GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OMPdecase - Orotidine 5-phosphate decarboxylase HUMPS family
Pfam: PF00215 (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: 226
Sequences: 4117
Seq/Len: 18.22
HH_delta: 0.133 (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
11_D14_E1.128714.305
218_D221_E0.822613.137
195_T207_I0.786893.001
52_K87_D0.72632.770
216_A222_A0.701572.676
221_E225_E0.630552.405
62_L86_A0.595072.269
183_Q205_D0.584872.230
220_R224_E0.581132.216
17_R21_E0.576712.199
20_D54_R0.541812.066
190_Q198_A0.53962.058
101_E105_K0.530162.022
18_I219_P0.512191.953
89_V114_G0.509921.945
20_D58_I0.494841.887
13_E17_R0.484931.849
196_P200_K0.483591.844
209_V212_A0.478861.826
76_E106_A0.465171.774
106_A109_K0.462331.763
174_I181_A0.46081.757
46_E49_E0.458451.748
64_L81_A0.439281.675
68_G71_V0.422651.612
93_P117_V0.412891.575
194_T198_A0.407691.555
76_E83_E0.406881.552
91_V100_L0.406721.551
21_E220_R0.397381.515
221_E224_E0.392871.498
104_V108_K0.384351.466
14_E17_R0.380581.451
17_R20_D0.369981.411
125_D128_D0.366341.397
204_A207_I0.36611.396
72_A105_K0.362971.384
199_A207_I0.362481.382
32_G66_D0.359641.372
97_D101_E0.358031.365
16_L50_E0.355071.354
52_K60_L0.354821.353
59_F88_A0.35421.351
91_V103_A0.353591.348
103_A106_A0.350141.335
106_A110_H0.34851.329
15_A18_I0.347361.325
95_A99_T0.347351.325
82_F114_G0.346641.322
49_E83_E0.345091.316
25_Y224_E0.344651.314
105_K109_K0.344411.313
61_D90_T0.337731.288
67_I73_R0.335131.278
127_E130_Q0.331141.263
192_R212_A0.330631.261
18_I22_L0.329631.257
156_I161_T0.323851.235
76_E110_H0.320111.221
49_E53_E0.318881.216
19_A29_I0.317291.210
39_Y47_I0.315271.202
90_T143_R0.314991.201
72_A103_A0.310491.184
126_S130_Q0.308661.177
144_A168_A0.307661.173
160_A194_T0.305941.167
197_A200_K0.30571.166
209_V213_I0.303891.159
219_P222_A0.303081.156
72_A106_A0.301431.150
50_E53_E0.299461.142
146_D168_A0.298031.137
194_T202_A0.298011.137
25_Y30_K0.295171.126
185_A208_I0.294351.123
125_D191_K0.291641.112
191_K194_T0.290631.108
48_I60_L0.288241.099
33_T37_L0.286891.094
20_D23_G0.286161.091
171_N175_L0.285191.088
174_I205_D0.28511.087
218_D222_A0.284821.086
75_A110_H0.279861.067
164_A167_K0.279811.067
126_S136_V0.278761.063
16_L20_D0.27721.057
91_V115_V0.27711.057
101_E140_I0.276191.053
142_H168_A0.275011.049
15_A219_P0.27341.043
48_I58_I0.272551.039
117_V143_R0.272121.038
98_D102_A0.271761.036
28_I31_V0.27071.032
198_A207_I0.270251.031
80_A83_E0.269911.029
222_A225_E0.26891.025
171_N174_I0.268661.025
98_D101_E0.268221.023
96_G103_A0.265961.014
12_L50_E0.262691.002
128_D131_D0.262261.000
72_A96_G0.261530.997
185_A212_A0.257910.984
37_L64_L0.257630.983
6_A210_G0.257560.982
7_L15_A0.25680.979
89_V107_A0.255650.975
140_I144_A0.254970.972
120_L124_P0.25470.971
108_K116_F0.250770.956
51_L60_L0.249850.953
156_I174_I0.247710.945
21_E219_P0.24690.942
163_P166_R0.246320.939
90_T119_D0.24610.939
164_A168_A0.246090.939
186_V189_G0.245260.935
4_Q28_I0.244680.933
46_E50_E0.243670.929
118_V141_V0.243440.928
138_Q164_A0.243340.928
75_A103_A0.242140.923
213_I223_A0.241840.922
108_K111_G0.241370.921
181_A185_A0.240190.916
105_K140_I0.239460.913
26_V30_K0.237020.904
184_G188_G0.236580.902
28_I57_P0.23650.902
98_D191_K0.236270.901
216_A219_P0.234860.896
100_L153_V0.233760.891
126_S137_D0.233240.889
101_E150_K0.232820.888
37_L81_A0.23140.882
181_A184_G0.229840.877
97_D150_K0.229280.874
127_E136_V0.228330.871
97_D151_A0.22810.870
198_A202_A0.227960.869
12_L47_I0.227850.869
100_L137_D0.226820.865
122_S126_S0.226810.865
15_A36_F0.226490.864
143_R206_I0.225160.859
60_L86_A0.225020.858
19_A22_L0.223990.854
25_Y28_I0.223640.853
57_P87_D0.223070.851
156_I172_F0.222960.850
