GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PhoU_div - Protein of unknown function DUF47
Pfam: PF01865 (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: CL0297
Length: 214
Sequences: 2990
Seq/Len: 13.97
HH_delta: 0.182 (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
161_A198_A0.593692.867
32_E36_E0.583432.818
129_E157_L0.565382.731
57_D92_D0.545062.632
162_D199_D0.511452.470
129_E153_E0.502212.425
88_D92_D0.494832.390
154_I205_A0.494022.386
53_E57_D0.488272.358
53_E92_D0.480072.319
158_E162_D0.427272.064
53_E88_D0.419912.028
86_S203_D0.404251.952
56_A91_A0.40181.941
115_E171_K0.40111.937
158_E199_D0.397331.919
57_D88_D0.380611.838
160_E163_K0.368371.779
158_E195_E0.361111.744
203_D206_D0.353551.708
31_L120_A0.348141.681
122_I160_E0.339211.638
195_E199_D0.332381.605
127_I201_C0.332031.604
58_E62_E0.325391.572
25_V29_E0.323931.564
129_E150_L0.323471.562
162_D195_E0.322431.557
47_E51_E0.305661.476
153_E157_L0.304791.472
157_L160_E0.303461.466
86_S200_K0.299761.448
83_L204_V0.298281.441
90_I127_I0.297091.435
90_I197_I0.293181.416
168_L191_Y0.292361.412
130_L201_C0.290091.401
122_I157_L0.286551.384
151_I209_E0.285281.378
47_E102_S0.282621.365
33_A38_D0.279841.352
62_E66_E0.2791.347
132_E136_E0.274421.325
126_A198_A0.273131.319
84_I207_R0.261631.264
126_A157_L0.260551.258
123_V194_L0.25851.248
153_E156_K0.258081.246
118_E160_E0.25791.246
49_I98_A0.256331.238
52_L55_E0.255751.235
48_E52_L0.253181.223
96_D193_H0.252811.221
55_E58_E0.251611.215
133_A154_I0.246261.189
64_R67_L0.244981.183
150_L153_E0.242321.170
125_E129_E0.235521.137
118_E121_E0.235311.136
115_E167_R0.23321.126
29_E52_L0.232641.124
29_E48_E0.228461.103
174_S179_M0.228151.102
124_V128_E0.227391.098
80_I134_I0.227341.098
50_K53_E0.226911.096
163_K167_R0.225711.090
57_D60_K0.22411.082
46_L50_K0.22371.080
159_E162_D0.223511.079
45_L48_E0.220891.067
67_L84_I0.220181.063
35_L117_Q0.219841.062
132_E150_L0.21961.061
46_L102_S0.219551.060
125_E157_L0.218761.057
130_L208_I0.218381.055
88_D91_A0.217461.050
122_I161_A0.21411.034
130_L204_V0.214061.034
48_E51_E0.212161.025
123_V161_A0.210271.016
80_I83_L0.209821.013
155_N202_E0.209691.013
175_N179_M0.20951.012
93_Y193_H0.208231.006
177_D180_D0.206570.998
44_E47_E0.206540.998
170_K174_S0.206520.997
53_E95_E0.205040.990
63_I84_I0.203710.984
99_K166_R0.203260.982
50_K57_D0.203170.981
60_K64_R0.202470.978
60_K82_R0.201990.976
97_A190_I0.19980.965
89_D196_D0.197160.952
93_Y196_D0.194930.941
30_L49_I0.194380.939
72_I79_D0.194040.937
71_F76_D0.193750.936
195_E198_A0.193480.934
109_P112_L0.191440.925
118_E164_L0.190980.922
60_K84_I0.189320.914
45_L49_I0.18840.910
82_R85_S0.186460.901
54_H57_D0.186250.900
111_E171_K0.185950.898
25_V28_A0.185580.896
114_E117_Q0.184990.893
28_A124_V0.184970.893
119_L194_L0.184360.890
123_V201_C0.183840.888
120_A194_L0.183630.887
114_E118_E0.183090.884
86_S207_R0.181580.877
73_T76_D0.180040.870
74_P78_E0.179720.868
96_D100_R0.1790.864
46_L53_E0.178330.861
71_F75_F0.178050.860
54_H58_E0.178010.860
26_L56_A0.177340.856
33_A45_L0.176840.854
82_R207_R0.176390.852
165_Y191_Y0.175110.846
60_K85_S0.175030.845
104_Y107_E0.174710.844
119_L165_Y0.173450.838
