GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lipase_GDSL_2 - GDSL-like LipaseAcylhydrolase family
Pfam: PF13472 (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: CL0264
Length: 179
Sequences: 8828
Seq/Len: 49.32
HH_delta: 0.144 (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
108_S146_F1.451183.522
92_R142_Y1.283643.115
96_E142_Y1.165512.829
88_E137_E1.156882.808
92_R141_K1.144542.778
2_F8_T1.11552.707
46_F69_F1.100292.670
65_V98_L1.058072.568
41_A49_R0.993072.410
43_S90_N0.917672.227
2_F66_V0.912392.214
92_R96_E0.911322.212
51_Q97_Q0.885832.150
103_P145_P0.874752.123
6_S170_H0.873782.121
148_D151_D0.847432.057
64_L105_I0.80891.963
139_A146_F0.735271.784
136_R146_F0.708821.720
9_A39_S0.694591.686
8_T37_G0.670721.628
174_A177_Q0.663871.611
22_R177_Q0.663071.609
108_S148_D0.662691.608
106_L139_A0.657721.596
88_E134_A0.656691.594
87_Y131_Y0.644671.565
109_P132_N0.641831.558
134_A137_E0.635621.543
7_I171_P0.622591.511
92_R138_L0.60041.457
64_L103_P0.600041.456
14_P173_P0.598931.454
133_Q137_E0.589711.431
138_L142_Y0.582631.414
41_A45_D0.566951.376
99_R142_Y0.56461.370
139_A144_V0.561821.364
95_I106_L0.561381.362
128_I132_N0.552721.341
47_L93_R0.547811.330
83_S86_Q0.545491.324
88_E92_R0.545381.324
105_I147_I0.540691.312
95_I144_V0.52991.286
137_E141_K0.527661.281
17_G173_P0.510991.240
97_Q101_H0.509691.237
108_S136_R0.509421.236
88_E141_K0.507451.232
133_Q136_R0.5051.226
136_R140_K0.499671.213
172_N175_G0.49661.205
42_T45_D0.49491.201
7_I71_T0.492171.194
93_R97_Q0.483571.174
91_L135_I0.482241.170
89_Q93_R0.478171.161
47_L90_N0.470811.143
2_F20_P0.469881.140
72_N170_H0.464641.128
43_S91_L0.46261.123
3_L46_F0.460811.118
134_A138_L0.45151.096
49_R53_D0.445971.082
132_N135_I0.443871.077
2_F19_Y0.439711.067
8_T68_S0.438291.064
68_S110_P0.435291.056
127_R130_R0.433041.051
136_R148_D0.432561.050
44_S86_Q0.430751.045
96_E100_P0.430691.045
95_I99_R0.427331.037
11_Y39_S0.424011.029
18_S21_D0.419371.018
47_L97_Q0.41811.015
6_S72_N0.417511.013
173_P177_Q0.417191.013
8_T19_Y0.414861.007
22_R25_E0.414841.007
95_I142_Y0.413841.004
43_S94_I0.411690.999
129_D133_Q0.401270.974
132_N136_R0.398640.967
91_L106_L0.396040.961
125_N129_D0.394260.957
75_L169_V0.393050.954
87_Y135_I0.391230.950
84_P88_E0.388910.944
89_Q92_R0.382030.927
85_E89_Q0.378890.920
167_D170_H0.378730.919
44_S90_N0.37850.919
137_E140_K0.378370.918
2_F23_L0.378260.918
50_L94_I0.378260.918
62_P65_V0.377960.917
10_G176_H0.376660.914
86_Q90_N0.376010.913
129_D150_F0.375870.912
13_A173_P0.373690.907
88_E138_L0.369980.898
86_Q89_Q0.367070.891
90_N94_I0.362140.879
138_L141_K0.358390.870
22_R26_R0.357740.868
19_Y176_H0.35230.855
84_P130_R0.351470.853
71_T169_V0.349430.848
165_F168_G0.348130.845
7_I169_V0.347570.844
97_Q100_P0.34550.839
41_A46_F0.343680.834
82_T86_Q0.343290.833
91_L95_I0.341870.830
54_V58_K0.339380.824
132_N148_D0.338550.822