172_F176_T0.222240.848
5_V213_I0.221850.846
32_G67_I0.221640.845
139_E177_P0.21950.837
93_P100_L0.219390.837
45_P49_E0.218960.835
16_L51_L0.218390.833
138_Q142_H0.217940.831
25_Y29_I0.217680.830
122_S125_D0.217590.830
71_V103_A0.216540.826
213_I216_A0.216320.825
127_E131_D0.214960.820
73_R80_A0.214430.818
158_C161_T0.214350.817
121_L126_S0.212980.812
9_P18_I0.210970.805
88_A115_V0.210710.804
20_D57_P0.209880.800
66_D157_V0.209430.799
39_Y46_E0.208970.797
31_V51_L0.207990.793
192_R222_A0.207140.790
69_N73_R0.206850.789
16_L54_R0.206630.788
104_V140_I0.206420.787
159_S197_A0.206280.787
96_G100_L0.206160.786
28_I206_I0.205810.785
142_H146_D0.204940.782
6_A211_R0.204840.781
12_L39_Y0.204690.781
51_L54_R0.204610.780
116_F153_V0.20390.778
192_R225_E0.202230.771
29_I51_L0.201590.769
83_E110_H0.20110.767
15_A47_I0.200880.766
146_D164_A0.20080.766
98_D128_D0.200630.765
119_D156_I0.200340.764
184_G225_E0.20.763
66_D71_V0.199880.762
166_R205_D0.199820.762
16_L19_A0.199520.761
217_E221_E0.198890.758
163_P177_P0.198280.756
195_T199_A0.197860.755
25_Y31_V0.197230.752
184_G187_A0.197140.752
35_L39_Y0.197020.751
48_I52_K0.196670.750
10_T54_R0.196330.749
118_V121_L0.196160.748
186_V204_A0.195950.747
64_L89_V0.195680.746
94_F124_P0.195590.746
31_V48_I0.195130.744
19_A51_L0.194980.744
22_L29_I0.194240.741
107_A116_F0.193260.737
121_L124_P0.193130.737
33_T36_F0.192270.733
93_P128_D0.192010.732
31_V60_L0.191780.731
72_A76_E0.191610.731
38_A80_A0.191290.730
75_A89_V0.190930.728
183_Q206_I0.19090.728
6_A15_A0.190740.727
196_P207_I0.190730.727
20_D55_G0.190650.727
88_A206_I0.190490.726
51_L58_I0.190370.726
116_F142_H0.190260.726
45_P80_A0.190090.725
165_I174_I0.189580.723
5_V26_V0.189490.723
93_P129_L0.189440.722
104_V141_V0.189340.722
45_P48_I0.188950.721
5_V154_D0.1880.717
5_V214_T0.1870.713
136_V139_E0.186380.711
118_V137_D0.18630.710
22_L220_R0.186050.710
142_H164_A0.185660.708
176_T179_I0.185120.706
126_S129_L0.185040.706
15_A19_A0.184160.702
122_S127_E0.184080.702
90_T117_V0.18290.698
94_F140_I0.182570.696
104_V154_D0.18240.696
120_L123_N0.182080.694
27_D223_A0.182020.694
45_P84_L0.1820.694
26_V48_I0.181610.693
9_P47_I0.18090.690
146_D149_A0.179770.686
63_K66_D0.179640.685
209_V223_A0.179580.685
144_A156_I0.179540.685
213_I219_P0.179260.684
21_E218_D0.178860.682
5_V189_G0.177610.677
154_D189_G0.177260.676
47_I50_E0.176730.674
33_T94_F0.176670.674
159_S162_E0.176660.674
82_F110_H0.176220.672
22_L223_A0.17490.667
166_R200_K0.174560.666
125_D131_D0.174510.666
160_A163_P0.174480.665
27_D206_I0.174460.665
67_I96_G0.173840.663
24_D220_R0.173690.662
59_F90_T0.173420.661
120_L130_Q0.172680.659
13_E16_L0.172630.658
50_E54_R0.172340.657
121_L125_D0.17160.654
124_P128_D0.171250.653
65_G92_H0.171210.653
127_E167_K0.171190.653
173_K176_T0.171080.652
71_V99_T0.171060.652
91_V104_V0.170420.650
4_Q206_I0.170410.650
80_A84_L0.170170.649
26_V60_L0.170130.649
28_I88_A0.168580.643
99_T150_K0.168250.642
181_A212_A0.168130.641
148_A153_V0.167920.640
52_K58_I0.167550.639
123_N130_Q0.166620.635
143_R146_D0.166590.635
142_H151_A0.166410.635
14_E18_I0.166320.634
29_I34_P0.165440.631
131_D136_V0.165330.631
211_R215_K0.165140.630
166_R170_P0.16510.630
165_I184_G0.164910.629
6_A209_V0.164880.629
64_L71_V0.164730.628
94_F144_A0.164140.626
200_K207_I0.163230.623
76_E80_A0.163070.622
36_F45_P0.162690.620
93_P148_A0.162690.620
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
3inpA0.90711000.133
3ctlA0.89821000.171
3ovpA0.88941000.178
1tqxA0.8851000.199
3cu2A0.89381000.238
1eixA0.91591000.266
1dbtA0.91151000.27
2yyuA0.91591000.286
3m47A0.8851000.301
1tqjA0.90271000.301

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