GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Dus - Dihydrouridine synthase (Dus)
Pfam: PF01207 (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: 309
Sequences: 3103
Seq/Len: 10.04
HH_delta: 0.341 (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
179_K208_D0.851674.660
19_E249_R0.822944.503
76_A122_P0.6313.452
193_F197_D0.550813.014
194_S197_D0.542442.968
200_R204_Q0.519452.842
68_L85_L0.511042.796
118_R153_S0.503952.757
54_R81_D0.465922.549
115_K119_K0.460752.521
114_V152_V0.457922.505
199_E203_E0.442772.423
173_E204_Q0.418872.292
13_F17_C0.414622.269
176_A180_E0.404472.213
177_E180_E0.403562.208
72_A121_V0.396472.169
148_E184_I0.385162.107
188_A201_M0.383522.098
105_K133_W0.382132.091
131_L174_A0.368692.017
192_I201_M0.364051.992
70_E73_E0.358451.961
148_E183_P0.355591.946
87_M110_L0.354711.941
293_T296_E0.354421.939
196_E200_R0.352661.930
193_F215_G0.352341.928
197_D200_R0.351081.921
252_D298_L0.344121.883
182_L186_V0.334761.832
250_H274_Y0.334131.828
66_E70_E0.33251.819
68_L117_V0.328311.796
106_D109_L0.3251.778
62_G68_L0.324591.776
98_G106_D0.320871.756
111_A150_A0.320081.751
171_D174_A0.321.751
112_E115_K0.315431.726
200_R203_E0.314531.721
25_L57_I0.313711.716
57_I82_G0.310661.700
248_L302_E0.307431.682
64_D67_D0.305621.672
110_L143_F0.303781.662
111_A115_K0.302721.656
140_T178_I0.299851.641
129_I157_V0.296681.623
76_A121_V0.294891.613
286_R290_K0.291831.597
248_L298_L0.290891.592
154_A187_I0.290261.588
188_A192_I0.288731.580
85_L117_V0.285861.564
175_I188_A0.285611.563
108_D146_I0.284161.555
250_H271_L0.282151.544
135_D164_Q0.280831.537
292_K296_E0.280671.536
111_A146_I0.279151.527
164_Q171_D0.278211.522
176_A204_Q0.277531.518
188_A207_A0.277161.516
1_I187_I0.27611.511
142_E145_R0.273631.497
298_L302_E0.273561.497
108_D112_E0.272631.492
291_C300_L0.271651.486
296_E299_E0.270451.480
176_A201_M0.26941.474
109_L112_E0.268421.469
114_V150_A0.266951.461
145_R181_A0.261621.431
121_V125_V0.261511.431
58_V75_V0.261321.430
187_I211_M0.259421.419
65_P69_A0.25751.409
104_L143_F0.256881.405
196_E234_P0.256131.401
257_F262_K0.255031.395
174_A177_E0.254221.391
295_E299_E0.249411.365
75_V83_I0.24741.354
141_I181_A0.245691.344
179_K186_V0.244841.340
157_V178_I0.244821.340
145_R148_E0.244811.339
144_A182_L0.244761.339
25_L82_G0.24161.322
73_E120_A0.240581.316
170_A191_D0.240031.313
111_A149_D0.239691.311
187_I209_G0.236591.294
148_E182_L0.233031.275
134_D137_P0.232191.270
76_A123_I0.231971.269
127_V152_V0.230861.263
287_E291_C0.230551.261
69_A120_A0.230141.259
199_E229_I0.230021.259
73_E77_E0.225921.236
127_V147_L0.225011.231
224_R242_E0.224621.229
101_A162_R0.221841.214
291_C296_E0.221591.212
34_K67_D0.220781.208
231_E235_E0.218871.198
104_L129_I0.217791.192
252_D256_E0.217441.190
18_R55_P0.216851.186
65_P109_L0.216671.185
115_K150_A0.214571.174
159_G175_I0.214261.172
198_A210_V0.213691.169
145_R149_D0.211061.155
145_R182_L0.205071.122
126_S154_A0.204021.116
12_P257_F0.203321.112
88_G189_N0.203241.112
27_Y57_I0.201981.105
283_K286_R0.201511.103
104_L110_L0.200061.095
141_I177_E0.199631.092
144_A178_I0.199051.089
118_R125_V0.197371.080
249_R253_Y0.196931.077
11_L48_P0.196881.077
40_N43_T0.196811.077
1_I25_L0.193941.061
140_T174_A0.19331.058
201_M207_A0.193011.056
201_M205_T0.192351.052
20_F246_I0.192181.051
177_E181_A0.191871.050
143_F147_L0.191491.048
157_V186_V0.191141.046
103_L113_I0.1891.034
114_V147_L0.188061.029
146_I150_A0.1881.029
283_K287_E0.187231.024
107_P142_E0.187061.023
118_R152_V0.186581.021
219_N225_E0.185951.017
