GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LTD - Lamin Tail Domain
Pfam: PF00932 (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: 116
Sequences: 1222
Seq/Len: 10.53
HH_delta: 0.311 (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
26_E91_N0.597423.402
31_Y65_Y0.458762.612
16_N29_E0.454142.586
47_D94_D0.45182.573
100_D104_E0.445772.538
37_T62_P0.369032.101
99_Y105_V0.364912.078
37_T59_T0.343831.958
60_L64_E0.330861.884
13_V43_W0.32211.834
55_P58_T0.316181.800
21_D91_N0.314471.791
16_N31_Y0.310561.768
43_W100_D0.290621.655
90_N94_D0.269221.533
20_P26_E0.268961.531
13_V30_L0.263151.498
13_V38_V0.260441.483
41_S58_T0.258281.471
97_T108_S0.255111.453
61_A64_E0.252311.437
37_T61_A0.243381.386
29_E67_V0.243271.385
97_T105_V0.236321.346
43_W106_V0.234841.337
46_V99_Y0.232151.322
17_E29_E0.227451.295
58_T66_V0.226981.292
17_E67_V0.222881.269
35_D63_G0.220981.258
16_N65_Y0.217841.240
69_W79_D0.217211.237
19_M22_G0.212281.209
12_D33_P0.209221.191
27_W111_Y0.205521.170
32_N38_V0.198791.132
21_D26_E0.195471.113
15_I28_V0.194751.109
30_L98_L0.194351.107
96_I111_Y0.193761.103
52_Y55_P0.189991.082
28_V45_L0.189881.081
45_L98_L0.188421.073
26_E111_Y0.186271.061
47_D90_N0.182141.037
15_I104_E0.181451.033
76_P81_Y0.179471.022
89_L96_I0.178281.015
30_L78_F0.177681.012
41_S57_G0.175741.001
14_V29_E0.175370.999
44_K103_G0.172590.983
14_V33_P0.171750.978
15_I109_V0.170990.974
19_M67_V0.170610.971
46_V97_T0.169860.967
11_G104_E0.166630.949
105_V108_S0.165380.942
94_D111_Y0.158410.902
26_E89_L0.158120.900
15_I45_L0.154930.882
26_E47_D0.154680.881
18_I96_I0.151840.865
11_G34_G0.151340.862
26_E88_G0.151320.862
19_M27_W0.150350.856
87_F91_N0.14980.853
16_N107_D0.147370.839
89_L93_G0.146340.833
26_E93_G0.146220.833
72_G85_S0.145480.828
48_S90_N0.145130.826
26_E90_N0.144220.821
70_T89_L0.143970.820
27_W87_F0.143970.820
76_P83_G0.143660.818
21_D24_D0.143240.816
18_I29_E0.143010.814
76_P80_L0.141980.808
47_D93_G0.141640.807
44_K99_Y0.140410.799
90_N111_Y0.140380.799
56_P61_A0.139260.793
90_N93_G0.138160.787
57_G61_A0.137810.785
95_T110_S0.137340.782
30_L66_V0.136930.780
54_F58_T0.136610.778
82_W85_S0.136220.776
47_D89_L0.133260.759
32_N60_L0.133220.759
44_K53_T0.132180.753
81_Y84_S0.131920.751
33_P62_P0.131220.747
77_P81_Y0.130840.745
20_P109_V0.130390.742
36_S59_T0.130320.742
35_D62_P0.130260.742
42_G100_D0.130190.741
77_P84_S0.130.740
89_L109_V0.129620.738
20_P25_N0.129490.737
30_L45_L0.129320.736
18_I21_D0.128860.734
31_Y105_V0.12880.733
20_P94_D0.128290.730
17_E27_W0.128210.730
77_P83_G0.126070.718
56_P62_P0.125680.716
95_T111_Y0.125580.715
38_V106_V0.123860.705
48_S95_T0.122790.699
22_G27_W0.122580.698
57_G101_P0.122480.697
45_L104_E0.122480.697
18_I26_E0.121760.693
22_G25_N0.121130.690
95_T100_D0.12090.688
19_M109_V0.120850.688
51_T54_F0.12050.686
32_N37_T0.120010.683
32_N62_P0.118260.673
24_D96_I0.118190.673
27_W47_D0.117760.671
39_D84_S0.117690.670
78_F84_S0.117310.668
45_L85_S0.116370.663
89_L111_Y0.1160.661
19_M26_E0.115230.656
77_P80_L0.1150.655
34_G38_V0.114430.652
13_V63_G0.114330.651
20_P111_Y0.114120.650
10_A36_S0.113850.648
15_I38_V0.113420.646
28_V46_V0.112270.639
27_W81_Y0.112020.638
71_G85_S0.111440.635
53_T68_V0.11070.630
30_L68_V0.109890.626
42_G68_V0.109690.625
26_E70_T0.109630.624
39_D106_V0.109370.623
14_V62_P0.10930.622
20_P47_D0.109050.621
101_P104_E0.108080.615
70_T87_F0.107920.615
48_S97_T0.10780.614
79_D101_P0.107390.611
42_G58_T0.105780.602
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
3jt0A0.965599.70.311
3hn9A0.965599.60.339
2lllA0.956999.60.34
1ufgA0.965599.60.366
1ifrA0.922499.60.369
1r17A0.836244.30.878
2ys4A0.887934.70.885
4f27A0.81916.40.901
3lafA0.982816.30.901
3dmkA0.956915.40.902

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