GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1492 - Protein of unknown function (DUF1492)
Pfam: PF07374 (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. )
Clan: CL0123
Length: 100
Sequences: 2234
Seq/Len: 22.34
HH_delta: 0.332 (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
67_R92_H0.646852.366
60_E98_E0.64252.350
87_T90_R0.615692.252
61_R65_R0.597692.186
66_M80_E0.58592.143
87_T91_I0.559462.046
64_L99_L0.535861.960
86_R89_Y0.533991.953
83_I88_Y0.531531.944
62_L80_E0.5181.895
18_N21_E0.468211.712
86_R90_R0.449431.644
72_L80_E0.417161.526
17_K21_E0.402591.472
66_M77_I0.391431.432
78_A88_Y0.377741.382
74_W89_Y0.362991.328
75_E85_R0.359781.316
62_L81_L0.358241.310
67_R74_W0.357931.309
20_Q71_K0.356951.306
45_K49_R0.352751.290
62_L66_M0.350831.283
75_E79_E0.346561.268
66_M72_L0.342141.251
83_I87_T0.337971.236
35_E39_D0.337831.236
41_L45_K0.334261.223
26_K29_D0.329951.207
59_D91_I0.329481.205
66_M81_L0.328441.201
62_L65_R0.312761.144
72_L76_Q0.312711.144
74_W88_Y0.310481.136
85_R89_Y0.301511.103
74_W92_H0.28981.060
60_E91_I0.288121.054
25_V28_I0.287011.050
21_E25_V0.277451.015
42_I49_R0.275691.008
63_I91_I0.275541.008
43_K47_E0.270980.991
18_N22_D0.270390.989
63_I95_A0.266590.975
92_H96_L0.263430.964
74_W78_A0.261250.956
84_S87_T0.261250.956
74_W86_R0.260940.954
94_K97_K0.258730.946
58_P65_R0.258350.945
81_L88_Y0.257110.940
39_D43_K0.253210.926
73_T76_Q0.253160.926
21_E71_K0.251330.919
74_W87_T0.250420.916
45_K50_R0.25040.916
63_I68_Y0.246250.901
20_Q24_I0.246120.900
38_I42_I0.24440.894
36_R40_E0.243730.891
56_E60_E0.243670.891
53_N61_R0.24110.882
19_K71_K0.2380.870
74_W90_R0.236980.867
74_W85_R0.233750.855
18_N23_K0.232670.851
19_K22_D0.232530.850
93_K96_L0.232330.850
59_D98_E0.232270.850
92_H95_A0.226720.829
43_K46_L0.226090.827
30_L33_E0.224980.823
46_L49_R0.224860.822
34_I37_E0.224720.822
86_R91_I0.224620.822
55_L60_E0.222790.815
60_E94_K0.218590.799
17_K20_Q0.212740.778
39_D42_I0.211320.773
40_E47_E0.209860.768
64_L68_Y0.208930.764
32_E36_R0.205540.752
79_E82_N0.202510.741
40_E44_E0.201490.737
60_E95_A0.201320.736
63_I81_L0.200390.733
65_R70_N0.200390.733
56_E98_E0.197670.723
21_E70_N0.195970.717
54_K58_P0.195870.716
20_Q25_V0.19140.700
29_D33_E0.188990.691
50_R53_N0.188740.690
23_K56_E0.186850.683
64_L95_A0.186750.683
55_L86_R0.185770.679
73_T89_Y0.183250.670
19_K23_K0.17960.657
73_T88_Y0.178880.654
54_K70_N0.177730.650
40_E72_L0.177280.648
34_I38_I0.177110.648
60_E81_L0.176950.647
37_E50_R0.176270.645
60_E63_I0.176140.644
48_I51_A0.175860.643
28_I43_K0.174430.638
84_S91_I0.174350.638
50_R54_K0.174180.637
20_Q70_N0.174120.637
41_L54_K0.174050.637
68_Y96_L0.173950.636
43_K50_R0.173780.636
24_I96_L0.170650.624
73_T84_S0.169890.621
35_E38_I0.169340.619
37_E53_N0.16930.619
18_N48_I0.169030.618
38_I46_L0.168140.615
27_I41_L0.167820.614
59_D83_I0.167160.611
28_I49_R0.165820.606
85_R95_A0.165770.606
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
4igcX0.9698.80.332
4kn7X0.9698.70.365
3iydF0.9698.70.366
2a6hF0.9598.60.386
1l9zH0.9598.60.39
3vdoA0.9998.60.398
3vfzA0.7698.60.399
3hugA0.8298.50.407
3t72q0.6498.50.409
1ttyA0.6398.50.413

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