GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
IGPS - Indole-3-glycerol phosphate synthase
Pfam: PF00218 (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: CL0036
Length: 254
Sequences: 5272
Seq/Len: 20.76
HH_delta: 0.143 (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
69_D72_E1.062183.162
225_R229_R0.876912.611
144_D173_R0.871522.595
155_H180_D0.866452.580
224_A235_V0.863872.572
248_G252_R0.828872.468
98_L130_A0.777112.314
105_R133_D0.761032.266
246_D249_E0.729942.173
197_N200_E0.723812.155
244_S250_A0.7192.141
218_I227_L0.710272.115
125_Y153_L0.700962.087
78_E110_L0.692532.062
152_E156_S0.670611.997
203_A233_D0.669981.995
143_S146_Q0.666341.984
153_L156_S0.640231.906
219_K223_D0.639681.904
206_I210_V0.623411.856
200_E226_R0.606911.807
172_E175_L0.594181.769
78_E109_D0.591981.762
125_Y157_L0.590371.758
79_E248_G0.569011.694
76_A247_P0.558511.663
211_I233_D0.538411.603
213_I234_A0.536121.596
154_A161_A0.534161.590
146_Q149_E0.530431.579
200_E230_A0.52871.574
168_E201_E0.520121.549
197_N201_E0.519291.546
226_R229_R0.516511.538
199_T232_A0.510661.520
71_A75_K0.501561.493
221_P225_R0.492181.465
219_K240_A0.487981.453
203_A212_V0.4851.444
172_E205_L0.481911.435
92_K119_I0.47721.421
97_S100_D0.475951.417
151_L155_H0.473521.410
137_L147_L0.473071.408
103_A106_K0.471951.405
214_S227_L0.465981.387
155_H161_A0.464691.384
199_T214_S0.461231.373
136_L164_E0.460831.372
148_E152_E0.456071.358
96_G188_D0.450471.341
148_E178_G0.449191.337
121_P149_E0.446931.331
109_D158_G0.44311.319
228_A235_V0.440161.310
95_G188_D0.440081.310
214_S232_A0.435991.298
99_E103_A0.434641.294
99_E102_R0.434611.294
128_R159_L0.43181.286
162_L181_I0.428271.275
203_A207_P0.422821.259
75_K79_E0.422421.258
57_A95_G0.419391.249
153_L157_L0.416691.241
151_L178_G0.406971.212
223_D226_R0.404591.205
135_V159_L0.403941.203
165_V171_L0.402491.198
120_D123_Q0.401181.194
125_Y129_A0.395541.178
119_I145_D0.394431.174
151_L161_A0.39431.174
247_P251_L0.388491.157
123_Q126_E0.388061.155
101_L112_V0.387891.155
171_L202_L0.387481.154
226_R230_A0.383381.141
222_E226_R0.377381.124
105_R112_V0.374231.114
218_I224_A0.37081.104
83_A116_D0.367371.094
84_A234_A0.366111.090
171_L205_L0.366021.090
134_A160_E0.361731.077
195_D198_R0.358521.067
149_E152_E0.356541.062
138_I169_E0.354851.056
201_E205_L0.354651.056
80_A248_G0.354391.055
172_E176_E0.354391.055
227_L232_A0.35031.043
78_E108_V0.346921.033
151_L177_A0.345511.029
122_Y150_L0.345061.027
75_K107_A0.341871.018
76_A80_A0.340771.015
168_E205_L0.339131.010
182_I210_V0.337021.003
87_V112_V0.335710.999
136_L181_I0.334430.996
175_L201_E0.331520.987
150_L153_L0.330470.984
139_A173_R0.330450.984
74_A104_V0.329690.982
122_Y142_L0.329410.981
87_V101_L0.329230.980
139_A147_L0.327830.976
192_F196_L0.326220.971
163_V179_A0.323490.963
75_K78_E0.322770.961
137_L142_L0.321440.957
140_A170_E0.319040.950
184_I212_V0.318380.948
84_A134_A0.317760.946
175_L205_L0.314620.937
92_K120_D0.310510.924
171_L206_I0.310210.924
183_G195_D0.308260.918
131_G143_S0.307520.916
100_D103_A0.303130.902
102_R106_K0.302440.900
181_I234_A0.302210.900
61_K85_I0.301890.899
114_R132_A0.301190.897
200_E227_L0.301110.896
151_L179_A0.300460.895
200_E204_P0.300450.895
211_I234_A0.299350.891
56_R100_D0.298720.889
214_S218_I0.295220.879
200_E232_A0.295160.879
186_N199_T0.295110.879
166_H185_N0.294720.877
111_P134_A0.293470.874
213_I236_L0.293450.874
198_R201_E0.291760.869
147_L163_V0.290410.865
86_S117_F0.290020.863
72_E75_K0.289480.862
