GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PDZ_2 - PDZ domain
Pfam: PF13180 (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: CL0466
Length: 82
Sequences: 16527
Seq/Len: 201.55
HH_delta: -0.035 (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
40_A68_T3.342543.674
69_V78_V2.679982.946
68_T77_T2.156982.371
36_D71_R2.152272.366
68_T75_E2.043192.246
66_T77_T1.877042.063
15_G37_I1.816851.997
23_P28_A1.745151.918
66_T79_E1.699021.867
59_G63_D1.658871.823
37_I70_L1.626411.788
64_T79_E1.51531.665
44_K55_I1.447471.591
17_V37_I1.389581.527
69_V76_L1.295491.424
49_S53_V1.295061.423
47_N51_D1.264971.390
21_V34_P1.231761.354
39_L70_L1.228541.350
70_L75_E1.189661.308
60_K63_D1.173531.290
26_P30_A1.083251.191
71_R76_L1.07761.184
40_A43_G1.076421.183
33_Q71_R1.069611.176
50_E53_V1.032091.134
21_V25_S1.031631.134
42_N59_G1.029991.132
41_I52_L1.029371.131
32_L69_V1.014651.115
48_S51_D0.991031.089
33_Q36_D0.983121.081
40_A45_P0.93971.033
24_G28_A0.929541.022
16_V49_S0.928531.021
70_L73_G0.920731.012
39_L68_T0.893750.982
41_I59_G0.889020.977
42_N66_T0.861630.947
39_L75_E0.859920.945
27_A32_L0.850590.935
32_L67_L0.828060.910
18_V32_L0.81390.895
54_N58_K0.804440.884
21_V28_A0.786610.865
41_I46_V0.763930.840
20_S34_P0.759280.835
41_I65_V0.753130.828
19_V34_P0.749050.823
19_V49_S0.745470.819
51_D54_N0.735880.809
52_L56_L0.7220.794
41_I67_L0.717710.789
28_A33_Q0.710530.781
53_V56_L0.708480.779
16_V52_L0.700560.770
42_N65_V0.699940.769
55_I59_G0.696960.766
18_V38_I0.691620.760
50_E54_N0.681420.749
16_V46_V0.673560.740
71_R78_V0.673270.740
17_V35_G0.659380.725
30_A80_V0.653370.718
22_I25_S0.650510.715
51_D55_I0.624590.686
67_L80_V0.622910.685
26_P80_V0.605050.665
43_G77_T0.581420.639
27_A30_A0.576440.634
43_G66_T0.572740.629
36_D69_V0.571210.628
42_N55_I0.569190.626
15_G49_S0.550560.605
46_V49_S0.531090.584
16_V48_S0.528520.581
27_A31_G0.52260.574
43_G68_T0.512520.563
46_V55_I0.498690.548
55_I58_K0.498530.548
21_V30_A0.49010.539
21_V27_A0.478970.526
76_L79_E0.47680.524
40_A77_T0.475820.523
63_D66_T0.472120.519
22_I28_A0.469780.516
71_R74_E0.467720.514
46_V52_L0.465720.512
59_G65_V0.453690.499
51_D56_L0.452690.498
27_A80_V0.444530.489
37_I49_S0.440720.484
16_V37_I0.435650.479
74_E77_T0.430620.473
24_G29_K0.424920.467
44_K51_D0.417570.459
16_V56_L0.401880.442
26_P29_K0.397620.437
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
3stjA199.2-0.035
1y8tA199.1-0.021
3pv2A199.1-0.012
4fgmA0.963499.1-0.009
1te0A199.10.003
4a8cA199.10.006
3qo6A1990.015
2l97A0.9878990.016
1ky9A1990.021
4ic6A1990.05

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