GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UDPG_MGDP_dh - UDP-glucoseGDP-mannose dehydrogenase family central domain
Pfam: PF00984 (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: CL0106
Length: 96
Sequences: 5434
Seq/Len: 56.6
HH_delta: 0.052 (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
9_Y71_A0.971292.080
73_I87_E0.960722.057
37_Y41_E0.938922.011
77_K87_E0.937122.007
87_E91_N0.936162.005
32_L79_L0.928081.987
82_P87_E0.926281.983
17_T21_F0.910851.950
29_C39_V0.894951.916
35_D38_E0.893931.914
84_Q91_N0.859471.840
10_A25_L0.829031.775
75_L78_E0.821591.759
16_A65_L0.805941.726
38_E41_E0.801361.716
31_K81_Y0.782791.676
88_A91_N0.778741.668
6_L29_C0.752281.611
76_A83_P0.740751.586
16_A69_P0.737831.580
30_E36_V0.734031.572
74_Y77_K0.719451.541
70_Y90_I0.718581.539
74_Y78_E0.70671.513
14_F18_K0.686841.471
17_T89_V0.659641.413
27_R31_K0.658711.411
28_L83_P0.633761.357
40_I44_N0.613191.313
13_A21_F0.60761.301
47_P51_P0.605331.296
18_K22_A0.555731.190
84_Q87_E0.553261.185
10_A29_C0.551261.180
3_E34_I0.545291.168
11_E43_A0.544721.166
20_A85_L0.540111.157
75_L79_L0.532991.141
6_L34_I0.520041.114
14_F25_L0.512611.098
70_Y74_Y0.51261.098
17_T85_L0.508381.089
27_R81_Y0.497681.066
24_E84_Q0.489481.048
13_A86_L0.486141.041
73_I77_K0.485191.039
84_Q88_A0.473041.013
48_R53_Y0.47091.008
61_G64_C0.466160.998
6_L32_L0.465260.996
31_K79_L0.463050.992
29_C36_V0.462790.991
8_K12_N0.459930.985
77_K90_I0.455790.976
47_P52_H0.455110.975
73_I90_I0.453580.971
12_N68_D0.453330.971
69_P86_L0.448020.959
73_I83_P0.444520.952
19_I65_L0.444050.951
28_L76_A0.439910.942
11_E15_R0.43840.939
27_R30_E0.426270.913
66_P90_I0.418680.897
26_A40_I0.413630.886
13_A72_L0.407190.872
20_A92_I0.401710.860
37_Y55_R0.397690.852
85_L88_A0.396720.850
60_F90_I0.390120.835
7_I42_A0.389850.835
7_I38_E0.383680.822
3_E38_E0.381120.816
16_A90_I0.373350.799
50_G53_Y0.372860.798
28_L75_L0.369710.792
5_E46_D0.366750.785
48_R51_P0.362910.777
11_E46_D0.362690.777
88_A92_I0.361720.775
38_E42_A0.355770.762
32_L75_L0.347940.745
9_Y72_L0.347190.743
42_A46_D0.34340.735
14_F43_A0.339510.727
5_E11_E0.326890.700
36_V40_I0.324340.695
10_A28_L0.324330.695
66_P70_Y0.323230.692
4_A11_E0.321810.689
14_F22_A0.319870.685
12_N15_R0.315530.676
10_A14_F0.315460.676
85_L89_V0.313140.671
70_Y73_I0.312140.668
10_A39_V0.311810.668
77_K82_P0.311550.667
12_N67_K0.307790.659
24_E83_P0.307340.658
82_P91_N0.306480.656
12_N64_C0.304560.652
3_E39_V0.304310.652
8_K68_D0.300390.643
47_P50_G0.300020.642
37_Y40_I0.298720.640
60_F70_Y0.294540.631
53_Y56_P0.294010.630
7_I39_V0.290390.622
10_A75_L0.289770.620
17_T86_L0.288360.617
77_K80_G0.287250.615
19_I64_C0.285870.612
22_A49_I0.285640.612
41_E80_G0.282720.605
18_K54_L0.281670.603
15_R19_I0.280470.601
64_C71_A0.27890.597
58_P64_C0.277370.594
55_R58_P0.276430.592
79_L82_P0.276330.592
3_E6_L0.273660.586
74_Y84_Q0.27350.586
15_R46_D0.267610.573
42_A45_T0.26740.573
70_Y77_K0.267190.572
7_I34_I0.265490.569
14_F21_F0.265260.568
26_A29_C0.260740.558
20_A88_A0.259220.555
69_P89_V0.258050.553
60_F64_C0.256260.549
24_E92_I0.251290.538
18_K21_F0.251120.538
23_N57_G0.249620.535
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
4a7pA199.80.052
3g79A199.80.054
3gg2A199.70.063
3ojoA0.947999.70.107
3vtfA199.70.116
3pidA0.979299.70.117
2o3jA199.70.128
1dljA0.979299.60.154
4gbjA0.989699.60.161
3obbA0.979299.60.182

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