124_I150_L0.286810.854
152_E178_G0.286680.854
137_L150_L0.286390.853
84_A211_I0.286010.852
114_R126_E0.283060.843
223_D227_L0.282370.841
98_L114_R0.282130.840
206_I233_D0.281670.839
128_R157_L0.280220.834
201_E204_P0.279810.833
237_V240_A0.275510.820
140_A169_E0.274990.819
148_E176_E0.273660.815
188_D191_T0.272490.811
124_I157_L0.272390.811
182_I202_L0.271780.809
76_A248_G0.270690.806
175_L182_I0.27060.806
175_L209_D0.269860.803
102_R130_A0.269570.803
102_R129_A0.269130.801
61_K239_E0.268520.799
175_L210_V0.267570.797
249_E252_R0.265250.790
136_L162_L0.264920.789
203_A206_I0.264130.786
144_D176_E0.263540.785
77_Y85_I0.262250.781
83_A111_P0.258950.771
227_L235_V0.258050.768
222_E225_R0.256890.765
116_D123_Q0.255210.760
171_L182_I0.254980.759
118_I123_Q0.252510.752
61_K100_D0.252480.752
181_I213_I0.251660.749
155_H178_G0.250940.747
239_E243_R0.248380.739
244_S247_P0.248080.739
68_F100_D0.247740.738
114_R127_A0.24530.730
196_L226_R0.244970.729
212_V232_A0.241260.718
124_I135_V0.240870.717
139_A174_A0.238860.711
134_A181_I0.238360.710
188_D193_E0.238260.709
237_V241_L0.238110.709
149_E153_L0.237610.707
181_I211_I0.23590.702
200_E229_R0.235710.702
70_P74_A0.234870.699
73_I247_P0.234860.699
221_P240_A0.234260.697
216_S236_L0.232570.692
101_L119_I0.2320.691
163_V174_A0.231860.690
84_A181_I0.229620.684
173_R176_E0.228190.679
73_I76_A0.227360.677
240_A244_S0.227170.676
104_V107_A0.226110.673
206_I212_V0.226010.673
127_A132_A0.225560.672
139_A163_V0.224340.668
178_G210_V0.224280.668
104_V112_V0.223660.666
126_E130_A0.222150.661
199_T212_V0.221890.661
241_L251_L0.220580.657
175_L206_I0.21970.654
145_D149_E0.219110.652
161_A180_D0.218680.651
68_F95_G0.218580.651
191_T219_K0.217190.647
121_P153_L0.216440.644
165_V184_I0.21630.644
192_F239_E0.215790.642
124_I153_L0.215550.642
135_V154_A0.214410.638
189_L192_F0.214320.638
227_L230_A0.21320.635
248_G251_L0.213120.635
126_E129_A0.212810.634
98_L102_R0.212380.632
203_A210_V0.212340.632
72_E76_A0.21210.631
122_Y153_L0.212050.631
194_V197_N0.211990.631
57_A251_L0.211730.630
160_E180_D0.211510.630
122_Y125_Y0.211130.629
71_A107_A0.208750.622
74_A107_A0.208120.620
197_N226_R0.207340.617
247_P250_A0.207050.616
146_Q185_N0.206810.616
155_H160_E0.206280.614
183_G236_L0.206170.614
221_P250_A0.205950.613
166_H215_E0.205180.611
80_A247_P0.20320.605
87_V108_V0.203080.605
183_G213_I0.202840.604
195_D201_E0.202720.604
108_V112_V0.2020.601
218_I237_V0.201560.600
71_A104_V0.200210.596
172_E206_I0.20.595
186_N198_R0.199880.595
179_A210_V0.198270.590
196_L223_D0.198270.590
202_L205_L0.198040.590
139_A142_L0.196890.586
167_N170_E0.196750.586
105_R108_V0.196660.586
164_E185_N0.196230.584
219_K222_E0.196090.584
154_A159_L0.195720.583
167_N198_R0.195560.582
246_D250_A0.195120.581
58_S234_A0.194930.580
148_E177_A0.19490.580
169_E172_E0.194760.580
179_A182_I0.194530.579
86_S162_L0.194520.579
194_V239_E0.194450.579
167_N184_I0.193180.575
85_I104_V0.192470.573
241_L247_P0.191510.570
82_A251_L0.191040.569
140_A190_K0.190660.568
85_I110_L0.190550.567
168_E185_N0.190540.567
203_A230_A0.190320.567
160_E211_I0.189850.565
183_G211_I0.189550.564
196_L199_T0.189420.564
148_E173_R0.1890.563
167_N190_K0.188870.562
80_A251_L0.188580.561
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
3tsmA11000.143
1piiA0.97641000.155
3qjaA0.99211000.17
4a29A0.95671000.188
1i4nA0.95671000.201
1vc4A0.9371000.265
3q58A0.830799.90.547
3igsA0.830799.90.554
4adtA0.818999.90.564
2yzrA0.807199.80.582

Page generated in 0.0194 seconds.