GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UMPH-1 - Pyrimidine 5-nucleotidase (UMPH-1)
Pfam: PF05822 (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: CL0137
Length: 246
Sequences: 3424
Seq/Len: 13.92
HH_delta: 0.376 (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
2_T181_N0.994056.093
186_G191_D0.553463.392
195_A204_V0.5193.181
178_K181_N0.430852.641
193_H197_G0.429772.634
171_P174_K0.421722.585
173_F182_V0.390082.391
32_K36_E0.373442.289
196_D219_E0.356182.183
6_F185_L0.349122.140
4_T183_L0.345272.116
206_K209_F0.327622.008
165_S168_E0.325671.996
184_L195_A0.323641.984
35_K68_E0.321471.970
96_E100_D0.314321.927
53_E57_P0.312831.918
204_V207_I0.312791.917
172_Y176_L0.303681.861
3_L176_L0.295751.813
212_D216_E0.294221.803
207_I210_L0.29141.786
56_I60_E0.275351.688
184_L198_V0.275351.688
100_D104_E0.273581.677
57_P61_E0.266341.633
33_K37_L0.263511.615
213_K216_E0.2631.612
94_G98_F0.262541.609
33_K36_E0.259681.592
51_S54_E0.258471.584
54_E57_P0.254051.557
171_P175_Q0.251961.544
28_E32_K0.242971.489
9_N187_D0.242771.488
12_R43_P0.241431.480
121_E125_R0.240241.473
204_V208_G0.239081.465
7_H11_K0.23861.463
115_G119_V0.230781.415
204_V209_F0.227671.396
206_K210_L0.226271.387
8_Y13_C0.222341.363
168_E179_R0.219221.344
204_V210_L0.212231.301
167_L194_M0.21221.301
97_E102_L0.211631.297
7_H187_D0.206421.265
206_K212_D0.199591.223
192_L196_D0.198831.219
163_N195_A0.195431.198
212_D217_N0.193891.188
124_L128_G0.190291.166
208_G212_D0.190031.165
78_S82_E0.18811.153
120_I123_V0.186681.144
8_Y11_K0.186571.144
163_N197_G0.185871.139
5_R44_I0.185711.138
9_N186_G0.185071.134
103_E109_L0.184921.133
191_D194_M0.184431.130
179_R182_V0.182261.117
77_K81_E0.181971.115
136_V140_F0.181681.114
3_L182_V0.179161.098
165_S194_M0.178181.092
194_M198_V0.177591.089
5_R182_V0.174261.068
195_A206_K0.173981.066
55_K188_S0.173261.062
206_K211_N0.171141.049
53_E66_A0.170371.044
57_P60_E0.16951.039
208_G214_V0.169121.037
34_L44_I0.168051.030
3_L40_K0.166111.018
184_L194_M0.161890.992
138_S141_M0.161480.990
97_E101_K0.160580.984
48_P72_E0.15930.976
79_E82_E0.158890.974
184_L191_D0.158610.972
214_V217_N0.158050.969
7_H12_R0.157910.968
118_D122_E0.156760.961
47_D50_M0.156090.957
183_L220_K0.155420.953
213_K217_N0.154190.945
2_T182_V0.153940.944
137_V140_F0.153830.943
118_D123_V0.152940.937
11_K194_M0.152790.937
121_E124_L0.152660.936
120_I126_Q0.151940.931
115_G122_E0.151080.926
5_R167_L0.150860.925
164_E197_G0.150810.924
52_I101_K0.147790.906
213_K223_E0.146490.898
12_R60_E0.146290.897
183_L205_L0.145830.894
160_F164_E0.145580.892
68_E72_E0.144910.888
162_K191_D0.144860.888
52_I74_G0.144480.886
120_I124_L0.144370.885
50_M58_H0.142060.871
56_I66_A0.142020.871
7_H162_K0.1420.870
218_L221_Y0.141950.870
210_L217_N0.141570.868
113_S120_I0.140810.863
205_L208_G0.140710.862
186_G194_M0.140520.861
125_R130_F0.140520.861
35_K65_K0.140470.861
49_T190_G0.140430.861
92_R140_F0.140360.860
35_K41_Y0.139840.857
161_N186_G0.138820.851
124_L127_A0.138610.850
48_P55_K0.138010.846
9_N12_R0.137640.844
215_E223_E0.137340.842
4_T39_E0.137160.841
8_Y12_R0.136630.837
3_L42_Y0.136490.837
3_L179_R0.136080.834
2_T39_E0.135860.833
33_K41_Y0.135780.832
168_E174_K0.135280.829
209_F217_N0.135250.829
220_K224_A0.134170.822
70_L74_G0.134050.822
116_L119_V0.133970.821
214_V223_E0.133750.820
121_E127_A0.133610.819
215_E218_L0.133130.816
44_I48_P0.133050.816
