GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TauD - Taurine catabolism dioxygenase TauD TfdA family
Pfam: PF02668 (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: CL0029
Length: 258
Sequences: 2720
Seq/Len: 10.54
HH_delta: 0.215 (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
138_R219_Y0.500073.170
141_P144_L0.443112.809
47_D50_Q0.42892.719
134_A138_R0.407522.583
117_C120_P0.400622.540
55_A257_V0.386792.452
126_E243_T0.386612.451
133_R182_R0.374552.374
42_R229_D0.370272.347
126_E222_R0.363312.303
208_A212_A0.360242.284
38_F129_F0.345592.191
40_V231_L0.341042.162
42_R226_Q0.33212.105
136_Y144_L0.326552.070
145_E149_E0.325572.064
152_R170_S0.322212.042
141_P145_E0.310461.968
31_E35_E0.30761.950
129_F231_L0.307051.946
138_R218_E0.305541.937
26_L57_R0.303951.927
204_Q208_A0.301541.911
126_E224_R0.295451.873
200_L204_Q0.291341.847
37_G133_R0.289411.835
137_E182_R0.289111.833
114_A230_L0.28781.824
33_L39_V0.285261.808
120_P227_P0.279561.772
127_T225_W0.2761.750
140_S143_L0.272151.725
55_A114_A0.270421.714
223_H229_D0.268151.700
134_A137_E0.266421.689
122_E250_G0.265631.684
143_L209_A0.265041.680
34_A179_E0.262821.666
52_E56_S0.256421.625
48_P255_L0.252431.600
222_R243_T0.250741.589
119_R251_D0.250421.587
50_Q53_A0.24841.575
118_L253_H0.247631.570
49_E53_A0.241781.533
37_G131_D0.241281.529
176_T183_K0.240371.524
34_A180_T0.232431.473
149_E183_K0.231311.466
73_I77_R0.22971.456
170_S195_Q0.229491.455
104_S155_R0.228071.446
43_G229_D0.227771.444
240_H252_R0.224311.422
99_W241_G0.223791.419
147_L210_L0.222131.408
153_Y173_I0.21981.393
134_A219_Y0.218991.388
174_V185_L0.21591.369
119_R227_P0.213751.355
25_E28_E0.21371.355
99_W130_A0.213161.351
27_E31_E0.212051.344
223_H231_L0.212021.344
131_D237_R0.20991.331
226_Q229_D0.207941.318
129_F233_W0.2041.293
235_N240_H0.203931.293
114_A232_I0.199811.267
117_C254_L0.199531.265
30_R179_E0.199521.265
40_V223_H0.198691.259
213_L216_D0.19731.251
145_E150_P0.193581.227
212_A216_D0.192551.221
118_L255_L0.192031.217
133_R184_I0.190761.209
132_A239_L0.190581.208
147_L174_V0.189881.204
112_Y232_I0.186091.180
43_G226_Q0.1861.179
153_Y191_A0.18451.170
177_H180_T0.184351.169
37_G237_R0.183821.165
54_L232_I0.180971.147
28_E31_E0.180231.142
130_A239_L0.178721.133
209_A213_L0.178411.131
133_R137_E0.1781.128
53_A56_S0.177491.125
146_R206_A0.176131.116
61_L257_V0.1761.116
30_R111_D0.174831.108
130_A135_V0.173351.099
128_T241_G0.172021.090
242_R245_F0.170971.084
191_A211_D0.169861.077
110_P113_L0.168671.069
140_S144_L0.165111.047
151_V206_A0.163841.039
142_E146_R0.163461.036
75_D255_L0.161851.026
103_G190_F0.16151.024
128_T220_T0.161011.021
33_L112_Y0.159511.011
128_T243_T0.159331.010
142_E145_E0.15921.009
104_S186_Y0.158931.007
26_L30_R0.15760.999
154_I168_S0.156820.994
194_F197_P0.15660.993
123_E249_D0.155950.989
43_G228_G0.154740.981
97_L242_R0.154440.979
135_V213_L0.153880.975
136_Y174_V0.153130.971
135_V185_L0.151820.962
75_D253_H0.151710.962
27_E30_R0.150210.952
154_I195_Q0.149020.945
187_S191_A0.148690.943
32_A36_Y0.148020.938
45_P228_G0.147690.936
213_L219_Y0.14570.924
38_F231_L0.14550.922
177_H234_D0.144390.915
99_W128_T0.144260.914
200_L203_S0.144040.913
201_E212_A0.143570.910
103_G110_P0.143360.909
73_I76_V0.143160.907
101_T132_A0.142930.906
116_Y228_G0.142470.903
131_D134_A0.142080.901
52_E72_D0.141730.898
133_R136_Y0.141440.897
205_E208_A0.141220.895
65_P68_T0.140470.890
173_I194_F0.139820.886
55_A58_L0.139720.886
252_R256_R0.139670.885
187_S207_L0.13920.882
137_E140_S0.139150.882
51_F116_Y0.139090.882
132_A214_L0.139060.881
37_G182_R0.138950.881
48_P116_Y0.138880.880
52_E61_L0.138630.879
44_F230_L0.138480.878
136_Y183_K0.13780.874
202_E205_E0.137630.872
152_R168_S0.136650.866
154_I193_R0.136320.864
97_L241_G0.135220.857
129_F221_Y0.134440.852
41_L232_I0.133780.848
205_E212_A0.132720.841
87_S90_P0.132420.839
109_P236_H0.131880.836
139_L143_L0.131850.836
42_R223_H0.130770.829
31_E34_A0.130710.829
146_R209_A0.130460.827
102_D125_G0.129810.823
30_R34_A0.128380.814
