GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF397 - Domain of unknown function (DUF397)
Pfam: PF04149 (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: 56
Sequences: 1207
Seq/Len: 21.55
HH_delta: 0.866 (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
19_E30_R0.745962.719
6_K10_S0.627482.288
7_S10_S0.620662.263
23_L28_A0.617362.251
32_S35_P0.573682.091
5_R22_R0.54481.986
34_D37_G0.480781.753
20_V47_W0.447691.632
42_F50_F0.432221.576
2_A21_A0.427921.560
6_K19_E0.408371.489
51_L55_K0.360681.315
35_P38_P0.35221.284
6_K17_C0.351351.281
47_W50_F0.346881.265
2_A23_L0.344871.257
29_V42_F0.342391.248
49_A53_G0.341041.243
31_D42_F0.339391.237
21_A28_A0.330951.207
5_R20_V0.328111.196
29_V33_K0.318991.163
10_S17_C0.312031.138
34_D40_L0.304951.112
39_V53_G0.301741.100
50_F53_G0.296231.080
2_A28_A0.28331.033
42_F46_E0.27240.993
28_A41_T0.267720.976
48_A52_A0.260020.948
49_A54_V0.259840.947
10_S19_E0.258960.944
5_R24_P0.249920.911
2_A26_G0.247290.902
18_V28_A0.243490.888
17_C32_S0.236820.863
12_G15_G0.236610.863
32_S38_P0.236080.861
10_S33_K0.235240.858
15_G27_V0.232950.849
36_D45_A0.230460.840
20_V50_F0.230150.839
4_W28_A0.224590.819
16_N20_V0.223520.815
6_K9_Y0.219490.800
28_A39_V0.217230.792
3_R25_G0.215390.785
31_D34_D0.21010.766
45_A56_A0.20620.752
31_D47_W0.203260.741
43_T55_K0.202570.738
52_A56_A0.192770.703
7_S31_D0.191810.699
4_W51_L0.191490.698
3_R14_G0.190610.695
36_D39_V0.190360.694
3_R56_A0.189950.692
3_R47_W0.187070.682
10_S31_D0.185780.677
3_R52_A0.185650.677
50_F54_V0.184720.673
43_T53_G0.184560.673
5_R50_F0.183890.670
53_G56_A0.182630.666
8_S48_A0.181990.663
9_Y17_C0.180780.659
46_E51_L0.18060.658
27_V42_F0.179580.655
46_E49_A0.178680.651
3_R55_K0.17640.643
22_R44_P0.176360.643
17_C29_V0.175530.640
7_S17_C0.173980.634
24_P40_L0.172890.630
18_V47_W0.172540.629
3_R22_R0.172030.627
7_S33_K0.171320.625
2_A25_G0.171150.624
2_A5_R0.170830.623
42_F49_A0.170550.622
26_G46_E0.16960.618
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
3tqcA0.589318.10.866
4hd4A0.514.80.871
3l6wA0.428611.20.878
1n10A0.92869.60.881
3aezA0.48218.50.883
3awuA0.42868.30.884
2hczX0.92868.30.884
1lnlA0.48217.60.886
1lrzA0.35717.40.887
2xb0X0.35717.40.887
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