GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GYF - GYF domain
Pfam: PF02213 (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: 57
Sequences: 820
Seq/Len: 14.39
HH_delta: 0.149 (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
37_R41_D0.503992.300
24_W29_Y0.47792.181
5_Y16_F0.412721.883
17_S20_Q0.407171.858
18_S21_M0.367891.679
5_Y24_W0.329741.505
8_P34_L0.31241.425
16_F24_W0.294211.342
37_R44_F0.292891.336
22_Q26_K0.290781.327
12_I37_R0.283281.293
4_Y39_V0.276831.263
6_K12_I0.274861.254
7_D13_Q0.273981.250
30_F34_L0.268721.226
25_Y48_F0.260851.190
26_K32_D0.259431.184
16_F29_Y0.256011.168
16_F30_F0.25551.166
3_W21_M0.254221.160
18_S22_Q0.250981.145
35_Q47_P0.246751.126
46_D50_S0.244611.116
49_G52_D0.234531.070
21_M25_Y0.23361.066
13_Q16_F0.232921.063
6_K35_Q0.23251.061
47_P50_S0.231651.057
37_R40_D0.225491.029
4_Y37_R0.217190.991
38_R51_I0.216610.988
9_D13_Q0.207460.947
6_K10_G0.202140.922
25_Y34_L0.199860.912
4_Y44_F0.198930.908
24_W30_F0.19860.906
20_Q52_D0.196160.895
2_M38_R0.19380.884
12_I42_T0.191830.875
33_D43_Q0.191620.874
13_Q24_W0.189760.866
41_D46_D0.189190.863
7_D34_L0.183460.837
21_M36_V0.181390.828
40_D43_Q0.180670.824
36_V51_I0.179630.820
23_A39_V0.177930.812
10_G13_Q0.175770.802
38_R41_D0.174640.797
27_Q39_V0.173810.793
23_A26_K0.173430.791
7_D11_N0.168380.768
23_A27_Q0.167220.763
11_N47_P0.166250.759
21_M34_L0.16480.752
39_V44_F0.162530.742
2_M17_S0.160580.733
40_D44_F0.160520.732
41_D44_F0.159920.730
16_F21_M0.158910.725
5_Y13_Q0.158220.722
22_Q37_R0.157870.720
6_K17_S0.157060.717
19_E23_A0.156570.714
3_W47_P0.156280.713
46_D52_D0.154660.706
10_G35_Q0.15440.705
9_D27_Q0.154360.704
13_Q29_Y0.151620.692
26_K36_V0.150720.688
10_G49_G0.149620.683
7_D16_F0.14850.678
20_Q23_A0.147710.674
20_Q26_K0.14520.663
33_D49_G0.144350.659
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
1wh2A0.964999.10.149
3k3vA0.982599.10.163
1syxB0.964998.90.222
2iukA0.877217.70.823
2iujA0.877217.20.824
1f8nA0.877216.10.826
1loxA0.87727.60.848
3rdeA0.87727.60.848
3d3lA0.87727.30.849
3v98A0.87726.70.852

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