GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GSHPx - Glutathione peroxidase
Pfam: PF00255 (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: CL0172
Length: 108
Sequences: 11163
Seq/Len: 103.36
HH_delta: 0.045 (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
5_S13_P2.058492.913
43_N86_T1.846182.613
5_S15_S1.811552.564
22_K55_E1.774862.512
46_Y50_K1.665582.357
7_K13_P1.612042.281
8_D12_K1.558422.205
15_S18_K1.420512.010
6_A90_F1.271141.799
8_D14_V1.245351.762
72_N91_E1.205571.706
45_L48_K1.165921.650
43_N47_E1.139891.613
46_Y86_T1.105891.565
3_D17_S1.090681.543
24_L55_E1.037451.468
50_K55_E1.013891.435
33_C36_T1.009231.428
17_S20_K1.007131.425
58_A87_F0.998391.413
14_V19_Y0.956091.353
47_E50_K0.950011.344
3_D15_S0.949041.343
7_K72_N0.935061.323
9_I79_C0.919751.302
71_S74_E0.910351.288
76_K80_K0.900971.275
59_F90_F0.900021.274
10_D76_K0.887381.256
30_A75_I0.872581.235
47_E86_T0.859061.216
23_V54_L0.840471.189
58_A89_V0.822351.164
48_K51_D0.798941.131
57_L90_F0.797931.129
55_E88_P0.780881.105
19_Y24_L0.769331.089
19_Y57_L0.757531.072
3_D16_L0.754851.068
73_E77_E0.732321.036
41_Q44_E0.720241.019
77_E81_E0.720231.019
72_N76_K0.717511.015
40_K44_E0.712071.008
14_V18_K0.706661.000
31_S75_I0.695960.985
37_K40_K0.675340.956
40_K43_N0.659680.934
9_I72_N0.658160.931
27_V39_Y0.657740.931
74_E77_E0.653130.924
27_V38_Q0.653070.924
9_I76_K0.649850.920
43_N46_Y0.646590.915
75_I78_F0.640660.907
77_E80_K0.633470.896
43_N87_F0.624810.884
28_N59_F0.620420.878
60_P75_I0.617910.874
46_Y56_I0.613330.868
4_F16_L0.613180.868
29_V58_A0.612870.867
25_L54_L0.600310.850
39_Y85_V0.593670.840
24_L57_L0.593030.839
14_V90_F0.58580.829
42_L56_I0.580690.822
6_A59_F0.570770.808
27_V42_L0.551430.780
48_K52_K0.550340.779
8_D90_F0.548470.776
76_K79_C0.543850.770
49_Y54_L0.539760.764
16_L20_K0.539530.764
50_K53_G0.538720.762
47_E51_D0.536040.759
41_Q45_L0.52490.743
59_F93_I0.524410.742
7_K12_K0.511010.723
46_Y55_E0.510330.722
8_D88_P0.510020.722
31_S35_Y0.5080.719
60_P70_G0.499150.706
45_L49_Y0.498110.705
40_K83_F0.497170.704
31_S83_F0.496640.703
7_K91_E0.492080.696
44_E48_K0.491690.696
20_K25_L0.488130.691
32_K35_Y0.484810.686
25_L42_L0.479370.678
49_Y56_I0.474380.671
16_L24_L0.472220.668
19_Y55_E0.471630.667
20_K24_L0.464710.658
30_A34_G0.463460.656
23_V55_E0.459120.650
70_G74_E0.457140.647
32_K77_E0.444530.629
78_F83_F0.441330.625
73_E76_K0.438860.621
50_K86_T0.437660.619
25_L56_I0.434890.615
71_S75_I0.433310.613
59_F92_K0.431340.610
49_Y52_K0.427460.605
29_V32_K0.427130.604
70_G75_I0.424920.601
79_C89_V0.421360.596
2_Y20_K0.408940.579
37_K81_E0.40470.573
30_A35_Y0.404020.572
32_K70_G0.402990.570
26_I59_F0.400810.567
29_V39_Y0.399710.566
61_C93_I0.399310.565
75_I92_K0.396420.561
29_V75_I0.395820.560
30_A33_C0.391320.554
16_L19_Y0.390360.552
8_D11_G0.38790.549
31_S74_E0.378330.535
27_V35_Y0.375350.531
29_V33_C0.372270.527
23_V53_G0.372220.527
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
2i3yA0.990799.80.045
2r37A0.990799.80.062
2f8aA0.990799.80.098
3dwvA199.80.125
3cmiA0.990799.80.148
3kijA199.80.149
2gs3A0.990799.70.156
2vupA0.990799.70.162
2obiA0.990799.70.168
2p31A199.70.174

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