GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UB2H - Bifunctional transglycosylase second domain
Pfam: PF14814 (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: 85
Sequences: 3111
Seq/Len: 36.6
HH_delta: 0.088 (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_L68_V1.702113.879
2_Y5_A1.065992.429
58_R74_L0.885732.018
64_S69_S0.870881.985
17_E33_Y0.863891.969
22_R32_E0.834461.902
40_I63_F0.81471.856
42_I61_L0.757981.727
9_P13_E0.722881.647
15_E18_L0.682011.554
1_L68_V0.671211.530
43_Y58_R0.662521.510
29_R32_E0.652181.486
12_L40_I0.651991.486
13_E23_K0.64211.463
62_T72_Q0.639481.457
57_R73_D0.631721.440
12_L63_F0.584511.332
8_S11_Q0.578051.317
11_Q15_E0.575221.311
6_P66_G0.5751.310
35_R40_I0.572031.304
9_P35_R0.56871.296
13_E35_R0.568071.294
62_T70_S0.560771.278
64_S67_R0.51151.166
14_Q18_L0.504281.149
44_T55_P0.495671.130
59_V73_D0.472611.077
15_E19_L0.470231.072
7_L12_L0.465631.061
41_E60_R0.463371.056
38_N62_T0.462221.053
41_E74_L0.441871.007
7_L15_E0.429280.978
55_P73_D0.419750.956
11_Q14_Q0.419140.955
13_E17_E0.413860.943
23_K35_R0.413030.941
27_P74_L0.409720.934
16_L33_Y0.407210.928
4_G67_R0.395820.902
6_P65_G0.390340.889
6_P67_R0.388540.885
37_G60_R0.385670.879
7_L63_F0.381510.869
26_N29_R0.373070.850
34_S41_E0.372420.849
24_V32_E0.364570.831
63_F68_V0.361890.825
13_E40_I0.359540.819
36_S41_E0.35910.818
19_L59_V0.353260.805
8_S14_Q0.349770.797
27_P32_E0.34850.794
10_A14_Q0.346690.790
23_K33_Y0.345930.788
21_Y26_N0.34450.785
7_L68_V0.340630.776
57_R75_D0.33670.767
39_R62_T0.335860.765
36_S58_R0.331070.754
3_P70_S0.329980.752
20_G27_P0.326910.745
55_P59_V0.325870.743
12_L16_L0.325420.742
24_V27_P0.321970.734
43_Y74_L0.319370.728
17_E23_K0.316190.721
10_A13_E0.308150.702
28_D32_E0.303750.692
10_A35_R0.302310.689
36_S60_R0.302220.689
38_N64_S0.29180.665
28_D58_R0.290020.661
22_R57_R0.289820.660
8_S63_F0.286870.654
65_G69_S0.28680.654
36_S39_R0.284970.649
30_P44_T0.280270.639
21_Y44_T0.277220.632
25_S28_D0.272140.620
1_L71_I0.271160.618
1_L12_L0.269850.615
22_R29_R0.268410.612
57_R76_N0.261290.595
2_Y55_P0.256780.585
58_R76_N0.255910.583
38_N70_S0.255850.583
27_P43_Y0.25470.580
1_L7_L0.24920.568
61_L71_I0.249140.568
25_S36_S0.249060.568
7_L11_Q0.248380.566
28_D34_S0.24820.566
27_P36_S0.245520.559
66_G69_S0.241240.550
14_Q17_E0.240430.548
28_D43_Y0.239030.545
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
2eyqA0.905999.80.088
3hjhA0.905999.80.113
1c4oA0.905999.80.139
2d7dA0.917699.70.151
3fwmA199.70.171
3fpnB0.917699.70.179
3reoA0.494130.30.872
2fi0A0.317629.20.873
3p9cA0.470628.70.873
4e70A0.470622.80.879

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