GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PGM_PMM_III - Phosphoglucomutasephosphomannomutase alphabetaalpha domain III
Pfam: PF02880 (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: 113
Sequences: 4866
Seq/Len: 43.06
HH_delta: 0.057 (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
57_K60_E1.515773.746
34_D46_R1.391363.438
39_K112_K1.070412.645
45_I57_K1.012012.501
22_T43_K0.995162.459
57_K61_E0.986022.437
11_D40_H0.929372.297
100_K104_E0.763511.887
6_L67_G0.759991.878
34_D38_E0.750891.856
14_L42_G0.743411.837
35_K38_E0.720991.782
100_K108_E0.717461.773
25_V44_V0.681451.684
101_T104_E0.656681.623
11_D105_L0.654851.618
103_S107_D0.651291.610
11_D108_E0.636281.572
37_A42_G0.626991.549
92_L95_L0.622751.539
8_L94_L0.614921.520
11_D15_E0.60691.500
16_E97_E0.585381.447
54_I66_G0.583491.442
34_D44_V0.573631.418
12_Y16_E0.571421.412
15_E98_E0.566551.400
91_L102_L0.565251.397
4_E106_L0.564761.396
58_M63_A0.541471.338
47_T57_K0.539811.334
25_V46_R0.537991.330
9_L75_F0.536961.327
100_K105_L0.535691.324
36_I40_H0.533411.318
50_G68_E0.531061.312
23_V37_A0.524061.295
7_A36_I0.522921.292
65_F73_F0.518261.281
10_A23_V0.5181.280
95_L105_L0.516361.276
45_I61_E0.510061.261
22_T45_I0.50851.257
93_E97_E0.489081.209
72_G82_K0.476931.179
14_L40_H0.476211.177
56_E60_E0.462591.143
32_A109_L0.461821.141
37_A44_V0.458051.132
22_T63_A0.455561.126
29_S33_L0.450481.113
105_L108_E0.447251.105
25_V29_S0.446591.104
12_Y97_E0.443961.097
25_V34_D0.441431.091
8_L106_L0.434631.074
12_Y94_L0.430841.065
11_D36_I0.425431.051
7_A32_A0.42411.048
14_L21_G0.419631.037
55_A74_I0.419621.037
75_F90_L0.4181.033
6_L33_L0.416881.030
53_N56_E0.415371.027
5_L91_L0.402860.996
35_K39_K0.398480.985
22_T61_E0.393710.973
33_L67_G0.389890.964
24_V57_K0.375850.929
48_K53_N0.369420.913
90_L93_E0.367790.909
28_V49_V0.367230.908
73_F87_A0.363580.899
9_L91_L0.363160.897
30_S67_G0.355920.880
64_V77_D0.354710.877
13_L90_L0.351640.869
8_L105_L0.349820.865
36_I39_K0.344650.852
51_F82_K0.331020.818
95_L102_L0.328990.813
8_L102_L0.328980.813
7_A11_D0.32740.809
12_Y93_E0.322690.797
9_L87_A0.322590.797
3_D29_S0.320950.793
7_A30_S0.316440.782
18_K21_G0.315980.781
26_T49_V0.313480.775
14_L37_A0.310020.766
98_E105_L0.309910.766
102_L106_L0.309120.764
10_A42_G0.306130.757
54_I58_M0.305010.754
5_L71_G0.304080.751
38_E43_K0.303510.750
51_F55_A0.302250.747
37_A72_G0.299970.741
28_V82_K0.297250.735
13_L75_F0.295670.731
1_N4_E0.295150.729
8_L108_E0.290620.718
104_E107_D0.28910.714
31_R35_K0.288980.714
10_A33_L0.287920.712
51_F72_G0.286980.709
62_N76_P0.286950.709
106_L109_L0.285510.706
95_L98_E0.281630.696
45_I63_A0.27770.686
93_E96_A0.277690.686
23_V33_L0.275870.682
107_D111_K0.275810.682
11_D109_L0.273550.676
47_T54_I0.271060.670
86_Y90_L0.270790.669
29_S67_G0.268040.662
107_D110_P0.266760.659
33_L44_V0.26460.654
24_V66_G0.264490.654
94_L98_E0.262650.649
59_R74_I0.262080.648
109_L112_K0.259050.640
15_E40_H0.258460.639
11_D112_K0.256380.634
38_E97_E0.256260.633
26_T51_F0.254420.629
75_F87_A0.253750.627
74_I79_S0.249740.617
70_S82_K0.248740.615
65_F75_F0.245980.608
25_V31_R0.245920.608
3_D82_K0.24590.608
50_G70_S0.245070.606
38_E44_V0.245010.605
11_D98_E0.244420.604
26_T82_K0.243930.603
58_M76_P0.243440.602
51_F70_S0.242920.600
2_G26_T0.241930.598
17_H21_G0.240720.595
28_V72_G0.238120.588
67_G70_S0.23810.588
26_T69_E0.238040.588
3_D28_V0.237960.588
68_E72_G0.237650.587
12_Y15_E0.235810.583
20_G63_A0.233570.577
49_V82_K0.233510.577
5_L9_L0.233360.577
3_D30_S0.233150.576
106_L110_P0.232640.575
9_L90_L0.232150.574
88_A92_L0.231490.572
70_S84_G0.231290.572
24_V61_E0.230690.570
52_K79_S0.228560.565
24_V63_A0.228260.564
52_K70_S0.227620.563
79_S86_Y0.227190.561
32_A35_K0.22690.561
95_L103_S0.225940.558
6_L29_S0.225730.558
58_M67_G0.225150.556
69_E72_G0.224570.555
5_L73_F0.224440.555
17_H110_P0.222410.550
28_V69_E0.222110.549
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
1wqaA0.991299.90.057
3pdkA199.90.06
3i3wA0.991299.90.063
2f7lA199.90.064
3na5A199.90.069
1tuoA0.991299.90.07
1p5dX0.991299.90.092
2z0fA199.90.092
3uw2A0.982399.90.095
3pmgA0.982399.90.122

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