GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SE - Squalene epoxidase
Pfam: PF08491 (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: CL0063
Length: 276
Sequences: 3080
Seq/Len: 11.16
HH_delta: 0.463 (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
184_H188_K0.534433.579
7_V15_F0.478623.205
127_N191_S0.429972.879
19_L132_V0.399942.678
155_N190_L0.370892.483
163_L186_K0.364532.441
126_P129_K0.359572.408
8_A135_L0.350632.348
162_D186_K0.346012.317
156_D187_R0.343852.302
159_L186_K0.333982.236
128_W181_K0.329632.207
163_L182_K0.321462.152
163_L179_A0.320292.145
7_V134_L0.317862.128
157_V161_R0.309762.074
93_V96_Q0.306182.050
14_K18_E0.306092.050
199_Q203_S0.298531.999
4_L180_L0.287981.928
159_L163_L0.284931.908
9_D13_S0.258531.731
11_C141_M0.251611.685
2_A5_T0.243031.627
128_W133_V0.239741.605
159_L162_D0.237851.593
167_I179_A0.235241.575
161_R165_S0.224861.506
122_L141_M0.223921.499
4_L133_V0.221261.482
16_R140_N0.220781.478
140_N156_D0.218641.464
5_T15_F0.215871.445
167_I182_K0.21571.444
133_V160_L0.215581.444
14_K17_K0.21521.441
163_L166_P0.215081.440
19_L129_K0.213241.428
140_N148_G0.209541.403
142_R152_V0.209391.402
15_F132_V0.208111.393
94_A114_I0.207261.388
13_S16_R0.201241.347
88_Y100_E0.200151.340
99_E103_P0.199691.337
130_P177_L0.198451.329
98_P102_R0.196661.317
21_D124_A0.193971.299
6_I135_L0.189891.271
134_L138_A0.187911.258
140_N187_R0.187821.258
123_P127_N0.18451.235
124_A134_L0.184011.232
42_K46_G0.183961.232
128_W177_L0.183541.229
12_F17_K0.180751.210
68_V71_D0.180451.208
35_L68_V0.180391.208
6_I160_L0.18021.207
126_P184_H0.179881.204
87_E91_E0.179021.199
159_L182_K0.178891.198
102_R107_K0.173891.164
4_L164_L0.173781.164
207_A212_L0.171981.152
57_L143_H0.17141.148
182_K186_K0.170521.142
209_D212_L0.168261.127
211_Y214_A0.167341.120
55_P145_L0.166811.117
57_L145_L0.164151.099
188_K192_S0.163971.098
4_L167_I0.16311.092
123_P188_K0.162471.088
135_L183_F0.162291.087
90_R116_S0.160371.074
21_D125_S0.160271.073
127_N184_H0.159021.065
148_G151_T0.158751.063
6_I161_R0.157161.052
7_V19_L0.156951.051
58_L105_F0.156911.051
67_R70_V0.156461.048
97_L101_L0.154711.036
101_L105_F0.154091.032
30_F69_L0.154041.031
162_D182_K0.152771.023
100_E103_P0.152761.023
48_V145_L0.152631.022
26_V31_V0.152621.022
137_D147_G0.152111.019
167_I178_E0.151911.017
148_G187_R0.151471.014
130_P133_V0.151061.011
137_D153_A0.149491.001
127_N139_A0.14880.996
208_D213_K0.148770.996
140_N191_S0.148260.993
110_E170_L0.148220.992
142_R198_A0.1480.991
5_T132_V0.147530.988
69_L145_L0.147320.986
7_V14_K0.146960.984
121_F199_Q0.146830.983
55_P143_H0.146510.981
162_D166_P0.145210.972
215_L218_G0.144750.969
99_E102_R0.144180.965
29_Y34_I0.144010.964
150_M154_L0.143420.960
50_L57_L0.142470.954
87_E90_R0.140410.940
48_V137_D0.140370.940
133_V180_L0.139830.936
213_K217_Q0.139790.936
13_S140_N0.139340.933
137_D191_S0.13860.928
137_D149_G0.138440.927
55_P59_Y0.137980.924
186_K189_P0.13780.923
67_R72_V0.137750.922
147_G194_I0.13760.921
150_M202_Y0.13760.921
221_K225_L0.137150.918
222_Y226_G0.136680.915
191_S195_N0.136310.913
57_L69_L0.135990.911
166_P179_A0.135820.909
29_Y75_P0.1350.904
94_A97_L0.134680.902
185_W189_P0.134640.902
138_A153_A0.134480.900
193_V196_I0.134360.900
140_N151_T0.134210.899
15_F183_F0.134160.898
7_V138_A0.134030.897
105_F108_A0.133990.897
28_S32_G0.133840.896
9_D15_F0.133680.895
31_V73_P0.133270.892
31_V110_E0.133180.892
158_V162_D0.133060.891
214_A218_G0.132840.889
146_T205_F0.132690.888
144_P148_G0.131910.883
69_L143_H0.131750.882
117_M150_M0.131130.878
146_T151_T0.130420.873
129_K177_L0.130260.872
166_P178_E0.129830.869
3_P7_V0.129410.867
110_E172_D0.129240.865
192_S196_I0.128650.861
62_S65_E0.128460.860
134_L204_L0.128460.860
59_Y143_H0.128350.859
17_K103_P0.128150.858