36_E128_E0.173410.838
126_A158_E0.170750.825
116_F187_L0.17050.823
92_D203_D0.169390.818
64_R207_R0.168750.815
86_S89_D0.168590.814
30_L94_I0.168330.813
122_I125_E0.168240.813
119_L191_Y0.167370.808
90_I201_C0.16710.807
192_E200_K0.166530.804
187_L191_Y0.166390.804
172_L184_I0.16490.796
181_P185_I0.164810.796
119_L161_A0.164810.796
162_D198_A0.164590.795
185_I188_K0.164390.794
118_E167_R0.164370.794
64_R68_Y0.164280.793
49_I52_L0.164270.793
115_E191_Y0.162440.785
151_I208_I0.162170.783
70_S79_D0.162090.783
172_L187_L0.162030.783
115_E118_E0.160650.776
61_R155_N0.160640.776
59_I62_E0.159860.772
180_D183_E0.158640.766
93_Y165_Y0.15850.765
149_E153_E0.158230.764
122_I164_L0.158060.763
130_L205_A0.15790.763
180_D184_I0.157890.763
116_F191_Y0.157510.761
100_R190_I0.157360.760
88_D203_D0.157180.759
201_C208_I0.157020.758
89_D203_D0.156980.758
132_E135_E0.156240.755
71_F74_P0.155990.753
149_E152_K0.155960.753
47_E50_K0.155850.753
125_E153_E0.154870.748
89_D200_K0.15420.745
170_K176_E0.153880.743
169_I189_E0.153770.743
73_T78_E0.153670.742
30_L33_A0.153360.741
30_L34_Y0.152820.738
169_I173_F0.152580.737
113_R183_E0.151960.734
72_I75_F0.151730.733
29_E45_L0.151630.732
56_A88_D0.151570.732
110_E114_E0.151190.730
110_E183_E0.150410.726
96_D99_K0.150310.726
176_E179_M0.150310.726
129_E132_E0.150160.725
200_K203_D0.150140.725
30_L98_A0.149550.722
165_Y169_I0.149520.722
26_L55_E0.149430.722
114_E121_E0.149290.721
27_L197_I0.149120.720
53_E56_A0.149020.720
196_D200_K0.148120.715
66_E69_K0.147890.714
126_A201_C0.14780.714
173_F185_I0.146840.709
60_K116_F0.145850.704
202_E206_D0.145780.704
83_L207_R0.144950.700
189_E192_E0.144630.699
152_K156_K0.144040.696
46_L101_L0.142940.690
172_L191_Y0.142930.690
72_I76_D0.142750.689
100_R186_K0.142480.688
43_E47_E0.142470.688
68_Y210_I0.142010.686
100_R193_H0.14180.685
59_I77_R0.140860.680
67_L81_L0.140360.678
133_A150_L0.139910.676
89_D93_Y0.139660.675
37_G104_Y0.139480.674
152_K209_E0.139450.673
123_V197_I0.139370.673
196_D203_D0.138860.671
169_I188_K0.138650.670
46_L49_I0.137930.666
165_Y193_H0.137870.666
125_E176_E0.137810.666
109_P176_E0.137670.665
50_K98_A0.137430.664
93_Y192_E0.137220.663
75_F79_D0.137010.662
133_A208_I0.136970.662
165_Y195_E0.136660.660
134_I137_L0.136590.660
93_Y200_K0.136350.659
131_V134_I0.135820.656
122_I129_E0.13550.654
81_L207_R0.135440.654
65_E68_Y0.134980.652
169_I185_I0.134030.647
95_E99_K0.133730.646
75_F78_E0.133230.643
84_I173_F0.132820.641
79_D210_I0.132470.640
29_E32_E0.131940.637
133_A136_E0.131410.635
155_N205_A0.131370.634
123_V198_A0.131230.634
36_E117_Q0.130360.630
155_N209_E0.130320.629
111_E178_E0.130230.629
37_G107_E0.129480.625
70_S104_Y0.129030.623
109_P172_L0.128390.620
120_A190_I0.128160.619
93_Y197_I0.127130.614
165_Y189_E0.126720.612
45_L52_L0.12590.608
27_L91_A0.125480.606
139_S209_E0.125290.605
119_L126_A0.12510.604
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
2oltA199.90.182
3l39A0.976699.90.22
1sumB0.934699.90.315
2i0mA0.939399.80.325
1xwmA0.939399.80.335
1t72A0.939399.80.346
1t72A0.509398.40.704
1xwmA0.490798.30.715
1sumB0.490798.10.737
2i0mA0.5047980.739

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