GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lipase_GDSL - GDSL-like LipaseAcylhydrolase
Pfam: PF00657 (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: 234
Sequences: 5911
Seq/Len: 25.26
HH_delta: 0.306 (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
3_V9_T0.828663.209
86_V122_L0.70562.732
1_I87_V0.692122.680
195_D198_S0.682272.642
7_S221_H0.550832.133
112_V176_E0.543872.106
53_S114_N0.538652.086
228_K232_E0.533782.067
86_V127_A0.524692.032
139_N193_Y0.517912.005
175_R193_Y0.508111.967
196_I230_I0.479741.858
3_V87_V0.479071.855
229_I232_E0.476781.846
178_A193_Y0.473461.833
116_R188_G0.470221.821
116_R120_K0.456131.766
112_V173_A0.451091.747
116_R189_A0.437741.695
8_L222_P0.42941.663
120_K189_A0.42171.633
7_S93_N0.413871.602
134_N138_I0.40771.579
116_R177_V0.395471.531
95_Y170_F0.393751.525
109_E173_A0.393171.522
111_F170_F0.381971.479
172_S176_E0.376061.456
9_T47_A0.36741.423
203_M226_G0.365251.414
10_D49_S0.36461.412
225_K228_K0.361761.401
9_T89_W0.359221.391
134_N139_N0.356191.379
3_V21_P0.353641.369
173_A177_V0.353041.367
120_K124_S0.352141.363
121_R125_N0.352081.363
218_D221_H0.351431.361
107_S110_E0.346821.343
27_N232_E0.343081.328
23_G228_K0.337441.307
172_S175_R0.334581.295
93_N221_H0.332211.286
134_N137_V0.33091.281
23_G231_A0.328291.271
113_E117_N0.321121.243
19_G22_E0.319891.239
20_W24_L0.319651.238
173_A176_E0.318431.233
53_S115_L0.315181.220
224_E228_K0.311031.204
122_L127_A0.310251.201
166_I169_A0.306171.185
165_A168_A0.305991.185
11_G227_H0.305861.184
197_Y201_S0.305331.182
137_V178_A0.303451.175
8_L92_T0.30271.172
135_I139_N0.299731.161
123_R128_R0.297491.152
115_L177_V0.296251.147
91_G94_D0.295781.145
171_N174_L0.294771.141
216_F219_G0.291931.130
137_V140_L0.288721.118
123_R189_A0.287871.115
222_P227_H0.285871.107
2_V46_Y0.285481.105
74_L78_K0.285141.104
8_L89_W0.28441.101
18_G26_N0.280561.086
112_V116_R0.279261.081
18_G224_E0.276481.071
89_W92_T0.275541.067
215_M226_G0.275071.065
170_F174_L0.274021.061
229_I233_Y0.273571.059
80_F83_P0.27171.052
161_E165_A0.271371.051
117_N121_R0.265661.029
20_W227_H0.262651.017
1_I43_V0.259471.005
27_N231_A0.258511.001
108_V169_A0.258040.999
67_I73_R0.257120.996
177_V189_A0.255590.990
45_N48_I0.25470.986
135_I138_I0.253990.983
168_A197_Y0.250660.971
48_I51_A0.250560.970
18_G22_E0.25040.970
70_Q74_L0.250140.969
18_G23_G0.248460.962
199_I233_Y0.24780.959
121_R124_S0.247130.957
227_H230_I0.247090.957
115_L174_L0.246560.955
83_P86_V0.245260.950
23_G27_N0.244180.945
3_V43_V0.243820.944
223_T226_G0.243340.942
222_P230_I0.243290.942
23_G26_N0.242570.939
9_T20_W0.241650.936
112_V177_V0.241560.935
171_N197_Y0.238780.925
2_V83_P0.238570.924
169_A173_A0.238340.923
225_K229_I0.237410.919
96_F220_V0.237230.919
108_V112_V0.232980.902
119_I191_V0.230330.892
24_L28_L0.22980.890
200_F226_G0.227980.883
137_V141_P0.227980.883
103_D106_T0.226690.878
138_I141_P0.226220.876
164_N168_A0.225160.872
78_K83_P0.224590.870
189_A192_P0.224280.868
167_V171_N0.223520.865
2_V79_S0.222860.863
51_A90_I0.222420.861
54_D110_E0.222340.861