241_A245_D0.185611.016
68_L113_I0.185031.012
232_G235_E0.185011.012
131_L171_D0.182821.000
74_I77_E0.182721.000
172_W201_M0.182130.997
147_L152_V0.181930.995
202_L207_A0.181060.991
72_A125_V0.180840.989
221_W243_R0.180310.987
191_D214_R0.17970.983
15_R50_L0.179540.982
33_A71_A0.179170.980
3_A213_G0.178830.978
66_E116_A0.177390.971
104_L139_E0.176550.966
244_L248_L0.175620.961
15_R253_Y0.175450.960
137_P177_E0.174590.955
295_E298_L0.173890.951
250_H267_M0.172450.944
166_Y191_D0.171690.939
216_A222_L0.171150.936
291_C297_F0.169690.928
248_L252_D0.169670.928
254_M267_M0.169030.925
299_E302_E0.168250.921
6_A30_M0.168050.919
137_P181_A0.168010.919
33_A68_L0.167810.918
27_Y156_T0.167250.915
259_G263_A0.166780.913
188_A204_Q0.166130.909
15_R19_E0.16570.907
36_I78_L0.165570.906
247_I271_L0.16480.902
192_I198_A0.164710.901
143_F146_I0.163540.895
91_A94_V0.163490.895
114_V127_V0.163410.894
152_V155_I0.161310.883
216_A223_F0.16020.877
258_Y266_Q0.159960.875
8_V273_W0.159770.874
112_E119_K0.159130.871
156_T211_M0.158450.867
155_I184_I0.157620.862
11_L15_R0.157350.861
142_E146_I0.157030.859
141_I178_I0.156970.859
252_D294_L0.156340.855
129_I143_F0.155720.852
154_A185_P0.155550.851
69_A116_A0.155290.850
2_L216_A0.154560.846
57_I126_S0.154050.843
32_S61_F0.153910.842
253_Y256_E0.153350.839
110_L147_L0.152340.834
131_L159_G0.152240.833
72_A117_V0.152180.833
36_I74_I0.152160.833
144_A155_I0.151130.827
2_L17_C0.151030.826
33_A67_D0.15090.826
250_H254_M0.150690.824
34_K38_R0.150650.824
36_I40_N0.150490.823
148_E185_P0.150360.823
110_L114_V0.150260.822
37_L67_D0.149660.819
129_I140_T0.149470.818
239_P242_E0.149310.817
69_A73_E0.149120.816
75_V80_F0.148930.815
72_A123_I0.147790.809
255_E259_G0.147780.809
148_E179_K0.147710.808
20_F224_R0.147210.805
257_F260_E0.145570.796
41_K45_R0.145470.796
265_R268_R0.144260.789
261_E292_K0.144250.789
245_D249_R0.144010.788
129_I155_I0.143950.788
243_R278_F0.143940.788
139_E143_F0.143710.786
294_L298_L0.143560.785
83_I121_V0.143480.785
108_D111_A0.143290.784
148_E155_I0.143040.783
173_E177_E0.142760.781
82_G126_S0.141880.776
134_D163_K0.141650.775
44_I48_P0.140860.771
156_T187_I0.139260.762
269_K273_W0.138530.758
31_I35_A0.13850.758
141_I144_A0.138240.756
159_G178_I0.138150.756
2_L9_T0.138040.755
67_D70_E0.137760.754
43_T46_L0.137720.754
17_C216_A0.137030.750
285_R289_N0.136890.749
37_L70_E0.136870.749
135_D174_A0.136640.748
92_P95_T0.136620.748
16_L253_Y0.136490.747
212_I223_F0.136320.746
15_R52_N0.136290.746
260_E263_A0.136090.745
192_I212_I0.135150.739
73_E76_A0.135040.739
32_S35_A0.134670.737
66_E112_E0.134620.737
65_P113_I0.134540.736
240_I243_R0.134490.736
275_F284_F0.133610.731
105_K134_D0.13360.731
275_F281_A0.133590.731
45_R48_P0.132860.727
94_V99_A0.132590.725
202_L210_V0.132210.723
3_A211_M0.132120.723
230_K233_E0.13210.723
175_I189_N0.132030.722
131_L138_E0.131660.720
65_P112_E0.130490.714
251_Y255_E0.130390.713
1_I154_A0.130340.713
109_L113_I0.129820.710
172_W197_D0.129370.708
1_I27_Y0.129040.706
87_M127_V0.128920.705
2_L223_F0.128890.705
18_R53_E0.128750.704
132_G140_T0.128580.704
17_C223_F0.128190.701
129_I144_A0.128120.701
119_K145_R0.127670.699
212_I222_L0.127640.698
28_T56_L0.127570.698
48_P78_L0.127560.698
197_D201_M0.127410.697
76_A83_I0.127360.697
49_F56_L0.127240.696
271_L288_L0.127060.695
18_R26_T0.126650.693
85_L114_V0.126620.693
117_V125_V0.126590.693
36_I48_P0.126460.692
159_G174_A0.126360.691
176_A205_T0.126070.690
44_I78_L0.125820.688
60_L117_V0.125720.688
34_K64_D0.12520.685
173_E203_E0.124790.683
