GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HMA - Heavy-metal-associated domain
Pfam: PF00403 (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: 62
Sequences: 9552
Seq/Len: 154.06
HH_delta: -0.168 (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_C12_C2.37193.179
5_P62_E1.848582.478
17_E21_S1.715692.300
13_A33_L1.608112.156
48_S51_K1.529552.050
28_S41_T1.449611.943
23_L55_A1.283711.721
32_D35_T1.281941.718
19_A59_A1.235261.656
20_L38_V1.227691.646
4_V38_V1.084621.454
27_K41_T1.051481.409
19_A55_A1.023071.371
43_D46_K1.008331.352
5_P36_K1.006661.349
50_E54_E0.93291.250
57_E62_E0.917361.230
49_I53_I0.909041.218
56_I62_E0.898321.204
13_A17_E0.89821.204
6_G62_E0.84141.128
4_V7_M0.840921.127
21_S29_V0.827251.109
7_M33_L0.826591.108
30_K39_T0.810951.087
10_E13_A0.806441.081
11_G15_K0.802811.076
19_A23_L0.800551.073
42_Y48_S0.791841.061
8_T11_G0.791351.061
16_V56_I0.791311.061
7_M31_V0.789581.058
31_V38_V0.78381.051
53_I57_E0.78091.047
27_K43_D0.775391.039
14_K18_K0.764291.024
55_A59_A0.755181.012
51_K54_E0.747161.002
23_L51_K0.725250.972
13_A31_V0.720260.965
8_T15_K0.715950.960
32_D39_T0.704040.944
42_Y46_K0.70230.941
20_L29_V0.696660.934
10_E14_K0.696040.933
11_G14_K0.680580.912
12_C61_Y0.661690.887
3_K36_K0.661320.886
40_V52_I0.653280.876
2_F53_I0.632830.848
10_E34_E0.626580.840
54_E58_K0.610910.819
7_M16_V0.602550.808
38_V56_I0.600410.805
21_S28_S0.595250.798
15_K19_A0.593110.795
17_E31_V0.580890.779
26_V29_V0.571340.766
20_L26_V0.564520.757
51_K55_A0.560030.751
7_M36_K0.543170.728
17_E29_V0.520920.698
26_V52_I0.520270.697
42_Y49_I0.504080.676
2_F38_V0.500830.671
32_D37_T0.490890.658
42_Y52_I0.48850.655
33_L36_K0.470590.631
49_I52_I0.469560.629
54_E57_E0.465480.624
35_T39_T0.460250.617
7_M13_A0.456140.611
15_K59_A0.455090.610
6_G36_K0.450840.604
50_E53_I0.449610.603
15_K61_Y0.442640.593
15_K18_K0.436440.585
17_E30_K0.428220.574
24_P46_K0.425010.570
20_L56_I0.422580.566
13_A32_D0.415420.557
34_E37_T0.411560.552
3_K39_T0.407110.546
16_V38_V0.403490.541
29_V38_V0.401820.539
8_T33_L0.401780.539
20_L52_I0.397980.533
10_E33_L0.396320.531
16_V31_V0.371740.498
48_S52_I0.369630.495
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
3j09A197.9-0.168
3dxsX197.7-0.136
1p6tA197.6-0.105
2ew9A197.6-0.102
4a4jA0.983997.6-0.097
2ropA197.6-0.097
2ofgX197.5-0.079
2g9oA197.4-0.06
3fryA0.919497.4-0.05
1q8lA197.3-0.046

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