GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PCRF - PCRF domain
Pfam: PF03462 (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: CL0328
Length: 115
Sequences: 3315
Seq/Len: 28.83
HH_delta: 0.04 (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
76_A103_I1.243543.187
50_L101_L1.191633.054
79_R111_Y1.027882.634
73_Q83_V1.020632.616
69_F99_A0.954812.447
69_F101_L0.942452.415
52_I65_A0.893682.290
28_E32_E0.843922.163
47_N104_S0.81292.083
84_E102_E0.78372.009
49_I102_E0.777751.993
83_V101_L0.765811.963
48_A110_G0.734151.882
25_E28_E0.723131.853
82_K104_S0.688161.764
69_F73_Q0.66151.695
21_Q25_E0.644651.652
84_E104_S0.640381.641
59_D91_G0.632331.621
76_A83_V0.617481.583
17_E21_Q0.615571.578
88_Y96_I0.613891.573
63_L93_E0.595861.527
13_E17_E0.554611.421
73_Q77_E0.531721.363
23_E27_E0.529451.357
69_F85_V0.527151.351
43_Y46_N0.525221.346
45_A107_G0.519061.330
85_V99_A0.512031.312
12_R16_E0.511211.310
24_E28_E0.51021.308
75_Y81_W0.508931.304
75_Y111_Y0.486841.248
9_E13_E0.486451.247
81_W108_A0.479631.229
81_W112_L0.478441.226
74_R77_E0.474561.216
16_E20_E0.4711.207
14_L18_E0.468311.200
103_I112_L0.467771.199
17_E20_E0.461251.182
75_Y79_R0.454181.164
73_Q101_L0.43941.126
7_E15_A0.431431.106
49_I86_L0.421231.080
19_I23_E0.419621.075
85_V88_Y0.418121.072
8_D11_M0.416891.068
45_A106_E0.406851.043
20_E24_E0.403111.033
21_Q24_E0.402841.032
13_E16_E0.40081.027
25_E29_L0.388510.996
19_I26_L0.383770.984
55_G87_D0.3810.976
47_N102_E0.374990.961
14_L17_E0.374770.961
44_D113_K0.374590.960
27_E30_E0.374350.959
69_F96_I0.372440.955
52_I99_A0.367240.941
27_E31_K0.364430.934
20_E23_E0.363890.933
7_E12_R0.362170.928
11_M14_L0.357040.915
59_D93_E0.353260.905
11_M15_A0.350020.897
50_L112_L0.346910.889
66_E88_Y0.341170.874
62_C97_K0.340850.874
50_L103_I0.340360.872
31_K39_P0.338860.868
54_A96_I0.338730.868
54_A89_S0.332740.853
61_A89_S0.32770.840
96_I99_A0.32760.840
62_C93_E0.326890.838
67_E96_I0.322770.827
69_F88_Y0.320070.820
9_E12_R0.319690.819
10_E13_E0.317030.813
32_E107_G0.31690.812
54_A61_A0.316510.811
63_L67_E0.314770.807
44_D110_G0.314330.806
54_A97_K0.313820.804
56_A59_D0.311230.798
86_L102_E0.310930.797
108_A112_L0.308320.790
54_A62_C0.304810.781
48_A109_Y0.304390.780
70_R73_Q0.303590.778
29_L52_I0.30210.774
81_W114_F0.301650.773
59_D62_C0.298010.764
59_D63_L0.297350.762
65_A96_I0.294010.754
88_Y99_A0.293450.752
62_C66_E0.275940.707
66_E91_G0.271010.695
43_Y110_G0.270460.693
70_R77_E0.270310.693
48_A112_L0.27020.693
41_D45_A0.269710.691
53_R98_S0.269570.691
55_G70_R0.26540.680
24_E27_E0.261850.671
89_S98_S0.255430.655
68_L72_Y0.253340.649
56_A61_A0.250590.642
21_Q28_E0.246870.633
28_E31_K0.245280.629
57_G60_E0.244960.628
63_L91_G0.244490.627
87_D100_T0.243760.625
49_I104_S0.242570.622
12_R15_A0.242120.621
104_S108_A0.239910.615
70_R74_R0.238950.612
30_E37_L0.237110.608
39_P94_G0.236610.606
64_F114_F0.236130.605
55_G97_K0.235540.604
41_D113_K0.23470.602
81_W111_Y0.234610.601
37_L51_E0.230480.591
54_A88_Y0.229840.589
41_D44_D0.228940.587
73_Q88_Y0.227850.584
15_A19_I0.224630.576
43_Y48_A0.223860.574
62_C92_E0.223320.572
38_L43_Y0.22330.572
53_R114_F0.222410.570
64_F91_G0.222360.570
54_A98_S0.220050.564
7_E16_E0.219960.564
64_F67_E0.21980.563
48_A108_A0.219260.562
29_L102_E0.218950.561
26_L29_L0.217630.558
17_E24_E0.217440.557
51_E60_E0.21570.553
40_S44_D0.212480.545
7_E20_E0.212450.545
87_D98_S0.211630.542
16_E19_I0.211370.542
10_E14_L0.210510.540
53_R113_K0.210.538
18_E37_L0.209220.536
62_C91_G0.208790.535
23_E106_E0.208250.534
52_I69_F0.2060.528
66_E96_I0.205420.526
42_P47_N0.204750.525
11_M18_E0.204550.524
49_I54_A0.204330.524
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
1zbtA11000.04
2b3tB0.97391000.064
3d5aX0.97391000.064
1gqeA0.96521000.068
2ihr10.92171000.133
1rq0A0.92171000.168
2qf9A0.408716.90.928
4djdD0.391316.80.928
3qneA0.965213.70.931
3g5sA0.513130.932

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