67_I71_I0.221740.859
123_R188_G0.219910.851
88_I118_A0.219190.849
127_A135_I0.217850.843
6_D89_W0.217620.843
75_L78_K0.217610.843
1_I85_L0.217610.843
109_E113_E0.216930.840
203_M215_M0.216680.839
139_N195_D0.215190.833
222_P226_G0.214760.832
85_L128_R0.213680.827
110_E114_N0.213380.826
89_W196_I0.212660.823
4_F46_Y0.212070.821
113_E116_R0.210770.816
73_R77_S0.20960.812
21_P25_A0.20880.808
10_D47_A0.208460.807
198_S201_S0.208260.806
21_P24_L0.207920.805
95_Y111_F0.207680.804
110_E113_E0.207390.803
106_T110_E0.206840.801
175_R195_D0.206060.798
117_N120_K0.203250.787
114_N118_A0.203190.787
109_E172_S0.202320.783
115_L119_I0.201910.782
120_K123_R0.201290.779
4_F69_Q0.199670.773
6_D9_T0.197970.767
171_N195_D0.197150.763
134_N140_L0.197120.763
88_I119_I0.19670.762
9_T87_V0.19650.761
165_A169_A0.195140.756
200_F222_P0.194520.753
136_V139_N0.19430.752
94_D114_N0.193870.751
67_I70_Q0.193070.748
8_L220_V0.192760.746
90_I93_N0.192350.745
21_P28_L0.192260.744
72_S76_D0.19210.744
115_L170_F0.191840.743
7_S218_D0.191010.740
20_W23_G0.190360.737
69_Q73_R0.190280.737
169_A172_S0.190230.737
3_V24_L0.190070.736
91_G231_A0.189910.735
8_L53_S0.189270.733
54_D114_N0.189080.732
22_E25_A0.188440.730
108_V173_A0.188290.729
38_N41_V0.187930.728
138_I193_Y0.187470.726
53_S111_F0.187230.725
68_S71_I0.187220.725
118_A121_R0.187110.724
90_I118_A0.186520.722
78_K120_K0.186390.722
115_L118_A0.186370.722
2_V81_Y0.18620.721
168_A172_S0.185660.719
162_R165_A0.185580.719
136_V140_L0.184470.714
217_W223_T0.183290.710
135_I140_L0.181650.703
178_A191_V0.181610.703
194_F199_I0.181470.703
215_M229_I0.180840.700
83_P127_A0.180070.697
92_T220_V0.180060.697
68_S121_R0.179460.695
2_V86_V0.177230.686
141_P160_I0.177040.685
125_N128_R0.176540.684
46_Y81_Y0.176480.683
75_L79_S0.176220.682
196_I200_F0.176160.682
167_V197_Y0.175990.681
11_G19_G0.175940.681
111_F114_N0.175470.679
25_A51_A0.174830.677
79_S83_P0.173380.671
50_G93_N0.173340.671
23_G224_E0.173190.671
75_L121_R0.173150.670
22_E227_H0.173040.670
24_L231_A0.17280.669
47_A51_A0.172750.669
39_S43_V0.171040.662
135_I143_I0.170620.661
214_Y225_K0.169390.656
140_L171_N0.168930.654
163_L167_V0.168730.653
10_D22_E0.167850.650
53_S92_T0.166960.646
118_A122_L0.166640.645
104_N108_V0.16650.645
135_I141_P0.165920.642
41_V85_L0.165760.642
43_V46_Y0.165370.640
10_D19_G0.165080.639
214_Y217_W0.165050.639
8_L91_G0.164750.638
127_A134_N0.164210.636
134_N141_P0.16360.633
88_I122_L0.162230.628
114_N117_N0.162070.628
111_F174_L0.161880.627
72_S77_S0.161080.624
22_E26_N0.159510.618
69_Q72_S0.158270.613
68_S72_S0.158040.612
20_W28_L0.157460.610
119_I189_A0.156830.607
88_I115_L0.156750.607
119_I137_V0.156220.605
216_F223_T0.155980.604
27_N208_N0.155530.602
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
3rjtA0.799199.90.306
3milA0.81299.90.31
4hf7A0.739399.90.316
3dc7A0.820599.90.326
3hp4A0.717999.90.328
3dciA0.790699.90.332
1vjgA0.790699.90.333
3bzwA0.829199.90.336
4hyqA0.837699.90.337
1k7cA0.790699.90.339

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