GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HRDC - HRDC domain
Pfam: PF00570 (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: CL0426
Length: 68
Sequences: 2519
Seq/Len: 37.04
HH_delta: -0.019 (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
13_E17_R1.423843.376
42_S45_E1.144862.714
11_W64_I1.060672.515
4_L39_L0.864692.050
55_R59_K0.852482.021
4_L68_I0.814391.931
43_I62_D0.801591.900
11_W15_L0.781321.852
34_E38_R0.764311.812
5_L36_A0.751871.783
62_D66_E0.734461.741
21_V25_R0.715011.695
7_A67_I0.706771.676
43_I47_L0.703891.669
15_L18_E0.631571.497
41_T45_E0.613851.455
35_I68_I0.590961.401
35_I52_M0.554551.315
15_L19_E0.55331.312
8_L32_L0.545891.294
47_L54_K0.536521.272
30_E50_P0.520721.235
15_L63_E0.516981.226
35_I64_I0.510281.210
46_L65_L0.502361.191
34_E50_P0.476711.130
34_E37_K0.462471.096
11_W67_I0.462071.095
63_E66_E0.457361.084
46_L57_V0.450521.068
54_K58_R0.44941.065
27_L52_M0.446881.059
13_E23_P0.443131.051
63_E67_I0.434671.031
11_W14_E0.431471.023
6_K9_K0.424771.007
25_R28_S0.422491.002
22_P25_R0.411680.976
22_P29_D0.408160.968
5_L32_L0.396520.940
10_E14_E0.394480.935
11_W63_E0.388510.921
38_R49_I0.386430.916
5_L9_K0.385570.914
27_L32_L0.382770.907
53_G56_K0.381270.904
43_I65_L0.373930.887
15_L64_I0.361590.857
61_G65_L0.360030.854
35_I46_L0.359550.852
34_E49_I0.350570.831
43_I57_V0.346140.821
31_A52_M0.345420.819
6_K33_L0.340040.806
46_L61_G0.333450.791
9_K32_L0.323840.768
24_Y29_D0.322970.766
41_T65_L0.317290.752
19_E59_K0.315160.747
2_L6_K0.309920.735
27_L56_K0.309420.734
55_R58_R0.309270.733
11_W35_I0.309230.733
47_L57_V0.307380.729
45_E48_Q0.30640.726
12_R29_D0.303520.720
18_E63_E0.297140.704
31_A51_G0.285470.677
19_E60_Y0.284910.675
56_K60_Y0.284610.675
27_L64_I0.28440.674
41_T66_E0.284080.674
33_L37_K0.283770.673
29_D56_K0.282440.670
39_L68_I0.281750.668
3_A54_K0.27470.651
5_L33_L0.274430.651
11_W46_L0.274230.650
14_E18_E0.268610.637
58_R62_D0.263110.624
24_Y53_G0.259540.615
12_R22_P0.258730.613
7_A10_E0.257860.611
40_P46_L0.253410.601
12_R23_P0.249230.591
16_A22_P0.247060.586
9_K29_D0.246540.585
28_S31_A0.243080.576
46_L64_I0.241870.573
40_P65_L0.236060.560
36_A39_L0.234840.557
43_I61_G0.234390.556
8_L64_I0.232140.550
16_A19_E0.2310.548
54_K57_V0.228030.541
13_E16_A0.226720.538
3_A18_E0.223990.531
14_E17_R0.219880.521
35_I39_L0.219530.520
44_E47_L0.217150.515
14_E38_R0.216620.514
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
1wudA199.5-0.019
3safA199.5-0.016
2rrdA199.50.002
2hbjA199.50.008
2rhfA199.50.013
2kv2A199.50.02
1yt3A0.985399.40.046
2dgzA0.985399.40.05
2e1fA0.985399.40.059
3cymA199.40.075

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