5_D73_D0.337150.818
164_Y178_L0.336390.816
58_K101_H0.335050.813
107_V149_L0.334680.812
29_R33_V0.333460.809
93_R96_E0.332310.807
20_P24_A0.332080.806
73_D90_N0.327630.795
59_D62_P0.325710.790
43_S47_L0.324370.787
95_I138_L0.322830.784
98_L104_V0.319420.775
85_E134_A0.319120.774
29_R32_E0.31680.769
2_F33_V0.316510.768
142_Y145_P0.315140.765
171_P176_H0.313750.761
68_S71_T0.313050.760
99_R102_G0.31210.757
13_A18_S0.310820.754
40_G72_N0.310740.754
66_V105_I0.309580.751
163_Y178_L0.30890.750
21_D24_A0.307940.747
46_F94_I0.306090.743
67_I106_L0.305940.743
8_T66_V0.305720.742
5_D70_G0.305510.741
5_D68_S0.304910.740
31_I63_D0.304090.738
7_I110_P0.303110.736
7_I68_S0.302410.734
84_P134_A0.296380.719
35_N38_V0.295780.718
125_N128_I0.295760.718
50_L98_L0.294470.715
10_G18_S0.294380.714
126_R130_R0.290960.706
44_S48_A0.290870.706
131_Y135_I0.289140.702
103_P107_V0.289110.702
98_L102_G0.286970.696
87_Y91_L0.286260.695
67_I94_I0.285740.693
150_F154_D0.285230.692
34_Y60_P0.284960.692
104_V144_V0.28450.690
87_Y134_A0.282890.687
37_G175_G0.282590.686
7_I109_P0.281830.684
50_L54_V0.281010.682
70_G73_D0.280290.680
6_S40_G0.279320.678
105_I145_P0.278110.675
38_V41_A0.276050.670
111_P114_P0.275370.668
95_I104_V0.274190.665
67_I95_I0.273070.663
129_D132_N0.27110.658
130_R133_Q0.270860.657
43_S87_Y0.268170.651
45_D48_A0.268010.650
152_A178_L0.267280.649
67_I104_V0.266460.647
68_S149_L0.264730.642
3_L65_V0.263160.639
149_L152_A0.258910.628
74_V87_Y0.257530.625
138_L144_V0.257110.624
82_T90_N0.256880.623
104_V108_S0.256840.623
34_Y62_P0.256740.623
90_N93_R0.255390.620
5_D69_F0.253740.616
38_V49_R0.253570.615
91_L138_L0.252770.613
43_S46_F0.252250.612
9_A37_G0.251070.609
71_T75_L0.251040.609
68_S107_V0.250820.609
132_N150_F0.249070.604
22_R176_H0.24730.600
13_A17_G0.246860.599
151_D154_D0.245880.597
108_S132_N0.245370.596
65_V104_V0.244840.594
50_L53_D0.244830.594
3_L94_I0.244630.594
3_L67_I0.24250.589
112_R115_D0.241080.585
74_V128_I0.24030.583
36_L53_D0.240210.583
65_V102_G0.240140.583
96_E99_R0.239990.582
107_V110_P0.239220.581
58_K62_P0.238470.579
47_L51_Q0.238320.578
163_Y174_A0.238210.578
85_E126_R0.237680.577
58_K61_K0.237320.576
111_P150_F0.236580.574
43_S73_D0.23610.573
113_G116_P0.236060.573
5_D67_I0.234410.569
163_Y166_S0.233980.568
19_Y66_V0.233470.567
171_P175_G0.23330.566
174_A178_L0.232630.565
49_R52_R0.232210.564
21_D25_E0.23190.563
20_P33_V0.231580.562
61_K101_H0.230980.561
130_R134_A0.230310.559
10_G13_A0.229530.557
54_V62_P0.22950.557
3_L36_L0.228990.556
108_S149_L0.228230.554
82_T87_Y0.227960.553
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
3milA0.988899.90.144
4hf7A0.927499.90.149
1vjgA0.977799.90.15
3dciA0.927499.90.153
3rjtA0.960999.90.17
4iyjA0.927499.90.176
2q0qA0.927499.90.182
3dc7A0.960999.90.183
3hp4A0.888399.90.192
1ivnA0.893999.90.194

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