GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oxidored_q4 - NADH-ubiquinoneplastoquinone oxidoreductase chain 3
Pfam: PF00507 (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. )
Length: 102
Sequences: 3281
Seq/Len: 32.17
HH_delta: -0.065 (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
79_S94_E0.528732.224
93_Y96_K0.499452.101
10_S14_S0.440381.852
75_F79_S0.437161.839
73_G76_S0.427091.796
70_Y73_G0.406311.709
65_W80_M0.39881.677
52_F55_F0.388451.634
78_I81_F0.377671.588
86_I90_G0.36421.532
59_I94_E0.34871.467
7_L10_S0.346541.458
95_W102_W0.338051.422
72_L76_S0.337281.419
86_I94_E0.335051.409
47_L100_L0.326891.375
23_K90_G0.321621.353
6_L9_L0.317361.335
92_L96_K0.313011.317
19_N24_L0.304271.280
45_F48_I0.303061.275
25_S33_P0.300191.263
71_S76_S0.293341.234
63_F66_A0.291071.224
70_Y74_F0.288841.215
11_F16_K0.285411.200
69_F72_L0.284731.198
71_S74_F0.284561.197
9_L14_S0.283451.192
68_S71_S0.281641.185
25_S31_F0.278011.169
88_L94_E0.274621.155
72_L77_L0.273441.150
81_F85_L0.271331.141
49_A52_F0.266521.121
5_L9_L0.264111.111
25_S29_C0.263521.108
85_L88_L0.260061.094
73_G77_L0.259161.090
26_P42_S0.256731.080
73_G83_F0.255991.077
69_F79_S0.255081.073
62_L84_L0.253941.068
8_L12_L0.253161.065
52_F56_D0.251971.060
31_F57_V0.251351.057
93_Y97_K0.251091.056
48_I55_F0.250321.053
77_L81_F0.24961.050
22_E25_S0.248951.047
88_L92_L0.248621.046
9_L13_L0.24761.041
35_G66_A0.247561.041
9_L15_P0.247491.041
40_P46_F0.242261.019
8_L11_F0.241421.015
76_S81_F0.239911.009
15_P74_F0.234940.988
70_Y79_S0.232780.979
49_A99_A0.232570.978
70_Y85_L0.231790.975
77_L80_M0.231690.974
20_N25_S0.230560.970
41_F65_W0.229310.964
15_P73_G0.228090.959
72_L75_F0.225260.947
48_I52_F0.223520.940
62_L99_A0.222850.937
59_I64_P0.221490.932
68_S74_F0.221350.931
78_I82_L0.21690.912
73_G78_I0.216650.911
29_C53_L0.216280.910
69_F73_G0.216150.909
42_S46_F0.215830.908
69_F77_L0.21490.904
68_S72_L0.214520.902
38_R41_F0.212570.894
62_L67_F0.211820.891
44_Q48_I0.209580.881
75_F78_I0.209440.881
53_L64_P0.209030.879
48_I101_D0.207090.871
69_F75_F0.205450.864
82_L85_L0.202790.853
48_I94_E0.201980.850
70_Y76_S0.201480.847
59_I91_L0.201460.847
64_P90_G0.201350.847
98_G102_W0.201110.846
10_S15_P0.20110.846
74_F78_I0.19970.840
6_L10_S0.198810.836
7_L11_F0.198150.833
25_S32_D0.197650.831
65_W79_S0.196630.827
54_I72_L0.196510.827
22_E101_D0.195050.820
36_S39_S0.193730.815
6_L11_F0.193380.813
7_L60_V0.192550.810
10_S43_I0.19190.807
71_S75_F0.19130.805
9_L24_L0.190610.802
60_V99_A0.189660.798
8_L17_K0.18960.797
14_S43_I0.189440.797
87_L90_G0.188620.793
51_L87_L0.185850.782
32_D64_P0.184890.778
29_C32_D0.184420.776
49_A55_F0.183540.772
70_Y78_I0.183530.772
46_F65_W0.183090.770
13_L84_L0.182890.769
23_K49_A0.182070.766
63_F76_S0.181910.765
43_I83_F0.181820.765
74_F77_L0.181540.764
27_Y67_F0.181460.763
44_Q66_A0.18110.762
44_Q98_G0.180680.760
75_F89_L0.180180.758
62_L65_W0.180.757
22_E31_F0.179920.757
57_V88_L0.177020.745
61_L97_K0.176910.744
32_D35_G0.176280.741
14_S18_P0.175750.739
11_F19_N0.175460.738
76_S85_L0.1750.736
26_P33_P0.174110.732
75_F83_F0.173810.731
14_S17_K0.172340.725
47_L55_F0.171990.723
33_P37_S0.171780.723
5_L8_L0.171370.721
62_L102_W0.17030.716
27_Y93_Y0.170190.716
31_F42_S0.169930.715
19_N79_S0.168290.708
7_L83_F0.168210.707
32_D40_P0.167810.706
10_S101_D0.167730.705
66_A83_F0.167540.705
74_F82_L0.167490.704
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
3rkoA0.9902100-0.065
4he8A0.980499.9-0.035
2ls2A0.25494.60.924
2z26A0.35292.90.931
1kf6C0.5491.80.938
4b19A0.18631.60.939
1olrA0.47061.60.94
1q90A0.35291.30.942
2ks1B0.23531.30.943
2kv5A0.20591.20.943

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