GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DFP - DNA pantothenate metabolism flavoprotein
Pfam: PF04127 (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: 185
Sequences: 45464
Seq/Len: 245.75
HH_delta: 0.252 (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
106_K114_T3.690653.014
106_K110_G3.521322.876
68_S71_E3.412072.787
6_V85_I3.399152.776
5_K45_E2.761952.256
110_G114_T2.748372.245
73_L122_K2.728762.229
11_G48_L2.698352.204
128_R158_K2.616182.137
49_I64_I2.571882.101
38_E42_R2.563062.093
120_T151_A2.497062.039
33_A37_E2.360611.928
53_S56_P2.305961.883
124_L155_L2.230241.822
134_N161_D2.213251.808
69_A102_E2.162871.766
141_K144_T2.148311.755
137_L148_I2.142181.750
31_M170_Q2.132221.741
64_I71_E2.128691.739
6_V39_A2.074791.695
109_S113_L2.007981.640
38_E41_R2.006151.638
76_V123_I2.001441.635
5_K47_T1.987471.623
27_S50_H1.971171.610
74_E78_E1.963011.603
53_S63_V1.950921.593
148_I164_V1.904381.555
47_T80_L1.874881.531
44_A85_I1.84211.505
71_E74_E1.834051.498
39_A44_A1.817611.485
69_A118_K1.803791.473
6_V44_A1.798331.469
73_L77_K1.794911.466
49_I75_A1.754271.433
101_A104_K1.749051.429
69_A73_L1.732211.415
34_A37_E1.720011.405
86_I119_P1.705651.393
4_K84_D1.703851.392
5_K82_S1.682591.374
114_T118_K1.660691.356
88_M137_L1.654221.351
88_M120_T1.622611.325
62_K78_E1.591351.300
72_M119_P1.573721.285
94_D107_K1.546291.263
64_I75_A1.542321.260
70_E74_E1.541821.259
134_N163_I1.540551.258
102_E118_K1.538511.257
7_L83_A1.527671.248
126_E130_N1.509111.233
86_I123_I1.492451.219
9_T88_M1.484921.213
109_S114_T1.481271.210
47_T62_K1.473921.204
36_A48_L1.463071.195
140_F144_T1.449631.184
8_I36_A1.440321.176
74_E77_K1.430881.169
67_E107_K1.41831.158
35_L87_I1.392911.138
145_E166_N1.387861.134
148_I162_L1.360031.111
140_F143_E1.352131.104
92_V111_D1.35121.104
94_D104_K1.329751.086
117_L147_L1.318291.077
62_K75_A1.31351.073
83_A123_I1.31271.072
70_E73_L1.287681.052
82_S130_N1.279831.045
37_E41_R1.275441.042
103_G107_K1.273961.040
7_L49_I1.271591.039
92_V107_K1.233881.008
145_E149_E1.226061.001
126_E129_K1.223160.999
45_E60_G1.216870.994
151_A162_L1.207780.986
146_E149_E1.203220.983
104_K107_K1.191990.974
127_L130_N1.181520.965
146_E150_N1.180410.964
111_D115_L1.170860.956
35_L89_A1.164170.951
102_E106_K1.16040.948
64_I72_M1.159740.947
34_A38_E1.149270.939
69_A121_P1.148160.938
4_K44_A1.144960.935
96_R104_K1.137940.929
47_T79_L1.13340.926
32_G89_A1.123860.918
102_E114_T1.115450.911
31_M35_L1.113570.909
120_T147_L1.10520.903
5_K84_D1.104840.902
105_I114_T1.085980.887
5_K80_L1.075520.878
67_E110_G1.075280.878
63_V71_E1.075240.878
7_L75_A1.071760.875
118_K122_K1.043150.852
45_E80_L1.037710.848
149_E152_K1.033310.844
116_E120_T1.032510.843
98_E128_R1.023860.836
122_K125_A1.017950.831
66_V90_A1.008920.824