30_F33_L0.128070.858
5_T131_G0.128010.857
34_I112_G0.127890.856
148_G156_D0.127840.856
133_V183_F0.127470.854
218_G221_K0.127180.852
126_P178_E0.126990.850
9_D16_R0.126940.850
143_H205_F0.126820.849
146_T201_L0.125910.843
59_Y69_L0.125340.839
145_L150_M0.125250.839
86_K89_L0.125070.837
23_K26_V0.124870.836
96_Q99_E0.124870.836
145_L202_Y0.124740.835
139_A153_A0.124390.833
30_F70_V0.124210.832
54_G57_L0.124120.831
211_Y215_L0.123890.830
21_D70_V0.123750.829
31_V70_V0.123440.827
123_P191_S0.122990.824
89_L92_V0.122610.821
46_G57_L0.122330.819
16_R122_L0.122140.818
31_V69_L0.121810.816
123_P192_S0.121050.811
88_Y91_E0.121020.810
142_R150_M0.120580.807
28_S31_V0.119580.801
101_L117_M0.119330.799
59_Y205_F0.118930.796
23_K27_R0.11890.796
22_N26_V0.118810.796
46_G143_H0.118690.795
181_K184_H0.118320.792
89_L93_V0.117840.789
143_H147_G0.11740.786
51_G54_G0.116590.781
3_P17_K0.116510.780
8_A128_W0.116230.778
46_G49_I0.116010.777
180_L183_F0.115890.776
164_L170_L0.115860.776
200_A211_Y0.115150.771
48_V56_I0.115050.770
22_N125_S0.114680.768
146_T150_M0.114530.767
209_D214_A0.114490.767
124_A127_N0.114340.766
140_N146_T0.114240.765
100_E104_S0.113190.758
48_V201_L0.113090.757
56_I104_S0.113090.757
28_S71_D0.112880.756
50_L145_L0.112420.753
26_V30_F0.112410.753
196_I199_Q0.112110.751
102_R106_E0.111820.749
88_Y92_V0.110930.743
209_D213_K0.11060.741
131_G177_L0.110470.740
221_K224_Q0.110410.739
28_S69_L0.110350.739
133_V179_A0.110270.738
7_V13_S0.110230.738
182_K185_W0.109440.733
19_L178_E0.109250.732
195_N198_A0.108660.728
6_I180_L0.108360.726
64_N87_E0.108230.725
24_P31_V0.108190.724
212_L215_L0.108170.724
48_V71_D0.107720.721
200_A219_C0.107710.721
35_L170_L0.107460.720
142_R195_N0.107120.717
157_V190_L0.10680.715
28_S199_Q0.106750.715
26_V32_G0.106670.714
172_D178_E0.106530.713
126_P133_V0.106320.712
90_R93_V0.106230.711
210_D214_A0.10620.711
193_V197_L0.106110.711
57_L71_D0.106020.710
222_Y225_L0.1060.710
50_L59_Y0.105890.709
121_F195_N0.105720.708
215_L219_C0.105530.707
160_L164_L0.105030.703
159_L166_P0.104760.701
69_L72_V0.104640.701
216_R220_F0.104610.700
99_E170_L0.104540.700
30_F71_D0.104440.699
99_E177_L0.104440.699
142_R145_L0.10440.699
93_V114_I0.104260.698
61_I135_L0.104150.697
23_K74_G0.103970.696
92_V96_Q0.103960.696
11_C122_L0.103920.696
16_R134_L0.103820.695
99_E181_K0.103810.695
146_T152_V0.103810.695
6_I126_P0.103510.693
10_G187_R0.10340.692
21_D26_V0.10320.691
49_I98_P0.103080.690
59_Y151_T0.102720.688
50_L55_P0.10270.688
186_K190_L0.102360.685
135_L157_V0.102350.685
29_Y70_V0.102240.685
106_E112_G0.10220.684
100_E188_K0.102120.684
10_G136_G0.101970.683
57_L118_P0.101560.680
103_P213_K0.101460.679
31_V68_V0.10140.679
147_G205_F0.101390.679
165_S179_A0.101360.679
50_L220_F0.101260.678
142_R146_T0.101060.677
31_V67_R0.101050.677
24_P29_Y0.100890.676
45_H63_S0.100880.675
140_N150_M0.100630.674
107_K113_R0.100590.674
144_P156_D0.100470.673
137_D140_N0.100350.672
122_L142_R0.100340.672
153_A156_D0.100250.671
103_P107_K0.100130.670
72_V89_L0.099940.669
142_R191_S0.099910.669
210_D215_L0.099870.669
5_T222_Y0.099820.668
114_I117_M0.099810.668
154_L226_G0.099760.668
119_N143_H0.099430.666
40_L46_G0.099380.665
31_V86_K0.099340.665
123_P195_N0.099340.665
2_A16_R0.099330.665
60_Q148_G0.099290.665
75_P103_P0.099270.665
177_L181_K0.099260.665
131_G179_A0.099210.664
129_K132_V0.099140.664
64_N178_E0.098690.661
2_A6_I0.098630.660
52_K74_G0.098630.660
137_D194_I0.098560.660
70_V205_F0.098520.660
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
3fmwA0.92751000.463
4k2xA0.94931000.468
2qa2A0.94571000.474
2qa1A0.94571000.476
3rp8A0.84061000.482
1k0iA0.85141000.494
2x3nA0.85511000.497
1pn0A0.94571000.499
4hb9A0.82251000.503
4k22A0.75361000.504

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