GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
G5 - G5 domain
Pfam: PF07501 (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: 79
Sequences: 1167
Seq/Len: 14.77
HH_delta: -0.092 (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
22_D74_E1.175643.274
54_E57_R1.055432.939
33_V74_E0.962432.680
18_I70_P0.902822.514
34_Q72_I0.894332.491
12_E38_P0.824012.295
41_K62_E0.777222.164
17_T71_R0.697141.941
19_Y75_V0.691951.927
10_E40_E0.682071.899
37_Q66_K0.65881.835
42_T65_Y0.640231.783
45_Y59_L0.6311.757
20_I33_V0.619741.726
26_P29_E0.618451.722
47_V57_R0.577211.607
19_Y30_E0.575671.603
50_V55_V0.574841.601
31_K74_E0.57361.597
16_E70_P0.557941.554
47_V54_E0.555371.547
43_V59_L0.538831.501
11_E41_K0.535951.493
21_E77_T0.529321.474
42_T63_E0.52661.467
27_P77_T0.520471.449
46_R58_E0.493261.374
34_Q69_V0.490291.365
49_Y54_E0.477431.330
46_R60_I0.476511.327
35_E71_R0.471451.313
14_P38_P0.445011.239
40_E66_K0.43461.210
45_Y57_R0.432231.204
43_V62_E0.411241.145
44_T61_S0.400491.115
32_V73_I0.390941.089
21_E75_V0.383311.067
37_Q69_V0.380911.061
10_E42_T0.372521.037
15_Y71_R0.366991.022
9_E45_Y0.353240.984
20_I74_E0.352050.980
26_P78_K0.340010.947
15_Y38_P0.338440.943
40_E65_Y0.3340.930
32_V71_R0.331460.923
8_T42_T0.319980.891
32_V35_E0.316220.881
22_D31_K0.304360.848
25_L29_E0.296430.826
13_I41_K0.28420.791
22_D25_L0.284070.791
25_L28_G0.283190.789
23_P77_T0.280490.781
15_Y68_P0.275910.768
17_T73_I0.268920.749
27_P78_K0.267260.744
11_E43_V0.261790.729
48_V56_S0.255750.712
41_K64_V0.254570.709
15_Y70_P0.245760.684
22_D33_V0.245390.683
15_Y36_G0.245090.683
50_V53_K0.240910.671
13_I36_G0.238860.665
18_I72_I0.238310.664
36_G71_R0.220530.614
8_T44_T0.215850.601
30_E75_V0.205250.572
7_V47_V0.198450.553
30_E71_R0.194050.540
25_L31_K0.190870.532
25_L30_E0.190790.531
59_L62_E0.188990.526
12_E40_E0.187890.523
18_I34_Q0.185540.517
17_T36_G0.184380.513
34_Q71_R0.182750.509
25_L74_E0.181330.505
19_Y73_I0.180350.502
22_D78_K0.178230.496
13_I17_T0.176350.491
11_E45_Y0.170850.476
38_P66_K0.168640.470
34_Q70_P0.168140.468
7_V57_R0.162130.452
48_V58_E0.161230.449
20_I72_I0.154950.432
23_P26_P0.151620.422
44_T60_I0.151260.421
7_V10_E0.150880.420
23_P27_P0.150330.419
16_E66_K0.149460.416
36_G39_G0.146910.409
21_E64_V0.145950.406
28_G77_T0.144920.404
13_I32_V0.14310.399
45_Y60_I0.143010.398
41_K65_Y0.142630.397
26_P46_R0.141650.394
39_G68_P0.140510.391
48_V55_V0.13950.388
25_L76_G0.139130.387
10_E59_L0.138060.384
8_T47_V0.137910.384
58_E68_P0.136450.380
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
3eo5A199.5-0.092
3tipA199.40.013
4fzqA0.987399.30.017
4fuoA199.30.045
2ltjA0.987399.30.047
3tiqA199.20.083
4fuoA0.987399.20.085
3tiqA0.987399.20.11
3tipA0.683595.70.613
2ae0X0.974727.10.806

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