GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Amidohydro_5 - Amidohydrolase
Pfam: PF13594 (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: CL0034
Length: 68
Sequences: 8785
Seq/Len: 129.19
HH_delta: -0.026 (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
4_E9_V2.517774.275
35_G66_T2.083083.537
1_V32_V1.543132.620
38_D41_T1.263592.145
33_M36_F1.198222.035
60_A68_V1.091941.854
27_A32_V1.089311.850
37_I67_T1.029011.747
54_E58_A1.002271.702
36_F65_V0.977971.661
2_L10_A0.966321.641
60_A63_G0.924311.569
43_L56_E0.88861.509
12_G15_S0.876681.489
41_T68_V0.813691.382
2_L9_V0.812961.380
57_A68_V0.801361.361
48_W51_L0.776181.318
57_A61_L0.741231.259
1_V11_V0.735631.249
2_L22_A0.719281.221
39_M44_G0.718181.219
56_E59_A0.707681.202
51_L56_E0.689051.170
27_A30_K0.67081.139
43_L68_V0.662891.126
50_S53_P0.650231.104
19_A22_A0.642441.091
44_G48_W0.641741.090
2_L21_A0.632731.074
55_T59_A0.619031.051
59_A63_G0.591461.004
52_D56_E0.573770.974
65_V68_V0.567520.964
58_A62_A0.55910.949
60_A65_V0.55830.948
41_T60_A0.555190.943
53_P65_V0.548050.931
59_A62_A0.527150.895
1_V8_I0.515990.876
49_Q55_T0.515040.875
43_L57_A0.507910.862
41_T50_S0.507860.862
50_S57_A0.499950.849
43_L63_G0.498730.847
44_G50_S0.494620.840
3_I8_I0.485860.825
21_A24_V0.484780.823
8_I11_V0.483760.821
20_D24_V0.476950.810
47_G50_S0.469520.797
43_L65_V0.441450.750
58_A61_L0.43710.742
3_I9_V0.433950.737
49_Q52_D0.429630.729
55_T58_A0.420870.715
47_G51_L0.418060.710
3_I6_G0.415160.705
39_M43_L0.412780.701
25_I29_G0.410450.697
36_F43_L0.408620.694
49_Q59_A0.407590.692
48_W52_D0.404650.687
2_L15_S0.403870.686
10_A15_S0.400070.679
51_L57_A0.395990.672
26_D29_G0.395740.672
33_M42_H0.385560.655
44_G47_G0.383970.652
39_M49_Q0.372980.633
2_L12_G0.371870.631
56_E63_G0.371410.631
41_T59_A0.371370.631
14_D20_D0.370850.630
44_G60_A0.365280.620
24_V28_K0.365040.620
43_L60_A0.358570.609
52_D55_T0.356110.605
39_M42_H0.353170.600
39_M59_A0.348590.592
35_G67_T0.346240.588
56_E60_A0.338590.575
41_T65_V0.332490.565
37_I63_G0.332110.564
26_D30_K0.331250.562
49_Q53_P0.331240.562
2_L6_G0.328690.558
44_G56_E0.326860.555
44_G49_Q0.326550.554
15_S18_P0.324880.552
40_H43_L0.322460.548
15_S19_A0.318950.542
25_I28_K0.318930.542
57_A63_G0.315820.536
33_M63_G0.312750.531
4_E22_A0.311760.529
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
4b90A0.985399.4-0.026
4b91A0.985399.30.039
4bknA0.985399.30.041
1e9yB0.882499.30.052
3gnhA199.30.054
2vunA199.30.055
2vm8A0.985399.30.055
2ftwA0.985399.30.059
2vr2A0.985399.30.063
3dc8A0.941299.30.065

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