GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PGM_PMM_II - Phosphoglucomutasephosphomannomutase alphabetaalpha domain II
Pfam: PF02879 (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: 104
Sequences: 5392
Seq/Len: 51.85
HH_delta: -0.014 (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
33_G94_A1.800983.853
78_I82_S1.643193.515
25_V84_A1.618113.462
77_K81_E1.196732.560
23_K47_D1.182352.530
78_I81_E1.146772.453
8_L43_R1.050762.248
76_I80_R0.985442.108
50_E53_C0.916161.960
39_R43_R0.915341.958
23_K49_I0.914781.957
25_V78_I0.888431.901
79_V87_G0.854191.827
52_N74_R0.822141.759
73_Q77_K0.802151.716
28_C53_C0.735151.573
4_I40_L0.728981.560
49_I82_S0.712741.525
26_V90_F0.711441.522
57_P60_P0.684631.465
38_P53_C0.65461.400
33_G90_F0.649061.389
6_S10_F0.647311.385
38_P42_E0.632011.352
75_L100_V0.621011.329
24_I86_L0.618141.322
91_D95_D0.601951.288
75_L89_A0.597011.277
22_L85_D0.588361.259
37_L90_F0.58261.246
73_Q76_I0.57831.237
5_E9_S0.573941.228
5_E43_R0.573211.226
75_L87_G0.569221.218
91_D96_R0.565211.209
74_R77_K0.554651.187
6_S9_S0.539521.154
77_K80_R0.536021.147
8_L44_L0.526951.127
88_I99_V0.516721.105
72_L98_G0.507931.087
79_V100_V0.506261.083
34_S38_P0.50391.078
30_N52_N0.497751.065
74_R78_I0.495051.059
11_I17_I0.490771.050
35_D39_R0.480981.029
34_S53_C0.478081.023
76_I100_V0.476911.020
93_D96_R0.471241.008
26_V33_G0.469081.004
39_R42_E0.465990.997
51_L74_R0.460540.985
51_L78_I0.45890.982
27_D75_L0.458840.982
2_A5_E0.458650.981
80_R83_G0.456650.977
4_I43_R0.455350.974
52_N61_N0.453410.970
42_E50_E0.443620.949
4_I36_I0.43290.926
12_D17_I0.424170.907
23_K82_S0.415550.889
63_H67_P0.405570.868
63_H66_N0.405430.867
49_I84_A0.402930.862
3_Y7_L0.400570.857
72_L89_A0.399730.855
86_L99_V0.394140.843
4_I39_R0.391380.837
41_L46_C0.390860.836
56_D60_P0.389930.834
26_V37_L0.385220.824
75_L79_V0.383840.821
4_I8_L0.376640.806
11_I44_L0.375850.804
72_L87_G0.371730.795
25_V51_L0.371330.794
49_I78_I0.367540.786
87_G100_V0.364580.780
31_G94_A0.362070.775
56_D63_H0.357440.765
5_E8_L0.357190.764
25_V87_G0.353740.757
25_V49_I0.352640.754
23_K83_G0.351990.753
2_A6_S0.345250.739
70_E73_Q0.339440.726
23_K85_D0.338690.725
34_S55_P0.337270.722
29_M92_G0.337110.721
37_L45_G0.336520.720
26_V41_L0.333120.713
89_A98_G0.332790.712
80_R103_N0.330910.708
17_I20_S0.328830.704
88_I97_L0.325040.695
64_A67_P0.319440.683
37_L41_L0.316910.678
41_L48_V0.313530.671
27_D52_N0.312350.668
63_H69_E0.304750.652
40_L44_L0.303640.650
30_N61_N0.302960.648
72_L100_V0.30290.648
89_A100_V0.301570.645
47_D82_S0.301050.644
7_L40_L0.292310.625
25_V82_S0.291440.624
25_V75_L0.288730.618
30_N55_P0.287070.614
51_L77_K0.28460.609
64_A69_E0.283250.606
79_V84_A0.281910.603
59_F67_P0.281280.602
24_I46_C0.28020.599
12_D19_K0.277430.594
71_S76_I0.274450.587
30_N63_H0.271190.580
27_D87_G0.267850.573
7_L99_V0.265220.567
38_P50_E0.263770.564
21_G45_G0.262760.562
61_N66_N0.262110.561
19_K47_D0.260970.558
36_I39_R0.259650.556
90_F94_A0.256780.549
32_A55_P0.256310.548
21_G47_D0.256160.548
69_E76_I0.255340.546
33_G92_G0.253720.543
32_A98_G0.250780.537
28_C34_S0.250010.535
92_G96_R0.249540.534
92_G95_D0.248350.531
5_E42_E0.247760.530
59_F65_P0.247270.529
18_K21_G0.24690.528
89_A93_D0.246540.527
28_C90_F0.24650.527
70_E98_G0.244020.522
78_I84_A0.243130.520
27_D89_A0.242090.518
80_R84_A0.24150.517
2_A43_R0.239130.512
66_N69_E0.238490.510
63_H71_S0.238270.510
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
2f7lA0.980899.9-0.014
1tuoA0.980899.9-0.005
1wqaA0.980899.9-0.003
3uw2A0.942399.80.021
3pmgA0.980899.80.022
1kfiA0.971299.80.033
1p5dX0.942399.80.037
3pdkA0.932799.80.068
3na5A0.951999.80.078
3i3wA0.942399.80.087

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