GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UN_NPL4 - Nuclear pore localisation protein NPL4
Pfam: PF11543 (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: CL0072
Length: 80
Sequences: 4790
Seq/Len: 59.88
HH_delta: 0.137 (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
30_K60_D1.648283.990
24_S28_D1.027662.488
62_K66_S1.018662.466
27_S31_E0.857982.077
24_S32_K0.826412.001
62_K67_L0.810641.963
22_P65_S0.748251.811
34_S44_Q0.728831.764
59_S62_K0.725511.756
27_S60_D0.685381.659
28_D31_E0.668461.618
21_S24_S0.660861.600
44_Q77_L0.643581.558
63_T66_S0.640961.552
33_I46_L0.63671.541
10_R74_M0.60181.457
70_K73_D0.59111.431
25_T28_D0.581211.407
47_S55_E0.580491.405
20_V24_S0.535341.296
41_D44_Q0.526891.276
34_S41_D0.514481.246
6_I17_R0.502131.216
16_K37_L0.502121.216
32_K35_E0.499071.208
47_S76_Y0.493411.195
30_K44_Q0.491521.190
6_I19_E0.490271.187
8_R17_R0.485611.176
5_M22_P0.473731.147
32_K36_Q0.471731.142
64_L69_L0.462681.120
63_T67_L0.451111.092
31_E35_E0.437331.059
7_L20_V0.423291.025
46_L75_L0.419711.016
27_S61_S0.418491.013
23_S65_S0.410050.993
50_R56_L0.39890.966
11_S16_K0.385510.933
26_L56_L0.383550.929
47_S50_R0.383070.927
34_S42_S0.37180.900
26_L64_L0.37150.899
33_I77_L0.366150.886
23_S63_T0.357770.866
9_V33_I0.352980.855
29_L37_L0.340560.824
10_R76_Y0.337240.816
29_L64_L0.330040.799
37_L40_P0.329370.797
24_S29_L0.328880.796
5_M19_E0.325380.788
69_L75_L0.323050.782
40_P44_Q0.320860.777
63_T68_G0.320130.775
5_M20_V0.318810.772
29_L75_L0.318590.771
45_S55_E0.315160.763
9_V29_L0.314520.761
33_I44_Q0.301140.729
7_L29_L0.300040.726
64_L67_L0.297630.721
13_D37_L0.295570.716
55_E59_S0.293970.712
25_T61_S0.291450.706
31_E38_S0.290820.704
6_I71_H0.28860.699
11_S77_L0.285230.691
28_D32_K0.281920.683
16_K36_Q0.277520.672
11_S76_Y0.276290.669
11_S14_G0.273660.663
21_S28_D0.27350.662
20_V64_L0.270940.656
26_L67_L0.26920.652
34_S40_P0.266110.644
39_I44_Q0.265130.642
31_E34_S0.261790.634
50_R54_E0.260050.630
8_R74_M0.259470.628
11_S17_R0.255190.618
9_V77_L0.252650.612
10_R16_K0.251740.609
19_E47_S0.251740.609
26_L46_L0.251170.608
17_R32_K0.249260.603
8_R72_G0.241120.584
28_D59_S0.238040.576
9_V18_I0.237010.574
48_K54_E0.236720.573
28_D61_S0.235050.569
35_E42_S0.23480.568
12_K45_S0.230970.559
5_M71_H0.229370.555
18_I24_S0.228260.553
50_R76_Y0.227440.551
5_M21_S0.225460.546
19_E32_K0.225370.546
56_L75_L0.223060.540
27_S30_K0.222280.538
20_V69_L0.220120.533
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
4k95A0.92599.10.137
1t0yA199.10.143
2hj8A0.937599.10.149
4hwiB0.912599.10.151
2pjhA199.10.152
1yqbA0.9375990.166
3phxB0.9375990.166
1v6eA0.975990.176
2bwfA0.9125990.179
2lwpA0.9375990.179

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