152_K163_I0.99160.810
88_M119_P0.990780.809
69_A122_K0.983670.803
53_S61_V0.979930.800
102_E121_P0.973220.795
11_G49_I0.969260.792
37_E40_A0.967860.790
116_E119_P0.966260.789
71_E75_A0.956420.781
77_K126_E0.953270.779
150_N153_E0.947460.774
149_E153_E0.93680.765
108_S112_E0.936770.765
66_V115_L0.932770.762
55_L61_V0.931950.761
117_L121_P0.919750.751
28_S33_A0.918030.750
39_A85_I0.916720.749
114_T117_L0.915410.748
50_H55_L0.913660.746
62_K79_L0.911340.744
27_S51_G0.908290.742
112_E116_E0.907680.741
28_S50_H0.901660.736
54_S57_P0.891360.728
106_K118_K0.885470.723
9_T90_A0.862370.704
100_P142_A0.859410.702
107_K110_G0.859270.702
36_A46_V0.858070.701
125_A128_R0.855250.699
67_E111_D0.854420.698
123_I127_L0.851540.695
150_N154_K0.849790.694
83_A126_E0.845030.690
76_V122_K0.838310.685
35_L39_A0.835040.682
92_V108_S0.834770.682
145_E164_V0.832110.680
52_P55_L0.83170.679
28_S52_P0.824030.673
88_M116_E0.822880.672
33_A57_P0.820570.670
127_L133_P0.812650.664
36_A40_A0.804030.657
155_L158_K0.801810.655
35_L38_E0.794680.649
60_G79_L0.79290.648
152_K156_E0.792140.647
72_M75_A0.791710.647
167_D170_Q0.789930.645
98_E155_L0.781980.639
50_H53_S0.77840.636
135_Q161_D0.773270.632
91_A112_E0.771550.630
28_S54_S0.767690.627
87_I138_V0.766540.626
89_A138_V0.763120.623
124_L158_K0.763110.623
90_A115_L0.763040.623
110_G118_K0.762330.623
50_H61_V0.759110.620
7_L86_I0.756180.618
65_R68_S0.755350.617
73_L125_A0.755330.617
88_M148_I0.75440.616
76_V86_I0.753140.615
124_L128_R0.751490.614
116_E137_L0.748410.611
29_G32_G0.744310.608
82_S126_E0.742870.607
118_K121_P0.742060.606
127_L132_K0.741390.606
153_E156_E0.740960.605
9_T119_P0.737160.602
120_T124_L0.731010.597
48_L61_V0.727830.594
40_A46_V0.727480.594
9_T89_A0.724990.592
47_T83_A0.724120.591
152_K162_L0.722490.590
4_K85_I0.722420.590
60_G80_L0.721760.589
120_T135_Q0.715790.585
125_A129_K0.713490.583
72_M122_K0.711750.581
151_A154_K0.708670.579
72_M118_K0.707440.578
123_I126_E0.700340.572
50_H63_V0.698050.570
151_A155_L0.694250.567
66_V72_M0.692340.565
112_E115_L0.686490.561
98_E158_K0.686430.561
147_L151_A0.685280.560
96_R99_E0.682220.557
75_A79_L0.677690.553
48_L59_P0.675760.552
155_L162_L0.668780.546
49_I71_E0.656340.536
107_K111_D0.654590.535
105_I113_L0.652870.533
39_A46_V0.651720.532
141_K145_E0.649290.530
72_M76_V0.644460.526
31_M167_D0.637690.521
69_A103_G0.63680.520
113_L117_L0.635180.519
47_T60_G0.631780.516
44_A84_D0.626850.512
97_P100_P0.625350.511
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
4ag3A0.913599.90.252
4g81D0.913599.90.261
4h15A0.913599.90.263
1u7zA199.90.263
4gkbA0.908199.90.265
4hp8A0.902799.90.272
4fgsA0.902799.90.276
4iuyA0.913599.90.28
4iqgC0.913599.90.284
3u49A0.913599.90.289

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