131_L157_V0.124530.681
8_V217_L0.124510.681
49_F54_R0.124330.680
62_G85_L0.123840.678
117_V120_A0.123820.677
116_A125_V0.123810.677
201_M204_Q0.123090.673
138_E174_A0.123040.673
115_K149_D0.122980.673
48_P51_P0.12260.671
296_E302_E0.122280.669
17_C22_A0.122270.669
110_L129_I0.122160.668
26_T56_L0.121620.665
282_R286_R0.12150.665
244_L301_L0.121180.663
63_N99_A0.12110.663
35_A47_L0.120950.662
259_G265_R0.120450.659
88_G211_M0.120360.659
104_L141_I0.12030.658
84_D156_T0.120150.657
17_C20_F0.120050.657
111_A152_V0.119680.655
141_I182_L0.119660.655
91_A165_R0.119580.654
186_V207_A0.119230.652
195_P225_E0.119190.652
287_E290_K0.118730.650
124_P153_S0.118490.648
98_G102_A0.118460.648
249_R252_D0.117790.644
6_A61_F0.117580.643
90_P162_R0.11730.642
29_E214_R0.11690.640
94_V97_G0.116720.639
251_Y264_L0.11670.639
180_E206_G0.116290.636
241_A246_I0.116230.636
72_A76_A0.116210.636
116_A119_K0.116140.635
36_I43_T0.116060.635
137_P174_A0.116010.635
137_P171_D0.115850.634
147_L155_I0.115710.633
61_F99_A0.115670.633
74_I78_L0.115630.633
212_I216_A0.115270.631
195_P234_P0.115140.630
8_V166_Y0.114920.629
164_Q168_G0.11490.629
268_R288_L0.114890.629
229_I233_E0.114480.626
275_F278_F0.114440.626
247_I275_F0.114210.625
176_A207_A0.114070.624
243_R247_I0.113570.621
175_I186_V0.113110.619
161_T164_Q0.112770.617
261_E264_L0.112770.617
268_R274_Y0.112480.615
79_G123_I0.11240.615
233_E237_F0.112060.613
35_A38_R0.111780.612
251_Y298_L0.111660.611
52_N256_E0.111460.610
172_W188_A0.111370.609
15_R256_E0.111290.609
60_L68_L0.111270.609
118_R121_V0.111270.609
215_G219_N0.111260.609
27_Y82_G0.111170.608
225_E237_F0.111050.608
242_E245_D0.1110.607
148_E151_G0.110740.606
113_I116_A0.110660.605
217_L273_W0.110630.605
93_K250_H0.110620.605
101_A104_L0.110330.604
40_N74_I0.110170.603
269_K274_Y0.109880.601
255_E294_L0.109730.600
141_I174_A0.109640.600
157_V175_I0.109530.599
217_L270_H0.109520.599
221_W224_R0.109520.599
42_K45_R0.109510.599
244_L247_I0.109490.599
296_E300_L0.10920.597
1_I156_T0.109180.597
63_N98_G0.109170.597
141_I145_R0.109150.597
155_I185_P0.10910.597
25_L156_T0.108940.596
132_G214_R0.108790.595
146_I149_D0.108690.595
231_E234_P0.108580.594
261_E265_R0.108560.594
2_L22_A0.108440.593
79_G132_G0.108390.593
136_S181_A0.108270.592
12_P253_Y0.107950.591
240_I247_I0.107910.590
111_A143_F0.107870.590
178_I181_A0.107840.590
95_T102_A0.107790.590
87_M147_L0.107740.589
109_L243_R0.107530.588
131_L140_T0.107170.586
5_M217_L0.107120.586
23_D233_E0.107090.586
65_P120_A0.106860.585
281_A285_R0.106850.585
30_M61_F0.106760.584
105_K137_P0.106730.584
49_F75_V0.106560.583
251_Y297_F0.106470.583
70_E74_I0.10640.582
173_E241_A0.106120.581
192_I210_V0.106070.580
1_I4_P0.106050.580
39_S44_I0.105870.579
1_I209_G0.105660.578
264_L297_F0.105660.578
118_R150_A0.105570.578
164_Q170_A0.105370.577
8_V13_F0.105230.576
188_A202_L0.105230.576
70_E77_E0.105170.575
263_A266_Q0.104570.572
279_P299_E0.104290.571
12_P15_R0.104270.571
10_D29_E0.104180.570
263_A268_R0.104080.569
263_A267_M0.10390.568
95_T162_R0.103780.568
77_E256_E0.103620.567
166_Y170_A0.103460.566
239_P245_D0.103340.565
159_G189_N0.103310.565
18_R54_R0.103310.565
135_D138_E0.103280.565
295_E302_E0.103020.564
16_L20_F0.102980.563
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
1vhnA0.97091000.341
3b0pA0.97091000.344
2r14A0.83821000.629
1icpA0.82521000.634
1jubA0.77991000.636
1z41A0.77991000.638
1vyrA0.80911000.64
1gteA0.9451000.641
2hsaB0.85111000.644
4ef8A0.78321000.647

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