GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cellulase-like - Sugar-binding cellulase-like
Pfam: PF12876 (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: CL0058
Length: 88
Sequences: 2844
Seq/Len: 32.32
HH_delta: 0.232 (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
61_T82_V0.77512.618
50_W54_V0.69992.364
55_D58_Q0.695712.350
50_W53_A0.686612.319
45_K49_R0.686072.317
52_R60_V0.640262.162
63_G86_H0.578191.953
48_F60_V0.559141.888
13_A82_V0.554461.873
14_W55_D0.510111.723
45_K79_N0.505381.707
48_F52_R0.505281.706
15_D86_H0.479071.618
11_I14_W0.462371.562
39_A42_E0.453321.531
49_R53_A0.448011.513
48_F80_L0.441581.491
62_S80_L0.421271.423
40_Y44_L0.38191.290
52_R81_D0.374931.266
36_K39_A0.349771.181
15_D84_S0.349081.179
51_I58_Q0.34131.153
16_L60_V0.331571.120
17_W43_W0.329641.113
71_D76_Q0.325441.099
15_D61_T0.322531.089
43_W47_A0.322461.089
42_E45_K0.317691.073
48_F79_N0.315121.064
46_E49_R0.306911.037
41_A45_K0.301621.019
7_Y57_S0.290630.982
47_A50_W0.28480.962
13_A59_P0.278760.941
49_R79_N0.2740.925
16_L47_A0.273370.923
38_E74_Q0.270610.914
59_P82_V0.26660.900
42_E46_E0.2660.898
72_L75_L0.265330.896
17_W21_P0.263450.890
53_A56_P0.262470.886
41_A74_Q0.260630.880
57_S74_Q0.258730.874
39_A70_E0.257260.869
14_W58_Q0.256270.866
46_E78_E0.252840.854
17_W44_L0.252240.852
17_W86_H0.246840.834
46_E50_W0.245960.831
12_L59_P0.244820.827
51_I60_V0.244420.825
44_L79_N0.244210.825
72_L76_Q0.241930.817
12_L82_V0.239660.809
54_V58_Q0.238610.806
8_D63_G0.234570.792
62_S83_I0.231330.781
6_G55_D0.229780.776
38_E42_E0.229130.774
41_A78_E0.228980.773
37_A68_D0.228860.773
22_N65_W0.227360.768
43_W88_Y0.225630.762
48_F62_S0.224890.760
17_W84_S0.222140.750
15_D88_Y0.220860.746
42_E50_W0.220320.744
44_L48_F0.220020.743
7_Y10_R0.219840.742
17_W47_A0.216030.730
17_W41_A0.21350.721
55_D85_F0.213390.721
71_D75_L0.212670.718
11_I81_D0.212630.718
48_F51_I0.207090.699
16_L51_I0.206250.697
11_I40_Y0.205180.693
17_W40_Y0.20370.688
19_E86_H0.203420.687
38_E70_E0.203070.686
38_E71_D0.202910.685
21_P52_R0.201450.680
23_N67_G0.2010.679
19_E88_Y0.200370.677
49_R52_R0.200250.676
16_L62_S0.198490.670
76_Q79_N0.195480.660
6_G40_Y0.194850.658
61_T84_S0.194220.656
66_G83_I0.192980.652
21_P44_L0.192810.651
69_W85_F0.188190.636
15_D65_W0.187850.634
38_E73_E0.187550.633
15_D87_P0.183960.621
62_S75_L0.183520.620
75_L79_N0.183230.619
24_W83_I0.18290.618
62_S66_G0.182350.616
75_L85_F0.181770.614
21_P65_W0.180760.610
41_A79_N0.180160.608
17_W22_N0.179920.608
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
4aweA0.988699.40.232
3zizA0.886499.30.243
1uuqA0.943299.30.252
3pzgA0.897799.30.264
1qnrA0.886499.20.283
1rh9A0.897799.20.296
2c0hA0.988699.20.303
3lpfA0.840999.20.316
4ekjA0.931899.10.319
3hn3A0.818299.10.325

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