GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PGM_PMM_IV - Phosphoglucomutasephosphomannomutase C-terminal domain
Pfam: PF00408 (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: 73
Sequences: 2888
Seq/Len: 39.56
HH_delta: 0.103 (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_A61_L1.133882.683
58_E62_E1.071462.535
34_D56_P1.069392.530
66_E70_E0.795591.882
62_E66_E0.787511.863
27_G64_I0.762461.804
4_V69_A0.751141.777
11_K14_E0.725031.715
2_I66_E0.708941.677
16_E20_K0.69711.649
53_V65_A0.682191.614
60_E63_E0.681921.613
46_E50_R0.678071.604
57_D60_E0.670471.586
60_E64_I0.612091.448
64_I67_E0.606911.436
30_I67_E0.600651.421
3_N48_K0.597991.415
4_V73_K0.58481.384
2_I69_A0.580791.374
25_I28_I0.57381.357
24_T40_V0.572141.354
65_A69_A0.558091.320
70_E73_K0.54581.291
63_E67_E0.532751.260
8_E11_K0.512051.211
69_A73_K0.506961.199
21_A26_D0.480771.137
34_D60_E0.475221.124
17_D20_K0.474461.122
59_E63_E0.468071.107
30_I63_E0.458231.084
16_E24_T0.45681.081
25_I29_K0.443031.048
5_K46_E0.435441.030
67_E71_A0.434351.028
6_V9_K0.423521.002
30_I64_I0.417520.988
2_I65_A0.414910.982
42_P49_I0.411990.975
12_I42_P0.409130.968
61_L65_A0.406080.961
26_D30_I0.399270.945
37_R68_I0.398010.942
8_E12_I0.386410.914
13_K17_D0.382390.905
66_E73_K0.378230.895
3_N46_E0.372070.880
44_G52_Y0.367180.869
51_V69_A0.367140.869
35_G38_L0.360070.852
36_W54_E0.359510.851
37_R53_V0.354360.838
24_T28_I0.351930.833
40_V49_I0.350920.830
5_K48_K0.35050.829
10_K42_P0.348510.824
26_D29_K0.347170.821
37_R52_Y0.344470.815
5_K47_P0.33980.804
2_I73_K0.334980.792
27_G67_E0.324240.767
10_K13_K0.323810.766
11_K15_L0.322180.762
3_N51_V0.319050.755
13_K16_E0.318780.754
53_V68_I0.310170.734
20_K26_D0.309150.731
6_V11_K0.306740.726
40_V68_I0.305170.722
38_L52_Y0.302110.715
24_T31_L0.299410.708
52_Y68_I0.298750.707
30_I60_E0.298310.706
29_K52_Y0.295760.700
27_G30_I0.292070.691
9_K42_P0.291690.690
67_E70_E0.287760.681
49_I72_I0.287730.681
46_E53_V0.285180.675
61_L64_I0.284440.673
6_V12_I0.281820.667
26_D67_E0.281510.666
32_F37_R0.276930.655
17_D21_A0.266840.631
35_G57_D0.265720.629
3_N50_R0.262770.622
3_N52_Y0.259970.615
17_D71_A0.259350.614
62_E65_A0.256090.606
6_V10_K0.255160.604
66_E69_A0.254520.602
37_R64_I0.248120.587
57_D61_L0.245660.581
52_Y65_A0.243610.576
44_G50_R0.243440.576
4_V51_V0.2410.570
5_K73_K0.236730.560
24_T37_R0.236320.559
21_A67_E0.236320.559
51_V65_A0.236160.559
19_F24_T0.236040.558
21_A27_G0.235980.558
44_G51_V0.235210.556
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
3uw2A0.986399.60.103
4bjuA0.986399.50.131
1p5dX0.986399.50.156
2dkaA0.986399.50.165
2f7lA0.986399.50.171
1wjwA0.986399.50.174
3i3wA0.958999.40.175
1wqaA0.986399.40.177
1tuoA0.986399.40.179
3pdkA0.945299.40.185

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