GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Limkain-b1 - Limkain b1
Pfam: PF11608 (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: CL0221
Length: 90
Sequences: 14872
Seq/Len: 165.24
HH_delta: 0.08 (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_N51_F2.197582.613
33_K47_P2.08282.477
15_D18_S1.809772.152
53_E73_F1.791912.131
8_S70_S1.734922.063
30_C58_R1.685822.005
49_Q73_F1.644931.956
12_T67_N1.589551.890
4_L45_R1.566961.863
35_L47_P1.491631.774
49_Q53_E1.437661.710
54_R58_R1.435551.707
18_S65_F1.387341.650
5_L56_Q1.380551.642
63_D68_K1.364931.623
30_C59_M1.31541.564
52_A73_F1.29821.544
61_G68_K1.235071.469
46_F55_A1.196391.423
64_V69_I1.127331.341
26_L62_E1.119971.332
25_Q28_D1.117721.329
47_P51_F1.11311.324
12_T40_G1.071751.275
35_L45_R1.053311.253
53_E57_K1.043961.241
33_K51_F1.005151.195
56_Q73_F0.986551.173
27_S44_L0.986111.173
26_L29_N0.958141.139
59_M62_E0.929611.105
26_L59_M0.917331.091
36_S45_R0.896961.067
63_D66_G0.888831.057
5_L52_A0.861291.024
54_R57_K0.84841.009
11_P14_K0.838240.997
13_N65_F0.818180.973
8_S41_T0.809860.963
6_Y41_T0.803830.956
14_K65_F0.793430.944
14_K64_V0.788950.938
27_S59_M0.75660.900
7_V27_S0.75450.897
50_E54_R0.742550.883
11_P67_N0.736630.876
43_I74_S0.736190.875
27_S55_A0.732390.871
59_M71_V0.727950.866
11_P65_F0.726430.864
8_S72_S0.722480.859
51_F54_R0.714610.850
19_I42_A0.691110.822
9_N67_N0.685070.815
7_V44_L0.675810.804
60_E70_S0.663340.789
4_L38_S0.659490.784
4_L36_S0.652180.776
14_K18_S0.648260.771
72_S75_P0.644730.767
9_N70_S0.629340.748
58_R62_E0.618860.736
56_Q71_V0.608450.724
10_L42_A0.607530.722
34_V46_F0.588670.700
34_V44_L0.586620.698
4_L74_S0.58140.691
5_L55_A0.573320.682
26_L69_I0.572390.681
51_F55_A0.566190.673
37_V42_A0.559540.665
27_S71_V0.556440.662
16_P37_V0.553390.658
43_I72_S0.551810.656
5_L73_F0.54780.651
50_E53_E0.541020.643
60_E71_V0.540220.642
40_G67_N0.534280.635
10_L14_K0.521860.621
29_N62_E0.521160.620
46_F51_F0.51930.618
7_V71_V0.518940.617
61_G70_S0.518930.617
17_S25_Q0.517580.615
32_G46_F0.508060.604
6_Y72_S0.505990.602
55_A59_M0.48860.581
18_S25_Q0.484510.576
6_Y74_S0.476410.567
26_L64_V0.475190.565
6_Y39_G0.461250.549
7_V19_I0.458510.545
12_T75_P0.454760.541
28_D34_V0.449030.534
4_L52_A0.442650.526
9_N68_K0.43920.522
45_R77_N0.437890.521
16_P19_I0.436980.520
30_C34_V0.435910.518
5_L71_V0.433490.515
56_Q60_E0.430480.512
10_L19_I0.423770.504
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
4f25A0.944499.40.08
2diuA0.988999.40.086
2a3jA0.988999.40.1
3u1lA0.922299.30.119
2dgxA0.911199.30.122
3egnA0.944499.30.122
1sjqA0.933399.30.125
3pgwS0.944499.30.128
4f02A0.944499.30.129
1rk8A0.944499.30.13

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