276
21_L25_R0.220151.230
28_F41_N0.213151.191
6_S45_S0.210641.177
27_F39_L0.210391.176
33_P38_L0.203371.137
34_T38_L0.202811.133
31_V46_H0.202171.130
11_S24_W0.198171.107
24_W29_Q0.196481.098
25_R46_H0.19291.078
21_L36_G0.18931.058
2_A13_G0.188931.056
7_F45_S0.188551.054
5_R9_P0.185671.038
25_R50_Y0.184821.033
2_A9_P0.183191.024
40_L48_A0.180481.009
32_R41_N0.180381.008
35_Q46_H0.179931.006
9_P29_Q0.179471.003
3_V6_S0.179231.002
7_F28_F0.175490.981
11_S19_G0.173350.969
35_Q47_T0.170820.955
8_F48_A0.170530.953
29_Q43_D0.170040.950
2_A6_S0.167320.935
21_L48_A0.165260.924
5_R23_A0.163760.915
6_S32_R0.163510.914
46_H50_Y0.162210.907
29_Q38_L0.161630.903
10_P24_W0.161620.903
5_R29_Q0.159510.891
13_G22_E0.159450.891
30_S41_N0.158030.883
11_S38_L0.156120.872
27_F48_A0.155410.869
12_G16_D0.154640.864
29_Q46_H0.154380.863
33_P36_G0.154010.861
32_R47_T0.153210.856
5_R24_W0.151280.845
10_P31_V0.150950.844
13_G16_D0.15030.840
9_P12_G0.148360.829
7_F16_D0.147820.826
3_V7_F0.147380.824
13_G42_V0.147340.823
35_Q43_D0.145950.816
42_V45_S0.144980.810
31_V50_Y0.142360.796
28_F49_F0.142340.795
7_F29_Q0.142180.795
23_A39_L0.139980.782
45_S48_A0.13980.781
24_W31_V0.139030.777
14_P22_E0.137730.770
39_L50_Y0.135860.759
11_S16_D0.135740.759
11_S14_P0.135520.757
35_Q40_L0.135140.755
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
4f3tA199.50.056
4kreA199.50.056
4f1nA199.30.138
1yvuA0.980899.20.211
1u04A0.903898.50.408
3ho1A0.961592.20.712
4dweA0.923112.10.854
4aw7A0.96157.50.866
3adoA0.92314.50.878
4h6uA0.754.30.879

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