GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DcpS_C - Scavenger mRNA decapping enzyme C-term binding
Pfam: PF11969 (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: CL0265
Length: 116
Sequences: 5316
Seq/Len: 45.83
HH_delta: 0.113 (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
2_C5_C1.918123.850
43_D56_H1.712683.438
19_E42_K1.668283.349
5_C45_H1.499973.011
2_C45_H1.359492.729
20_D59_L1.173812.356
22_D62_R1.153182.315
15_R27_K1.130462.269
24_V42_K1.039542.087
53_T56_H0.963181.933
10_G16_V0.925411.858
16_V24_V0.895941.798
6_I11_E0.871481.749
26_F40_I0.86531.737
17_L37_L0.835271.677
5_C9_R0.823181.652
84_I99_L0.788231.582
35_V103_S0.787881.582
22_D59_L0.750811.507
52_L97_L0.737371.480
27_K74_E0.73211.470
48_S51_D0.71541.436
43_D46_I0.714591.434
25_V37_L0.696811.399
47_R51_D0.668891.343
39_V101_V0.657531.320
16_V19_E0.645231.295
23_F63_M0.640251.285
70_L74_E0.63361.272
65_E69_E0.626411.257
46_I97_L0.603891.212
20_D62_R0.602281.209
69_E73_E0.591311.187
46_I52_L0.586631.178
46_I56_H0.582591.169
14_E24_V0.569041.142
18_Y63_M0.562031.128
18_Y66_V0.555711.115
57_L65_E0.553461.111
25_V39_V0.541911.088
54_P65_E0.539731.083
64_R99_L0.536781.077
46_I53_T0.52951.063
62_R66_V0.523851.052
58_P62_R0.502311.008
66_V70_L0.496150.996
5_C96_H0.490180.984
45_H96_H0.483190.970
43_D53_T0.483110.970
82_D86_L0.46670.937
38_L100_H0.461420.926
81_S85_R0.457680.919
81_S104_P0.455890.915
68_R72_K0.455340.914
71_L75_Y0.451370.906
48_S86_L0.451180.906
59_L62_R0.449680.903
37_L101_V0.449510.902
66_V69_E0.447230.898
4_F40_I0.442890.889
36_H100_H0.441590.886
22_D43_D0.43950.882
52_L60_L0.434410.872
84_I97_L0.431040.865
33_A102_I0.422960.849
59_L63_M0.420460.844
63_M99_L0.418360.840
23_F62_R0.41580.835
22_D56_H0.415080.833
32_K93_S0.409050.821
80_D86_L0.403930.811
73_E76_P0.403890.811
62_R65_E0.403830.811
27_K37_L0.40030.804
7_I14_E0.398030.799
83_D102_I0.395560.794
27_K35_V0.395070.793
57_L61_E0.394830.793
81_S90_Y0.394040.791
60_L64_R0.391630.786
6_I12_E0.390870.785
31_P36_H0.38920.781
48_S95_Y0.389060.781
43_D55_E0.387080.777
54_P58_P0.382430.768
8_I24_V0.378930.761
88_F95_Y0.378590.760
3_I6_I0.378240.759
54_P62_R0.377330.757
82_D92_P0.376810.756
2_C96_H0.375810.754
76_P103_S0.374060.751
47_R87_G0.372160.747
24_V40_I0.367390.737
61_E64_R0.363460.730
67_A71_L0.361390.725
5_C8_I0.35840.719
3_I12_E0.356390.715
37_L67_A0.355590.714
3_I29_I0.355490.714
54_P57_L0.351370.705
56_H59_L0.348750.700
32_K102_I0.339540.682
85_R104_P0.339540.682
26_F38_L0.336610.676
22_D55_E0.334150.671
54_P69_E0.328820.660
48_S87_G0.32710.657
20_D66_V0.327060.657
37_L103_S0.324190.651
50_R80_D0.318870.640
64_R68_R0.316120.635
69_E72_K0.313840.630
72_K75_Y0.309640.622
60_L99_L0.308760.620
27_K103_S0.307010.616
67_A82_D0.306260.615
4_F7_I0.303550.609
92_P95_Y0.301960.606
17_L27_K0.298750.600
28_D38_L0.293180.589
46_I51_D0.292960.588
8_I42_K0.292860.588
10_G14_E0.292170.586
47_R95_Y0.291890.586
64_R71_L0.289110.580
88_F91_P0.289070.580
64_R84_I0.288590.579
4_F94_V0.28840.579
20_D23_F0.288110.578
71_L74_E0.287630.577
22_D58_P0.287310.577
3_I94_V0.286830.576
80_D85_R0.282160.566
50_R86_L0.278350.559
28_D36_H0.278140.558
17_L25_V0.278040.558
52_L56_H0.277970.558
4_F26_F0.277560.557
70_L76_P0.277340.557
23_F59_L0.276610.555
8_I26_F0.275710.553
50_R72_K0.269240.540
10_G19_E0.268830.540
23_F60_L0.267230.536
65_E68_R0.266130.534
61_E65_E0.26490.532
25_V63_M0.264880.532
83_D89_H0.264660.531
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
3l7xA0.991499.90.113
3ksvA0.991499.90.116
3n1sA0.991499.90.117
3lb5A0.991499.90.118
3o0mA0.991499.90.123
3imiA0.991499.90.124
4eguA0.982899.90.126
4incA0.939799.90.133
3o1cA0.939799.90.139
1y23A0.991499.80.15

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