GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GIY-YIG - GIY-YIG catalytic domain
Pfam: PF01541 (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: CL0418
Length: 80
Sequences: 4436
Seq/Len: 55.45
HH_delta: 0.166 (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
55_E66_L1.271992.910
19_S64_L1.132292.590
25_K29_E0.959062.194
68_Q72_K0.935622.140
22_N25_K0.87462.001
66_L69_Y0.845681.935
2_Y19_S0.811851.857
8_Y50_E0.758251.735
6_I70_L0.754731.726
28_N32_S0.753881.725
17_I70_L0.738761.690
6_I17_I0.718221.643
9_N13_K0.698321.597
57_F66_L0.698131.597
59_T62_E0.680871.557
60_K64_L0.66971.532
7_I27_L0.662581.516
4_I70_L0.617971.414
38_K41_Q0.592121.354
8_Y52_I0.576091.318
16_Y26_R0.566791.297
7_I46_W0.555981.272
8_Y12_N0.549581.257
36_S40_K0.548851.256
3_G20_T0.539731.235
23_L54_I0.526761.205
8_Y14_K0.5221.194
31_F49_F0.518081.185
19_S60_K0.514461.177
69_Y73_K0.508291.163
61_S65_K0.502641.150
27_L31_F0.502621.150
46_W49_F0.479751.097
58_N62_E0.468031.071
26_R67_E0.466851.068
65_K69_Y0.451571.033
21_K60_K0.44291.013
37_K40_K0.438891.004
4_I17_I0.432260.989
2_Y60_K0.416450.953
14_K74_L0.416240.952
18_G26_R0.407480.932
53_I66_L0.40580.928
3_G23_L0.391470.895
26_R30_H0.389610.891
6_I53_I0.388030.888
3_G56_E0.385490.882
34_N37_K0.37830.865
18_G67_E0.377990.865
69_Y72_K0.377810.864
24_K28_N0.37470.857
6_I15_I0.372430.852
31_F47_D0.365890.837
16_Y30_H0.360910.826
8_Y48_N0.360290.824
5_Y30_H0.359680.823
13_K38_K0.354010.810
20_T23_L0.351380.804
2_Y21_K0.345150.790
7_I49_F0.343340.785
4_I19_S0.34210.783
59_T63_A0.340880.780
36_S41_Q0.340770.780
35_K40_K0.339110.776
59_T64_L0.33630.769
9_N48_N0.330110.755
70_L74_L0.329930.755
41_Q47_D0.326780.748
57_F62_E0.324240.742
5_Y16_Y0.318070.728
25_K28_N0.312020.714
32_S37_K0.310620.711
3_G54_I0.308460.706
12_N51_F0.307180.703
20_T31_F0.298850.684
19_S29_E0.291350.666
20_T30_H0.290860.665
13_K75_K0.290030.663
3_G27_L0.287940.659
33_G36_S0.286720.656
2_Y20_T0.28660.656
10_K47_D0.284560.651
11_D46_W0.278930.638
32_S75_K0.278860.638
6_I52_I0.278470.637
10_K49_F0.278450.637
37_K41_Q0.277040.634
36_S39_K0.276870.633
61_S64_L0.275950.631
9_N15_I0.275210.630
12_N48_N0.27360.626
8_Y13_K0.26850.614
12_N49_F0.268360.614
17_I73_K0.267380.612
61_S68_Q0.266520.610
7_I30_H0.266450.610
6_I55_E0.264380.605
9_N12_N0.263880.604
32_S35_K0.263710.603
66_L72_K0.261530.598
17_I74_L0.257650.589
2_Y63_A0.257530.589
41_Q51_F0.257490.589
33_G47_D0.257280.589
37_K61_S0.257210.588
34_N46_W0.257120.588
21_K25_K0.254660.583
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
1mk0A0.987599.30.166
1yd6A0.9599.20.206
1yd0A0.92599.20.214
2wshA0.97598.90.304
1zg2A0.937598.80.328
1ywlA0.962598.80.328
2lwfA0.87597.50.563
3mx1A0.937596.20.643
2o8rA0.819.70.84
1xdpA0.962512.10.854

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