GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PX - PX domain
Pfam: PF00787 (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: 113
Sequences: 2789
Seq/Len: 24.68
HH_delta: 0.109 (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
48_H90_Y1.152534.596
21_Y24_Y0.705372.813
81_E84_R0.641912.560
39_R44_F0.564052.249
88_E92_Q0.555482.215
19_K22_Y0.518852.069
19_K24_Y0.504192.010
48_H52_K0.504052.010
27_E34_S0.45821.827
20_T24_Y0.449141.791
87_L90_Y0.411681.642
67_Q79_F0.406651.622
80_I83_R0.400531.597
104_E108_E0.384771.534
48_H63_F0.381521.521
44_F91_L0.370991.479
44_F87_L0.367861.467
23_I38_Y0.363971.451
95_L106_L0.363851.451
40_R83_R0.352131.404
45_Y49_R0.346011.380
40_R66_K0.343421.369
50_K53_K0.338381.349
25_Q36_S0.337071.344
76_D80_I0.332021.324
84_R88_E0.331761.323
42_S45_Y0.324511.294
35_W111_E0.32411.292
89_K93_S0.323271.289
55_F103_S0.317691.267
54_R105_A0.314211.253
45_Y66_K0.31271.247
106_L110_L0.303881.212
24_Y28_L0.300691.199
76_D79_F0.29711.185
41_Y83_R0.291431.162
82_E86_A0.291291.162
54_R103_S0.284711.135
83_R87_L0.284091.133
45_Y63_F0.27731.106
25_Q34_S0.27561.099
43_D46_E0.275191.097
84_R87_L0.262821.048
44_F47_L0.261131.041
97_H100_L0.25971.036
15_G29_Q0.245320.978
94_L106_L0.243560.971
88_E91_L0.242820.968
41_Y87_L0.242160.966
75_L79_F0.239860.956
44_F63_F0.237670.948
79_F83_R0.235230.938
21_Y40_R0.233490.931
67_Q70_S0.229940.917
105_A108_E0.22710.906
41_Y66_K0.225560.899
95_L102_S0.225110.898
71_N76_D0.224510.895
92_Q96_S0.223580.892
70_S80_I0.22150.883
43_D70_S0.220040.877
71_N75_L0.219010.873
85_Q89_K0.218480.871
60_L63_F0.216430.863
35_W95_L0.212710.848
19_K40_R0.21260.848
92_Q95_L0.211790.845
41_Y63_F0.210720.840
29_Q34_S0.205970.821
17_K105_A0.204890.817
101_R106_L0.204410.815
39_R43_D0.203610.812
101_R111_E0.201370.803
44_F109_F0.200850.801
67_Q71_N0.197340.787
56_P59_K0.196680.784
46_E50_K0.196480.783
16_N19_K0.196220.782
97_H101_R0.195150.778
46_E89_K0.194960.777
15_G18_K0.194890.777
20_T80_I0.193420.771
91_L110_L0.192430.767
93_S96_S0.192090.766
64_P98_P0.1910.762
103_S106_L0.189570.756
50_K105_A0.189050.754
56_P68_W0.187740.749
33_E102_S0.187480.748
58_R97_H0.187350.747
46_E57_S0.186290.743
46_E108_E0.185530.740
41_Y44_F0.179650.716
37_V44_F0.179040.714
55_F100_L0.177230.707
98_P102_S0.174550.696
50_K107_K0.17090.681
50_K103_S0.170320.679
39_R47_L0.169920.678
77_P84_R0.16960.676
26_I47_L0.169390.675
66_K69_F0.168740.673
28_L111_E0.166640.664
58_R102_S0.16640.664
63_F90_Y0.166280.663
15_G42_S0.164150.655
40_R65_P0.164110.654
78_E82_E0.164010.654
48_H62_P0.163560.652
58_R71_N0.163430.652
94_L100_L0.162980.650
40_R64_P0.162750.649
75_L80_I0.161740.645
108_E111_E0.161370.643
48_H67_Q0.161220.643
54_R99_E0.160820.641
36_S88_E0.160540.640
67_Q76_D0.16030.639
100_L106_L0.16020.639
25_Q89_K0.159620.636
18_K22_Y0.158920.634
22_Y28_L0.158340.631
22_Y26_I0.15750.628
43_D109_F0.156690.625
59_K65_P0.156360.623
90_Y94_L0.156260.623
20_T79_F0.156170.623
37_V110_L0.155510.620
77_P81_E0.155220.619
90_Y100_L0.154640.617
23_I36_S0.15450.616
15_G19_K0.154360.616
15_G52_K0.153770.613
65_P77_P0.152780.609
27_E94_L0.152730.609
76_D104_E0.15220.607
27_E36_S0.151730.605
34_S85_Q0.151520.604
29_Q33_E0.149630.597
89_K104_E0.149510.596
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
1xteA0.973599.70.109
4akvA0.955899.70.117
1ocsA0.982399.70.12
3dytA0.955899.70.12
4ikdA0.973599.70.12
4hasA0.938199.70.136
2cskA0.991299.70.137
3iq2A199.70.143
2ar5A0.982399.70.15
2i4kA199.70.156

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