GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
F420_oxidored - NADP oxidoreductase coenzyme F420-dependent
Pfam: PF03807 (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: 96
Sequences: 63293
Seq/Len: 659.3
HH_delta: 0.08 (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
3_G62_A3.805833.464
1_K27_E2.817512.565
1_K29_I2.430372.212
36_P40_A2.317592.110
85_L88_K2.219332.020
2_I18_L2.092611.905
1_K63_D2.056171.872
29_I62_A2.053411.869
35_S38_K1.910561.739
7_A33_S1.841621.676
75_P79_S1.792271.631
14_L66_I1.773441.614
54_D57_E1.706581.553
40_A44_K1.663151.514
29_I61_E1.63761.491
7_A30_I1.626481.481
3_G58_A1.619661.474
76_E80_E1.591731.449
40_A43_A1.551491.412
2_I26_H1.542991.405
64_V89_L1.540041.402
84_L88_K1.470491.339
41_E45_E1.462031.331
18_L66_I1.414371.287
2_I64_V1.407641.281
41_E44_K1.394021.269
69_V77_V1.371471.248
67_L90_V1.308641.191
4_I15_A1.306251.189
37_E40_A1.300811.184
56_E80_E1.286131.171
1_K61_E1.272141.158
13_A16_R1.239021.128
10_M68_A1.224481.115
38_K41_E1.217071.108
29_I51_T1.216411.107
17_G21_S1.21041.102
39_A43_A1.197771.090
16_R20_A1.187621.081
13_A17_G1.18521.079
67_L70_K1.174291.069
4_I66_I1.171021.066
14_L68_A1.168011.063
7_A12_S1.166011.061
7_A15_A1.164951.060
36_P39_A1.160631.057
17_G20_A1.145031.042
3_G65_V1.135191.033
27_E49_Q1.093250.995
9_N12_S1.075320.979
33_S39_A1.056450.962
15_A30_I1.033560.941
33_S38_K1.030230.938
12_S16_R1.026530.934
65_V88_K1.020650.929
73_Q76_E1.002050.912
3_G31_V0.992920.904
58_A62_A0.983290.895
70_K73_Q0.979810.892
71_P74_L0.968580.882
12_S45_E0.965360.879
9_N13_A0.965110.879
10_M14_L0.964020.878
56_E60_Q0.96290.877
5_I65_V0.955450.870
2_I66_I0.938560.854
43_A50_A0.932670.849
76_E79_S0.924190.841
12_S41_E0.914010.832
10_M71_P0.908940.827
77_V80_E0.907380.826
78_L81_I0.907360.826
36_P52_A0.902550.822
73_Q77_V0.899830.819
37_E41_E0.889420.810
63_D85_L0.881150.802
48_V51_T0.865480.788
57_E60_Q0.861250.784
11_G68_A0.853150.777
22_G26_H0.835270.760
11_G15_A0.830240.756
21_S26_H0.82820.754
55_N58_A0.82360.750
48_V52_A0.812570.740
7_A31_V0.802240.730
14_L18_L0.790660.720
78_L90_V0.786640.716
67_L78_L0.779160.709
42_L45_E0.778220.708
1_K62_A0.777470.708
29_I49_Q0.771140.702
35_S40_A0.753660.686
74_L78_L0.74960.682
59_A62_A0.735660.670
79_S85_L0.73240.667
38_K42_L0.729010.664
51_T58_A0.725780.661
18_L26_H0.725230.660
5_I69_V0.720590.656
64_V91_I0.714520.650
49_Q52_A0.710820.647
39_A50_A0.702220.639
16_R45_E0.691440.629
62_A65_V0.688160.626
59_A81_I0.68680.625
5_I77_V0.681440.620
69_V74_L0.675870.615
14_L21_S0.67110.611
86_K89_L0.668430.608
5_I67_L0.66780.608
4_I11_G0.665790.606
61_E88_K0.66230.603
5_I31_V0.655440.597
63_D88_K0.653560.595
9_N70_K0.651670.593
75_P78_L0.644950.587
8_G68_A0.643050.585
67_L91_I0.635210.578
55_N80_E0.632430.576
84_L90_V0.624660.569
4_I14_L0.623790.568
55_N77_V0.623090.567
19_L47_G0.617430.562
42_L46_Y0.612770.558
71_P75_P0.610220.555
9_N71_P0.60670.552
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
3triA0.9792990.08
3dttA0.9479990.096
4hujA0.9479990.097
3gt0A0.9792990.099
1z82A0.916798.90.113
2zydA0.947998.90.119
3d1lA0.947998.90.123
3k96A0.947998.90.134
2p4qA0.947998.90.135
1evyA0.947998.90.14

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