GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oxidored_q2 - NADH-ubiquinoneplastoquinone oxidoreductase chain 4L
Pfam: PF00420 (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: 95
Sequences: 3495
Seq/Len: 36.79
HH_delta: -0.025 (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
16_G29_S1.08354.445
22_H85_D0.560252.298
10_F36_G0.541732.222
84_S89_S0.535872.198
15_Y19_T0.521822.141
20_R25_R0.479241.966
13_G32_L0.441331.810
78_L90_L0.433761.779
27_L71_G0.398441.635
6_A40_L0.396421.626
17_I26_I0.387761.591
38_F60_F0.366471.503
7_F11_F0.360221.478
53_P56_L0.353921.452
6_A36_G0.349911.435
31_E67_E0.332021.362
13_G36_G0.327811.345
6_A43_F0.327441.343
17_I29_S0.321551.319
77_S80_R0.308551.266
86_D89_S0.300971.235
49_N52_I0.299461.228
5_V9_L0.291861.197
77_S81_S0.291811.197
15_Y47_F0.287251.178
15_Y58_L0.278321.142
27_L75_L0.269151.104
34_M64_S0.264911.087
43_F47_F0.261261.072
23_L30_L0.260011.067
10_F33_M0.257691.057
31_E68_S0.25721.055
65_V69_A0.256161.051
45_G50_D0.251181.030
16_G20_R0.249831.025
31_E76_V0.249711.024
33_M36_G0.247131.014
71_G75_L0.246551.011
14_L54_Q0.245461.007
13_G29_S0.244551.003
9_L39_L0.244031.001
45_G55_A0.240980.989
67_E71_G0.240960.988
18_L54_Q0.236190.969
38_F61_L0.235970.968
27_L31_E0.234910.964
30_L44_M0.2320.952
82_Y92_L0.230350.945
37_V40_L0.230160.944
18_L44_M0.228750.938
68_S72_L0.226950.931
26_I54_Q0.225180.924
31_E71_G0.222140.911
74_L90_L0.22210.911
74_L77_S0.221630.909
70_L73_S0.220940.906
40_L44_M0.220490.905
41_L56_L0.220320.904
6_A39_L0.218330.896
33_M40_L0.21690.890
31_E80_R0.216280.887
35_L61_L0.215780.885
32_L91_N0.212660.872
51_P56_L0.210690.864
8_F11_F0.209590.860
8_F12_I0.209150.858
45_G56_L0.208470.855
38_F57_I0.207490.851
56_L59_T0.207250.850
16_G65_V0.206010.845
50_D54_Q0.205440.843
28_I86_D0.205230.842
45_G51_P0.205010.841
26_I87_V0.204480.839
13_G33_M0.200220.821
27_L40_L0.199810.820
60_F65_V0.199440.818
47_F56_L0.198870.816
37_V63_I0.198080.813
21_R86_D0.197950.812
15_Y52_I0.197710.811
34_M38_F0.197070.808
28_I75_L0.196170.805
42_V51_P0.194930.800
64_S69_A0.194610.798
6_A33_M0.194520.798
59_T62_V0.194070.796
60_F64_S0.191580.786
82_Y90_L0.189570.778
10_F71_G0.188450.773
11_F49_N0.188210.772
31_E35_L0.187670.770
46_Y55_A0.187490.769
32_L69_A0.187480.769
50_D53_P0.186780.766
65_V68_S0.186390.765
13_G20_R0.185870.763
12_I16_G0.185660.762
24_L87_V0.182710.750
40_L57_I0.182170.747
62_V77_S0.181820.746
18_L51_P0.18140.744
46_Y90_L0.181010.743
5_V10_F0.180910.742
28_I71_G0.180590.741
41_L53_P0.180140.739
38_F66_C0.180030.739
66_C72_L0.178450.732
51_P59_T0.177230.727
7_F49_N0.176910.726
28_I92_L0.176730.725
34_M67_E0.176430.724
42_V57_I0.176220.723
58_L81_S0.175950.722
23_L85_D0.175560.720
45_G60_F0.175110.718
65_V71_G0.173850.713
9_L36_G0.173480.712
46_Y49_N0.172320.707
20_R42_V0.172180.706
49_N55_A0.170920.701
22_H78_L0.17040.699
6_A12_I0.169950.697
53_P59_T0.169040.693
25_R28_I0.168890.693
41_L57_I0.167630.688
20_R76_V0.166840.684
23_L88_S0.166150.682
36_G40_L0.164320.674
44_M84_S0.164280.674
38_F64_S0.163670.671
11_F15_Y0.163660.671
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
3rkoK199.7-0.025
4he8K0.989599.70.053
4he8L0.968478.60.791
4he8M0.957966.60.809
3rkoN0.968463.90.812
3rkoL0.968456.50.82
3rkoM148.10.829
4he8N0.947434.80.841
4he8J0.936815.20.865
3lb6C0.36849.10.877

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