GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
z-alpha - Adenosine deaminase z-alpha domain
Pfam: PF02295 (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: CL0123
Length: 66
Sequences: 50649
Seq/Len: 767.41
HH_delta: 0.039 (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
12_F27_A3.006032.331
20_T23_A2.591052.009
45_E52_K2.262571.755
6_E40_V2.177391.689
25_A34_K2.166691.680
6_E47_Q2.164011.678
31_S35_K2.125681.649
6_E43_R1.976231.533
12_F16_L1.900031.474
5_L40_V1.846351.432
16_L19_S1.745041.353
21_A38_N1.731811.343
52_K58_P1.691741.312
38_N42_Y1.665021.291
43_R47_Q1.649951.280
21_A34_K1.623561.259
31_S36_E1.594691.237
35_K38_N1.589791.233
10_L49_K1.585721.230
22_T26_K1.501551.165
23_A27_A1.490411.156
9_I40_V1.474631.144
12_F19_S1.471811.141
19_S27_A1.454591.128
41_L60_W1.425081.105
8_K12_F1.414921.097
22_T34_K1.382391.072
19_S23_A1.381781.072
12_F28_L1.362741.057
42_Y45_E1.334021.035
42_Y46_K1.321771.025
35_K39_R1.30211.010
16_L27_A1.296871.006
25_A37_V1.283210.995
18_G59_K1.282530.995
30_L37_V1.273060.987
45_E50_V1.267890.983
18_G53_E1.263510.980
34_K38_N1.210770.939
20_T57_P1.207850.937
12_F15_E1.20560.935
7_E11_D1.186530.920
9_I37_V1.124120.872
5_L8_K1.115490.865
30_L36_E1.110810.861
39_R42_Y1.10350.856
21_A60_W1.10220.855
10_L14_K1.082530.840
24_I37_V1.08140.839
5_L30_L1.060960.823
36_E39_R1.056730.820
39_R43_R1.052020.816
8_K11_D1.046810.812
9_I24_I1.044050.810
36_E40_V1.041030.807
8_K28_L1.040090.807
52_K60_W1.027030.797
13_L19_S1.003440.778
23_A26_K0.996690.773
55_G58_P0.995260.772
14_K17_G0.972870.755
13_L50_V0.917450.712
13_L17_G0.912320.708
40_V43_R0.910990.707
8_K13_L0.896190.695
24_I41_L0.893620.693
21_A41_L0.88380.685
43_R46_K0.87230.677
21_A37_V0.85110.660
53_E59_K0.843870.654
28_L37_V0.807560.626
6_E10_L0.799940.620
13_L16_L0.797490.618
42_Y52_K0.787650.611
31_S34_K0.769960.597
20_T59_K0.767820.595
22_T25_A0.767810.595
41_L50_V0.756860.587
21_A25_A0.754410.585
56_T59_K0.754120.585
12_F24_I0.751670.583
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
3qphA0.969798.30.039
2wteA0.954598.30.065
1qgpA0.969798.20.075
1qbjA0.969798.20.079
1xmkA0.969798.20.09
3hsrA0.969798.10.098
1oyiA0.954598.10.101
3g3zA0.969798.10.107
2qwwA0.969798.10.109
3tgnA0.954598.10.109

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