GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pyr_redox_2 - Pyridine nucleotide-disulphide oxidoreductase
Pfam: PF07992 (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: CL0063
Length: 201
Sequences: 20374
Seq/Len: 101.36
HH_delta: 0.295 (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
180_D184_Q2.239893.719
1_D24_K1.966383.265
2_V18_L1.886553.132
170_E178_K1.885993.131
1_D112_D1.710062.839
30_K80_K1.697052.818
14_A115_V1.675162.781
89_K189_G1.635372.715
111_Y114_L1.554662.581
3_V28_I1.553512.579
28_I109_I1.505092.499
172_D176_F1.428292.372
3_V111_Y1.401182.327
113_Y189_G1.385482.300
170_E186_S1.33762.221
3_V109_I1.325592.201
10_A193_A1.315652.184
86_P187_V1.264432.099
3_V26_L1.17341.948
1_D26_L1.149791.909
184_Q188_P1.136151.886
183_L197_A1.114661.851
2_V115_V1.109921.843
115_V193_A1.109131.842
179_V197_A1.103231.832
172_D198_G1.078151.790
85_D88_S1.057241.755
179_V192_A1.055631.753
113_Y191_Y1.043331.732
118_T196_C1.040661.728
177_I192_A0.996581.655
24_K74_E0.977181.622
172_D178_K0.946591.572
7_G29_E0.943861.567
4_I15_A0.92091.529
141_D144_R0.91621.521
14_A193_A0.916151.521
86_P190_I0.914881.519
2_V23_A0.891361.480
178_K186_S0.889141.476
65_V69_K0.854091.418
32_P78_N0.853791.418
4_I11_G0.846351.405
15_A27_I0.84521.403
26_L109_I0.844591.402
103_T106_G0.844291.402
30_K88_S0.843141.400
91_V114_L0.832561.382
121_R161_E0.82881.376
79_A105_D0.825151.370
177_I196_C0.821331.364
126_N130_E0.818581.359
161_E165_E0.816811.356
117_A193_A0.814221.352
26_L85_D0.812941.350
90_R110_K0.810351.345
79_A107_R0.772051.282
185_T192_A0.770111.279
184_Q189_G0.758371.259
5_I116_I0.758181.259
192_A196_C0.756451.256
3_V91_V0.743031.234
140_D144_R0.732281.216
90_R108_E0.724591.203
140_D148_L0.69291.150
18_L25_V0.68941.145
18_L23_A0.672911.117
116_I196_C0.663251.101
5_I118_T0.656761.090
1_D23_A0.656071.089
28_I81_V0.654451.087
83_S102_E0.646611.074
187_V190_I0.645881.072
171_L178_K0.642161.066
179_V183_L0.629641.045
17_E20_R0.628251.043
52_H55_E0.625911.039
17_E21_P0.62441.037
171_L177_I0.622671.034
2_V113_Y0.614591.020
66_D69_K0.614571.020
1_D110_K0.608341.010
4_I25_V0.60541.005
169_V186_S0.604981.005
63_K66_D0.602491.000
114_L190_I0.596540.990
162_F166_K0.590450.980
63_K67_Q0.581460.965
5_I89_K0.581060.965
184_Q187_V0.569930.946
184_Q191_Y0.566960.941
11_G15_A0.561440.932
173_E178_K0.56140.932
79_A104_G0.560930.931
160_T171_L0.560410.930
64_L71_R0.560350.930
102_E108_E0.558610.928
14_A18_L0.558130.927
19_A25_V0.558030.927
55_E58_P0.557940.926
48_E52_H0.557140.925
167_L187_V0.554410.921
7_G27_I0.551780.916
40_C44_P0.54360.903
192_A197_A0.54170.899
64_L67_Q0.54080.898
122_P141_D0.536120.890
15_A73_V0.536080.890
48_E51_P0.535270.889
1_D109_I0.535070.888
24_K112_D0.527380.876
19_A73_V0.525930.873
83_S166_K0.523460.869
53_R57_L0.522850.868
125_P130_E0.521940.867
143_Q146_L0.52070.865
169_V177_I0.520120.864
23_A112_D0.516890.858
13_S17_E0.514070.854
82_V104_G0.510650.848
142_A145_F0.508710.845
3_V114_L0.504440.838
4_I14_A0.500390.831
176_F198_G0.497980.827
42_P45_L0.494260.821
85_D109_I0.490130.814
38_S143_Q0.487740.810
43_S46_L0.486690.808
27_I77_L0.485190.806
44_P47_V0.484860.805
85_D89_K0.483810.803
50_A53_R0.479960.797
5_I81_V0.478110.794
28_I79_A0.477750.793
11_G117_A0.476540.791
143_Q147_E0.47550.790
