GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LigT_PEase - LigT like Phosphoesterase
Pfam: PF02834 (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: CL0247
Length: 87
Sequences: 2088
Seq/Len: 24
HH_delta: 0.116 (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
75_G87_W0.638553.118
13_Q17_R0.407981.992
46_P49_Q0.394541.927
19_R29_W0.355821.738
52_E55_E0.339031.656
27_I35_P0.322921.577
15_Q35_P0.320831.567
9_E13_Q0.274341.340
78_P83_P0.27211.329
76_L79_S0.27171.327
15_Q19_R0.268631.312
50_L54_I0.266831.303
49_Q52_E0.261611.278
27_I78_P0.259531.267
55_E59_N0.254581.243
51_P54_I0.254491.243
25_L29_W0.246571.204
41_F85_V0.245671.200
52_E56_A0.24431.193
10_Q13_Q0.244061.192
63_R68_T0.242681.185
53_L57_L0.238761.166
60_I63_R0.236891.157
15_Q18_L0.234581.146
15_Q79_S0.229361.120
38_T71_V0.224611.097
11_L71_V0.22411.094
15_Q32_P0.222821.088
77_F87_W0.222041.084
69_L77_F0.220761.078
9_E12_N0.219921.074
37_I87_W0.218571.067
45_V53_L0.215861.054
29_W86_I0.213311.042
10_Q14_L0.213051.040
42_L45_V0.212241.036
33_F41_F0.211161.031
47_P51_P0.21091.030
16_E48_D0.209921.025
48_D58_A0.209711.024
45_V49_Q0.20911.021
54_I58_A0.207021.011
44_E50_L0.199190.973
39_L57_L0.198450.969
9_E17_R0.198030.967
41_F87_W0.196540.960
9_E16_E0.193950.947
79_S84_R0.193890.947
12_N70_T0.192510.940
14_L74_F0.190360.930
43_G86_I0.188440.920
8_K18_L0.187320.915
10_Q56_A0.186590.911
49_Q53_L0.18640.910
43_G84_R0.185120.904
60_I67_F0.184270.900
16_E19_R0.181250.885
11_L41_F0.178650.872
60_I64_F0.178380.871
14_L79_S0.177780.868
34_N44_E0.17730.866
32_P37_I0.176840.864
8_K32_P0.176680.863
33_F79_S0.175860.859
40_A71_V0.175620.858
31_R40_A0.175290.856
8_K37_I0.174490.852
34_N42_L0.174480.852
9_E59_N0.174380.852
47_P55_E0.174030.850
55_E82_R0.172950.845
27_I40_A0.172850.844
9_E32_P0.172030.840
48_D51_P0.169590.828
41_F84_R0.169220.826
76_L87_W0.166970.815
29_W39_L0.166450.813
26_G35_P0.165290.807
28_R31_R0.163720.800
57_L60_I0.163710.799
48_D65_P0.162560.794
27_I34_N0.160960.786
11_L35_P0.160140.782
51_P57_L0.160090.782
35_P87_W0.159950.781
82_R85_V0.158920.776
34_N53_L0.157010.767
47_P66_P0.156010.762
46_P75_G0.15590.761
43_G85_V0.155790.761
37_I43_G0.154840.756
63_R70_T0.152870.747
42_L53_L0.151660.741
65_P70_T0.149460.730
11_L69_L0.149440.730
34_N78_P0.149270.729
29_W57_L0.148310.724
12_N15_Q0.146740.717
59_N72_D0.145450.710
35_P79_S0.145080.708
12_N51_P0.14480.707
30_V35_P0.144620.706
55_E58_A0.143740.702
11_L59_N0.143550.701
25_L28_R0.142780.697
29_W42_L0.142690.697
35_P41_F0.141940.693
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
1iuhA0.965599.30.116
1vgjA0.97799.30.117
2vfkA0.95499.10.199
4h7wA0.95498.90.267
2d4gA0.885198.80.294
1jh6A0.873698.60.347
1vgjA0.965597.90.482
1iuhA0.862197.70.52
1jh6A0.95497.70.522
2d4gA0.896697.30.566

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