GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HD_assoc - Phosphohydrolase-associated domain
Pfam: PF13286 (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: 92
Sequences: 1459
Seq/Len: 15.86
HH_delta: 0.092 (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
41_E90_Y0.796364.161
42_L86_A0.544592.845
46_F89_L0.463532.422
81_M85_Y0.441782.308
18_N23_Y0.362871.896
89_L92_R0.356421.862
80_G85_Y0.350221.830
43_F78_I0.343821.796
16_K20_E0.342371.789
18_N22_I0.309581.617
38_I90_Y0.298761.561
8_K12_K0.291961.525
38_I86_A0.284311.485
12_K16_K0.280081.463
49_N53_L0.260541.361
28_V32_E0.253481.324
38_I87_L0.251471.314
19_Y24_Q0.250631.309
54_L74_V0.251.306
4_S7_V0.245211.281
42_L46_F0.238511.246
31_E34_K0.237831.243
39_I86_A0.233391.219
5_P9_E0.232611.215
39_I78_I0.228111.192
72_R75_C0.227471.188
56_E59_R0.226291.182
25_S28_V0.225911.180
45_Y53_L0.225121.176
50_P70_R0.222411.162
47_M74_V0.220561.152
43_F75_C0.220061.150
42_L78_I0.219441.147
44_D48_E0.211891.107
15_K19_Y0.210141.098
47_M71_A0.210131.098
83_D86_A0.207741.085
77_Y85_Y0.206981.081
38_I41_E0.206391.078
5_P8_K0.204421.068
61_R73_V0.201581.053
40_R44_D0.197381.031
29_V32_E0.197141.030
57_D82_T0.1971.029
43_F71_A0.196131.025
82_T91_Q0.193471.011
54_L73_V0.192431.005
42_L83_D0.18980.992
59_R62_Y0.187730.981
66_E69_S0.18520.968
9_E13_E0.184930.966
15_K45_Y0.184460.964
8_K67_D0.183830.960
26_P30_E0.183190.957
29_V34_K0.181180.947
69_S73_V0.181140.946
56_E60_E0.177550.928
34_K90_Y0.177220.926
34_K37_R0.177180.926
25_S29_V0.17670.923
37_R41_E0.176150.920
39_I75_C0.174630.912
50_P54_L0.168770.882
57_D60_E0.164360.859
24_Q84_R0.163880.856
41_E88_R0.16350.854
45_Y49_N0.163170.853
29_V36_R0.16190.846
81_M89_L0.161410.843
73_V77_Y0.155370.812
3_F22_I0.154670.808
10_A31_E0.152720.798
33_E48_E0.150570.787
36_R40_R0.149990.784
64_Q67_D0.149520.781
17_F21_N0.149370.780
27_R84_R0.149010.779
62_Y69_S0.148050.774
55_P77_Y0.14690.768
51_E67_D0.146380.765
88_R92_R0.14560.761
77_Y80_G0.145030.758
11_I15_K0.144350.754
22_I58_Y0.142860.746
48_E63_E0.142520.745
18_N32_E0.142480.744
5_P50_P0.142040.742
32_E35_G0.141770.741
17_F23_Y0.141630.740
14_L22_I0.141010.737
15_K92_R0.140690.735
25_S30_E0.139820.731
33_E53_L0.138160.722
9_E67_D0.13810.722
59_R63_E0.137890.720
9_E16_K0.137440.718
11_I14_L0.136070.711
78_I86_A0.135680.709
26_P32_E0.135580.708
9_E51_E0.135480.708
18_N43_F0.135310.707
25_S84_R0.134440.702
24_Q28_V0.134080.701
28_V35_G0.133680.698
55_P58_Y0.133650.698
59_R65_A0.133650.698
28_V86_A0.133390.697
20_E69_S0.133070.695
48_E88_R0.133030.695
67_D70_R0.132830.694
51_E56_E0.132690.693
6_E9_E0.13190.689
87_L91_Q0.13190.689
39_I88_R0.131790.689
77_Y82_T0.131560.687
30_E92_R0.131030.685
22_I75_C0.130090.680
58_Y75_C0.129580.677
56_E67_D0.129260.675
12_K42_L0.128950.674
35_G79_A0.128860.673
37_R40_R0.128670.672
38_I42_L0.127930.668
14_L81_M0.127550.666
75_C88_R0.127510.666
10_A74_V0.127310.665
3_F89_L0.127250.665
19_Y39_I0.126390.660
4_S13_E0.126240.660
20_E65_A0.12620.659
73_V76_D0.125820.657
62_Y70_R0.125360.655
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
2dqbA0.956599.90.092
2pgsA199.80.135
3bg2A0.956599.80.135
2q14A0.989192.60.802
3irhA0.923940.80.873
2hekA0.891336.90.876
2ekeC0.945729.60.882
1nkzB0.152222.90.888
1lghB0.206512.60.9
2x5qA0.576112.10.9

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