28_E32_A0.128230.813
147_L173_I0.127810.810
40_V229_D0.127590.809
129_F238_V0.126650.803
76_V85_D0.126610.803
111_D232_I0.126380.801
140_S213_L0.126280.800
133_R237_R0.126250.800
100_H240_H0.126010.799
207_L210_L0.125810.798
138_R213_L0.12540.795
74_W90_P0.125090.793
138_R145_E0.124910.792
146_R202_E0.124310.788
53_A57_R0.124170.787
111_D236_H0.123280.781
32_A35_E0.122570.777
32_A39_V0.121470.770
142_E205_E0.120980.767
46_L230_L0.120760.765
46_L228_G0.12070.765
35_E182_R0.119920.760
176_T181_G0.119630.758
225_W231_L0.118910.754
136_Y149_E0.118620.752
101_T186_Y0.118310.750
146_R150_P0.118240.750
211_D214_L0.117920.747
174_V183_K0.117290.743
51_F114_A0.117060.742
220_T223_H0.116960.741
203_S207_L0.116510.739
154_I170_S0.116450.738
189_P215_K0.116430.738
127_T140_S0.116310.737
51_F230_L0.116180.736
74_W85_D0.116070.736
178_P181_G0.115530.732
38_F238_V0.11490.728
85_D89_T0.114440.725
157_F160_S0.11430.725
146_R205_E0.113940.722
115_L254_L0.113830.722
124_G252_R0.113780.721
72_D75_D0.113390.719
99_W220_T0.11330.718
152_R195_Q0.113270.718
85_D88_Y0.113090.717
191_A207_L0.112910.716
140_S147_L0.11280.715
174_V206_A0.112450.713
188_S191_A0.112440.713
144_L176_T0.112070.710
98_P189_P0.112040.710
46_L50_Q0.111740.708
59_G256_R0.111660.708
131_D255_L0.111530.707
129_F241_G0.110860.703
113_L256_R0.110640.701
115_L225_W0.110250.699
71_G85_D0.110160.698
76_V254_L0.109770.696
35_E53_A0.109750.696
26_L58_L0.109680.695
41_L51_F0.10930.693
111_D248_P0.10920.692
187_S211_D0.1090.691
139_L209_A0.108840.690
65_P190_F0.108770.689
66_R70_Y0.108410.687
207_L211_D0.10830.687
188_S211_D0.107760.683
251_D254_L0.107710.683
73_I78_S0.107660.682
79_V84_E0.107240.680
100_H252_R0.107110.679
142_E218_E0.106960.678
30_R112_Y0.106930.678
74_W79_V0.106340.674
140_S209_A0.106250.674
212_A215_K0.105940.672
173_I191_A0.105810.671
71_G74_W0.105230.667
49_E145_E0.105160.667
70_Y74_W0.104990.666
75_D86_S0.104590.663
88_Y91_S0.104430.662
139_L144_L0.104280.661
36_Y57_R0.104250.661
140_S202_E0.104190.660
78_S90_P0.103970.659
54_L230_L0.103680.657
210_L213_L0.103640.657
107_P169_Q0.103510.656
101_T104_S0.10340.655
172_P220_T0.10330.655
104_S153_Y0.103120.654
127_T223_H0.103070.653
193_R203_S0.102760.651
84_E87_S0.102480.650
117_C227_P0.102280.648
63_S68_T0.101590.644
45_P227_P0.101560.644
113_L233_W0.101280.642
102_D124_G0.100730.639
34_A112_Y0.100650.638
131_D137_E0.100590.638
38_F115_L0.100450.637
128_T222_R0.100280.636
128_T217_P0.099810.633
78_S86_S0.099660.632
175_R183_K0.099390.630
147_L150_P0.099350.630
42_R222_R0.099340.630
158_P162_Y0.099260.629
149_E202_E0.099070.628
214_L239_L0.098530.625
113_L242_R0.098530.625
193_R200_L0.098190.622
86_S90_P0.098120.622
40_V129_F0.097660.619
145_E201_E0.097180.616
205_E209_A0.096860.614
37_G116_Y0.096740.613
99_W151_V0.096730.613
112_Y135_V0.096560.612
76_V90_P0.096450.611
67_S72_D0.096290.610
115_L233_W0.096020.609
199_D203_S0.095830.607
64_H103_G0.095610.606
70_Y76_V0.095590.606
142_E209_A0.095530.606
76_V123_E0.095520.605
221_Y229_D0.095480.605
131_D182_R0.09530.604
151_V173_I0.095160.603
168_S193_R0.094830.601
127_T231_L0.094790.601
151_V194_F0.094750.601
191_A194_F0.094740.601
155_R190_F0.094580.600
156_R159_S0.094480.599
200_L207_L0.094410.598
122_E249_D0.09430.598
221_Y238_V0.093720.594
144_L147_L0.093530.593
232_I239_L0.093490.593
171_H185_L0.093280.591
44_F59_G0.09320.591
105_Y161_R0.093090.590
25_E58_L0.092990.589
176_T209_A0.092940.589
71_G75_D0.092830.588
234_D237_R0.092730.588
146_R197_P0.092680.587
62_M65_P0.092470.586
38_F233_W0.09190.583
48_P59_G0.091760.582
119_R201_E0.091680.581
31_E39_V0.091440.580
204_Q211_D0.091330.579
56_S88_Y0.091330.579
100_H125_G0.091270.579
73_I90_P0.091230.578
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
3eatX0.95351000.215
1oihA0.9381000.222
4j5iA0.94571000.223
3pvjA0.94961000.225
3r1jA0.9381000.227
1otjA0.94571000.236
1nx8A0.94571000.255
2q4aA0.95741000.288
3o2gA0.94961000.293
2og5A0.94571000.349

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