GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Rio2_N - Rio2 N-terminal
Pfam: PF09202 (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: CL0123
Length: 82
Sequences: 51953
Seq/Len: 633.57
HH_delta: 0.196 (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
14_A33_I3.473392.655
26_P29_L2.797622.139
11_V44_R2.786912.130
8_D51_L2.633962.013
8_D44_R2.600511.988
54_V69_L2.560631.957
8_D47_R2.532781.936
16_E74_L2.179991.666
49_V56_R2.114781.617
5_S8_D2.044591.563
13_R17_M2.006561.534
29_L32_K1.968041.504
36_L40_E1.933621.478
37_S40_E1.926051.472
16_E66_L1.896581.450
42_E46_K1.753451.340
14_A34_S1.670381.277
7_E36_L1.649581.261
57_R65_R1.641991.255
14_A17_M1.577711.206
12_L16_E1.526511.167
27_L45_L1.509541.154
28_E38_E1.494611.142
67_T70_G1.491461.140
13_R74_L1.468131.122
31_E38_E1.450251.109
72_D75_A1.439921.101
71_Y75_A1.411561.079
39_G43_K1.398281.069
46_K50_K1.392131.064
28_E32_K1.35461.035
10_R14_A1.346091.029
43_K47_R1.34371.027
55_S67_T1.33271.019
39_G42_E1.307130.999
43_K46_K1.302390.996
12_L74_L1.300550.994
44_R47_R1.260060.963
55_S65_R1.258120.962
7_E44_R1.234990.944
11_V41_V1.226410.937
40_E43_K1.193280.912
17_M33_I1.187260.908
68_F71_Y1.184370.905
52_K55_S1.175560.899
31_E41_V1.173180.897
53_L56_R1.171760.896
40_E44_R1.150070.879
37_S43_K1.141180.872
68_F72_D1.138640.870
59_K62_D1.137340.869
46_K49_V1.122170.858
27_L42_E1.121070.857
16_E71_Y1.099360.840
29_L33_I1.091820.835
7_E10_R1.08980.833
27_L64_Y1.089620.833
69_L72_D1.088690.832
38_E42_E1.054520.806
11_V36_L1.044190.798
14_A30_I1.043930.798
53_L57_R0.997830.763
36_L41_V0.990450.757
59_K63_G0.982270.751
5_S44_R0.964090.737
47_R51_L0.962260.736
30_I41_V0.951540.727
55_S58_N0.943880.722
71_Y74_L0.943710.721
60_P63_G0.942940.721
9_F13_R0.920850.704
6_K10_R0.906360.693
12_L48_L0.900720.689
10_R13_R0.893470.683
27_L41_V0.874880.669
58_N65_R0.87090.666
27_L31_E0.869780.665
69_L73_Y0.851450.651
7_E47_R0.841980.644
15_I30_I0.83070.635
52_K69_L0.830640.635
46_K56_R0.830080.635
66_L71_Y0.824910.631
67_T71_Y0.815040.623
47_R50_K0.806470.616
53_L73_Y0.801380.613
58_N63_G0.797850.610
32_K35_G0.786190.601
45_L64_Y0.781680.598
5_S47_R0.763820.584
70_G73_Y0.75370.576
41_V45_L0.746740.571
34_S41_V0.745060.570
8_D11_V0.739930.566
66_L70_G0.720130.550
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
3nqoA0.975698.60.196
1hsjA0.975698.60.201
2qq9A0.951298.60.207
1fx7A0.951298.60.212
4aikA0.963498.60.212
3k0lA0.951298.60.213
3hrsA0.926898.60.215
3echA0.951298.60.216
3fm5A0.963498.50.218
4hblA0.951298.50.22

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