122_E126_Q0.132910.815
55_K59_M0.132450.812
78_S81_E0.132290.811
161_N195_A0.132250.811
81_E85_K0.131890.808
168_E173_F0.131150.804
208_G217_N0.13110.804
77_K105_H0.1310.803
101_K105_H0.130630.801
30_Y41_Y0.130460.800
36_E40_K0.130110.798
148_V190_G0.129710.795
44_I47_D0.129540.794
116_L123_V0.129480.794
71_V74_G0.128520.788
173_F179_R0.128420.787
106_N147_G0.128350.787
76_T137_V0.127960.784
114_A118_D0.127820.783
204_V211_N0.126990.778
192_L195_A0.126750.777
111_I130_F0.126260.774
219_E224_A0.125950.772
161_N166_A0.125920.772
119_V126_Q0.125860.771
209_F212_D0.125240.768
5_R172_Y0.125190.767
115_G123_V0.125160.767
113_S124_L0.124410.763
89_I92_R0.124180.761
30_Y34_L0.124020.760
4_T7_H0.123770.759
118_D126_Q0.123650.758
159_T163_N0.123630.758
119_V123_V0.123230.755
173_F198_V0.123050.754
94_G97_E0.122940.754
41_Y190_G0.12280.753
8_Y55_K0.122620.752
183_L204_V0.122410.750
15_S186_G0.121680.746
99_F103_E0.121670.746
110_L113_S0.121390.744
95_V106_N0.120770.740
137_V141_M0.120720.740
136_V139_N0.12040.738
167_L186_G0.120280.737
78_S175_Q0.120230.737
205_L209_F0.120170.737
190_G194_M0.119830.735
113_S128_G0.11980.734
112_F138_S0.119770.734
162_K187_D0.119140.730
71_V75_L0.119140.730
163_N167_L0.118890.729
5_R184_L0.118720.728
32_K35_K0.118650.727
215_E221_Y0.118590.727
118_D124_L0.118370.726
164_E168_E0.118230.725
93_D99_F0.117460.720
47_D188_S0.11710.718
34_L38_F0.117020.717
114_A120_I0.116880.716
166_A182_V0.116760.716
163_N218_L0.116710.715
11_K95_V0.116190.712
119_V128_G0.11610.712
188_S191_D0.115810.710
40_K176_L0.115740.709
92_R102_L0.115680.709
221_Y224_A0.115380.707
222_L226_D0.115190.706
172_Y194_M0.115190.706
11_K191_D0.115090.705
125_R216_E0.114920.704
78_S85_K0.114420.701
73_Q77_K0.113870.698
11_K52_I0.113850.698
42_Y175_Q0.113760.697
8_Y43_P0.113630.696
72_E95_V0.113520.696
44_I186_G0.113280.694
42_Y70_L0.113120.693
161_N187_D0.112820.692
73_Q76_T0.112450.689
48_P190_G0.112430.689
50_M55_K0.112360.689
111_I124_L0.112280.688
222_L225_Y0.112070.687
117_G121_E0.112030.687
100_D136_V0.111880.686
82_E174_K0.111880.686
94_G106_N0.111780.685
36_E88_D0.111720.685
9_N161_N0.111550.684
95_V116_L0.111420.683
47_D190_G0.111240.682
96_E99_F0.111180.681
210_L215_E0.110080.675
91_L129_V0.109660.672
166_A194_M0.109630.672
211_N215_E0.109320.670
11_K167_L0.109180.669
212_D215_E0.109120.669
46_I90_M0.109060.668
6_F30_Y0.108680.666
85_K126_Q0.108570.665
185_L207_I0.108330.664
68_E174_K0.108120.663
93_D96_E0.10810.663
78_S171_P0.108080.662
62_W205_L0.108070.662
60_E66_A0.107940.662
94_G208_G0.107920.661
53_E104_E0.107690.660
111_I140_F0.107510.659
119_V122_E0.10750.659
2_T41_Y0.107490.659
101_K104_E0.107440.659
165_S197_G0.10690.655
219_E222_L0.106820.655
45_E48_P0.106690.654
74_G77_K0.106220.651
59_M75_L0.106070.650
29_E32_K0.106040.650
5_R165_S0.105810.649
9_N194_M0.105660.648
207_I212_D0.105260.645
79_E83_A0.105020.644
61_E65_K0.105010.644
131_H136_V0.104940.643
167_L195_A0.104910.643
59_M63_W0.104910.643
40_K61_E0.10490.643
217_N221_Y0.104780.642
174_K177_K0.104630.641
89_I108_P0.104550.641
80_I84_V0.103880.637
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
3kbbA0.857799.90.376
4fe3A0.995999.90.395
4gibA0.882199.90.4
3e58A0.849699.90.412
4ex6A0.865999.80.416
2ah5A0.808999.80.42
3dv9A0.861899.80.421
4eekA0.894399.80.426
3l5kA0.869999.80.427
2hcfA0.87899.80.427

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