169_V187_V0.473470.786
54_H58_P0.472670.785
103_T109_I0.471310.783
67_Q71_R0.470570.781
174_N198_G0.457730.760
4_I117_A0.455810.757
140_D145_F0.455080.756
160_T196_C0.453920.754
136_L145_F0.451890.750
16_L20_R0.450930.749
127_I130_E0.450280.748
136_L142_A0.450280.748
168_G171_L0.44860.745
111_Y189_G0.447930.744
4_I27_I0.447120.742
124_T141_D0.445390.740
80_K104_G0.441380.733
13_S16_L0.437620.727
84_I114_L0.437390.726
144_R147_E0.437060.726
54_H57_L0.436910.725
178_K198_G0.436690.725
68_L72_G0.436350.725
51_P55_E0.436220.724
104_G107_R0.435850.724
40_C43_S0.435380.723
103_T107_R0.435270.723
51_P54_H0.43520.723
39_G42_P0.433540.720
26_L111_Y0.432750.719
123_R126_N0.428910.712
145_F148_L0.427990.711
169_V190_I0.427730.710
148_L152_P0.427720.710
181_E199_I0.427170.709
91_V111_Y0.42510.706
169_V185_T0.423010.702
177_I185_T0.421770.700
39_G44_P0.419850.697
90_R102_E0.41580.690
9_P13_S0.415250.689
160_T163_L0.413040.686
45_L48_E0.412070.684
25_V73_V0.411810.684
82_V106_G0.411320.683
87_E90_R0.408350.678
141_D145_F0.407980.677
167_L171_L0.403850.671
74_E77_L0.402630.669
37_N40_C0.402090.668
165_E168_G0.401130.666
121_R160_T0.400670.665
183_L191_Y0.399660.664
44_P48_E0.398810.662
15_A25_V0.397830.661
60_R63_K0.395030.656
34_T77_L0.394510.655
63_K68_L0.39070.649
40_C46_L0.390180.648
44_P50_A0.386860.642
26_L74_E0.385030.639
71_R75_I0.384880.639
43_S47_V0.384450.638
79_A82_V0.380610.632
2_V14_A0.380530.632
185_T190_I0.380310.631
102_E107_R0.377330.627
121_R162_F0.376740.626
57_L60_R0.37590.624
29_E35_P0.3740.621
165_E171_L0.373880.621
9_P12_L0.373860.621
183_L199_I0.373520.620
68_L71_R0.373330.620
178_K181_E0.371610.617
12_L27_I0.371290.616
65_V68_L0.37020.615
86_P111_Y0.368380.612
162_F165_E0.36830.612
147_E151_S0.368020.611
150_E153_K0.366710.609
85_D90_R0.366640.609
114_L189_G0.365260.606
140_D143_Q0.362340.602
79_A103_T0.361070.600
142_A146_L0.359550.597
45_L49_I0.359330.597
102_E106_G0.359290.597
162_F167_L0.358550.595
12_L16_L0.357710.594
35_P40_C0.35710.593
28_I103_T0.353460.587
3_V112_D0.35230.585
66_D70_N0.351760.584
56_F59_A0.350140.581
136_L144_R0.350080.581
38_S43_S0.346230.575
139_V143_Q0.346040.575
19_A71_R0.345830.574
173_E176_F0.345730.574
168_G187_V0.344950.573
171_L186_S0.344110.571
26_L77_L0.34380.571
90_R166_K0.343440.570
170_E173_E0.342760.569
180_D188_P0.342440.569
146_L150_E0.341250.567
11_G27_I0.340270.565
5_I114_L0.339780.564
23_A113_Y0.339670.564
180_D186_S0.337210.560
75_I79_A0.336130.558
85_D102_E0.336060.558
68_L73_V0.335760.557
37_N42_P0.333640.554
137_R141_D0.332870.553
15_A19_A0.332550.552
91_V187_V0.332070.551
167_L190_I0.331020.550
36_Y41_I0.330710.549
42_P48_E0.330380.549
81_V84_I0.330130.548
42_P49_I0.329710.547
193_A197_A0.329060.546
130_E139_V0.328150.545
19_A72_G0.327450.544
124_T130_E0.326980.543
19_A24_K0.32580.541
138_G141_D0.325780.541
69_K72_G0.325470.540
170_E185_T0.325260.540
46_L50_A0.323180.537
48_E55_E0.322760.536
36_Y39_G0.32260.536
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
4eqsA0.950299.90.295
4fk1A0.935399.90.315
3kljA0.910499.90.324
3ntdA0.950299.90.353
3icsA0.955299.90.355
4gcmA0.915499.90.357
3oc4A0.930399.90.358
3kd9A0.920499.80.359
4fx9A0.920499.80.36
4g6hA0.970199.80.363

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