GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Thr_dehydrat_C - C-terminal regulatory domain of Threonine dehydratase
Pfam: PF00585 (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: CL0070
Length: 91
Sequences: 5377
Seq/Len: 59.09
HH_delta: 0.268 (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
65_E69_E0.881552.285
68_I72_K0.858542.226
34_R70_R0.78112.025
17_F23_A0.745521.933
20_R26_R0.707051.833
38_T57_E0.697971.809
10_E38_T0.65181.690
14_A53_L0.624811.620
29_D33_P0.606851.573
30_A74_L0.602141.561
70_R73_A0.592371.536
25_K29_D0.564081.462
16_E77_P0.546291.416
34_R66_E0.538671.396
15_V27_F0.534881.387
23_A26_R0.526631.365
10_E57_E0.524021.358
60_D63_D0.523551.357
25_K32_G0.514891.335
33_P70_R0.514061.333
24_L40_F0.510981.325
26_R74_L0.493351.279
24_L28_L0.480111.245
69_E73_A0.478731.241
13_F68_I0.47411.229
72_K77_P0.473891.229
66_E69_E0.47241.225
17_F52_V0.462981.200
12_L55_G0.458171.188
69_E72_K0.456041.182
22_G36_N0.447371.160
16_E49_F0.443581.150
14_A81_L0.436261.131
18_P76_Y0.419481.087
66_E70_R0.415951.078
26_R30_A0.409181.061
58_V64_L0.408591.059
20_R23_A0.408091.058
19_E36_N0.406481.054
28_L37_I0.400181.037
31_L52_V0.396791.029
30_A70_R0.386641.002
27_F54_V0.386511.002
19_E50_A0.381010.988
11_A80_D0.379090.983
59_P63_D0.377380.978
62_E65_E0.370040.959
42_Y50_A0.369540.958
42_Y52_V0.365930.949
62_E66_E0.363660.943
31_L56_I0.359210.931
19_E22_G0.358660.930
72_K78_Y0.358320.929
28_L52_V0.350350.908
31_L54_V0.350310.908
26_R29_D0.345270.895
61_A65_E0.343560.891
10_E55_G0.343010.889
19_E48_D0.339510.880
17_F27_F0.337630.875
68_I78_Y0.327510.849
25_K28_L0.326870.847
58_V63_D0.326470.846
63_D66_E0.324920.842
49_F54_V0.323870.840
16_E51_R0.323740.839
24_L36_N0.323360.838
56_I67_L0.321430.833
40_F54_V0.319460.828
65_E72_K0.30840.800
27_F52_V0.306040.793
17_F50_A0.301540.782
39_E55_G0.299020.775
21_P24_L0.296870.770
17_F24_L0.291240.755
48_D51_R0.283690.735
41_H55_G0.281730.730
27_F74_L0.281340.729
30_A33_P0.276890.718
70_R74_L0.275520.714
33_P73_A0.271730.704
14_A79_E0.269950.700
12_L53_L0.269540.699
68_I80_D0.267070.692
31_L34_R0.266870.692
64_L68_I0.265420.688
18_P39_E0.265340.688
64_L80_D0.26460.686
65_E68_I0.263590.683
13_F71_L0.262670.681
40_F52_V0.259250.672
62_E79_E0.258030.669
64_L78_Y0.254570.660
9_R60_D0.250880.650
50_A56_I0.250610.650
16_E79_E0.250160.649
43_R52_V0.248230.644
44_Y52_V0.247260.641
11_A64_L0.247140.641
18_P40_F0.246620.639
10_E18_P0.245760.637
39_E42_Y0.244990.635
9_R61_A0.242440.629
51_R61_A0.241120.625
31_L71_L0.237580.616
37_I42_Y0.237060.615
13_F64_L0.23330.605
15_V78_Y0.232690.603
14_A51_R0.231580.600
41_H81_L0.22990.596
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
1tdjA0.989990.268
1tdjA0.96798.40.431
1zpvA0.9341980.506
2ko1A0.923197.90.511
2f1fA0.901197.60.555
2pc6A0.912197.60.556
2lvwA0.945197.60.558
1y7pA0.890197.50.569
2fgcA0.98997.30.589
2qmxA0.97897.10.604

Page generated in 0.0391 seconds.