GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PDZ - PDZ domain (Also known as DHR or GLGF)
Pfam: PF00595 (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: 81
Sequences: 12887
Seq/Len: 159.1
HH_delta: -0.118 (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
51_E79_T2.837314.618
34_P39_E1.645942.679
26_G48_R1.427212.323
43_L80_V1.187021.932
15_T31_S1.130211.840
61_S64_E1.112061.810
32_V45_V1.09591.784
17_R30_S1.082341.762
28_F48_R1.044651.700
51_E54_G0.98111.597
35_G39_E0.962891.567
32_V36_S0.921121.499
65_V69_L0.888581.446
60_M64_E0.868181.413
57_V60_M0.835511.360
37_P41_A0.819271.333
44_K47_D0.818021.331
19_G28_F0.812771.323
71_S74_N0.811391.321
50_L79_T0.809221.317
55_Q68_L0.795141.294
62_H66_V0.782551.274
43_L78_L0.777841.266
53_N77_T0.771251.255
51_E56_S0.766511.248
63_D67_Q0.757061.232
64_E67_Q0.753821.227
52_I57_V0.742131.208
32_V39_E0.731481.191
29_V43_L0.711011.157
64_E68_L0.706291.150
18_G60_M0.684451.114
18_G62_H0.650481.059
17_R28_F0.650381.059
70_K74_N0.650211.058
66_V70_K0.648131.055
52_I70_K0.638261.039
39_E44_K0.619461.008
15_T33_V0.612740.997
31_S45_V0.604690.984
54_G77_T0.586310.954
67_Q70_K0.576320.938
11_P37_P0.571380.930
33_V36_S0.553690.901
16_L60_M0.544430.886
18_G26_G0.543310.884
29_V32_V0.536730.874
30_S45_V0.529570.862
67_Q72_A0.527280.858
68_L71_S0.527170.858
11_P33_V0.526890.858
52_I76_V0.520530.847
15_T30_S0.520230.847
38_A42_G0.516690.841
17_R20_S0.508210.827
32_V38_A0.504460.821
27_V65_V0.487260.793
35_G40_R0.481570.784
38_A41_A0.470680.766
32_V41_A0.470640.766
52_I78_L0.462750.753
15_T18_G0.457540.745
47_D50_L0.453790.739
62_H69_L0.437170.712
58_R62_H0.428050.697
54_G79_T0.426510.694
72_A76_V0.418030.680
18_G27_V0.414040.674
57_V65_V0.4090.666
67_Q74_N0.40750.663
18_G21_D0.403060.656
27_V60_M0.396130.645
29_V49_I0.393470.640
10_G73_S0.382550.623
74_N77_T0.379530.618
28_F46_G0.378770.616
14_F43_L0.377920.615
69_L72_A0.377280.614
70_K76_V0.377010.614
11_P16_L0.368640.600
53_N76_V0.367750.599
14_F38_A0.367530.598
11_P15_T0.3670.597
27_V62_H0.365420.595
38_A43_L0.365220.594
21_D26_G0.363520.592
56_S59_G0.36280.590
39_E42_G0.352860.574
37_P40_R0.352420.574
19_G27_V0.342990.558
52_I65_V0.342970.558
63_D66_V0.342240.557
13_G29_V0.340830.555
16_L69_L0.336540.548
49_I80_V0.335740.546
47_D80_V0.332150.541
60_M68_L0.331530.540
32_V35_G0.325260.529
10_G74_N0.323980.527
16_L27_V0.323330.526
32_V43_L0.315980.514
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
4f8kA0.975399-0.118
1z87A0.987798.8-0.062
3l4fD198.8-0.027
2xkxA0.987798.8-0.024
3shwA0.938398.7-0.01
3k1rA0.975398.7-0.009
3b76A198.7-0.008
2iwoA198.7-0.008
3eggC0.987798.7-0.005
2lobA0.987798.7-0.005

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