GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pyr_redox - Pyridine nucleotide-disulphide oxidoreductase
Pfam: PF00070 (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: 80
Sequences: 42899
Seq/Len: 536.24
HH_delta: 0.085 (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
26_T58_H3.779663.375
65_E76_T3.394733.032
1_R24_E3.229932.885
30_R62_K2.888122.579
67_E76_T2.772782.476
3_V28_I2.703192.414
26_T56_E2.569682.295
2_V18_L2.364022.111
3_V75_V2.263442.021
1_R26_T2.230131.992
24_E56_E2.141611.913
7_G29_E1.985161.773
47_E51_R1.880621.680
32_D60_N1.858311.660
64_K76_T1.847681.650
58_H61_T1.80821.615
15_A27_L1.70891.526
4_V11_G1.59661.426
19_A55_V1.594161.424
1_R23_K1.549011.383
11_G29_E1.523011.360
49_Y53_R1.444181.290
18_L23_K1.410631.260
2_V23_K1.396271.247
3_V26_T1.392141.243
28_I58_H1.347011.203
16_E53_R1.302721.163
5_I63_V1.277351.141
14_L18_L1.232471.101
15_A55_V1.190451.063
45_I49_Y1.149171.026
29_E59_T1.148391.026
16_E20_E1.140221.018
16_E49_Y1.129671.009
63_V75_V1.126211.006
20_E53_R1.123981.004
19_A54_G1.121391.001
12_I50_L1.119060.999
34_L59_T1.118890.999
67_E70_G1.107920.989
14_L17_A1.103210.985
49_Y52_K1.09920.982
47_E59_T1.087420.971
15_A25_V1.070280.956
7_G27_L1.047560.936
44_K48_E1.043110.932
48_E52_K1.031610.921
41_D44_K0.990320.884
17_A21_L0.957020.855
19_A53_R0.953480.852
42_A45_I0.918150.820
10_I13_E0.905540.809
17_A20_E0.896130.800
19_A24_E0.89260.797
19_A25_V0.882030.788
50_L55_V0.862160.770
13_E17_A0.860250.768
48_E51_R0.855340.764
44_K47_E0.849670.759
12_I27_L0.840940.751
2_V25_V0.826890.738
4_V15_A0.810590.724
66_I75_V0.803560.718
4_V14_L0.794940.710
43_A47_E0.781150.698
33_R43_A0.774870.692
39_D43_A0.770720.688
9_F13_E0.761540.680
28_I61_T0.759440.678
4_V25_V0.757790.677
33_R47_E0.756680.676
45_I48_E0.754740.674
10_I14_L0.733460.655
40_P44_K0.716960.640
16_E50_L0.712030.636
32_D35_L0.697010.622
18_L25_V0.691610.618
33_R44_K0.674540.602
51_R59_T0.668990.597
12_I35_L0.667370.596
34_L47_E0.661050.590
9_F38_F0.644720.576
9_F17_A0.637670.569
64_K67_E0.627070.560
38_F45_I0.618240.552
41_D45_I0.597930.534
33_R40_P0.595930.532
40_P43_A0.590320.527
63_V66_I0.578110.516
22_G25_V0.576830.515
2_V22_G0.574450.513
13_E16_E0.569180.508
11_G15_A0.567140.506
2_V14_L0.566620.506
32_D59_T0.563560.503
12_I57_V0.561680.502
9_F43_A0.558890.499
17_A53_R0.555360.496
50_L57_V0.551220.492
61_T64_K0.546270.488
13_E42_A0.534220.477
43_A46_L0.527190.471
9_F35_L0.521910.466
5_I8_G0.521650.466
5_I66_I0.521030.465
39_D42_A0.512730.458
25_V55_V0.51250.458
31_S35_L0.511380.457
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
2yquA198.70.085
1ojtA198.70.086
2r9zA198.70.091
2eq6A198.70.092
1onfA198.70.092
2hqmA198.70.096
2a8xA198.70.1
1gesA198.60.106
1dxlA198.60.11
1ebdA198.60.114

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