GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oxidored_q6 - NADH ubiquinone oxidoreductase 20 Kd subunit
Pfam: PF01058 (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: 131
Sequences: 1795
Seq/Len: 13.7
HH_delta: 0.107 (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
67_K76_V0.59022.931
76_V108_V0.574152.851
4_C119_P0.514162.553
64_E68_E0.499092.478
105_L113_N0.465862.313
82_C117_C0.465572.312
79_V124_I0.453422.251
76_V110_V0.409172.032
126_E130_A0.404172.007
78_A84_S0.399951.986
60_E64_E0.373421.854
119_P124_I0.352661.751
49_L73_A0.334951.663
63_L67_K0.33021.640
46_A74_K0.324121.609
78_A83_A0.307481.527
50_I124_I0.304071.510
114_I127_T0.299841.489
81_T85_F0.299311.486
31_M34_P0.296791.474
55_V66_L0.296111.470
120_H123_W0.29031.441
8_F52_E0.289971.440
24_I29_S0.289161.436
49_L70_R0.288781.434
47_D72_K0.284321.412
47_D74_K0.283521.408
4_C82_C0.281841.399
67_K71_P0.279481.388
32_A35_G0.279031.385
114_I119_P0.273371.357
48_I77_I0.268951.335
4_C117_C0.262221.302
5_T27_H0.259061.286
24_I30_L0.252281.253
61_E65_W0.249341.238
60_E68_E0.247411.228
6_I9_L0.237171.178
81_T87_G0.231811.151
28_P128_L0.228961.137
5_T52_E0.226251.123
56_P96_S0.224121.113
50_I79_V0.217931.082
48_I128_L0.217281.079
67_K74_K0.215181.068
18_L28_P0.212971.057
2_T5_T0.211141.048
14_S17_D0.207161.029
49_L69_L0.206891.027
33_S45_E0.205211.019
55_V63_L0.203871.012
49_L76_V0.202451.005
29_S32_A0.202061.003
17_D25_R0.199530.991
51_V66_L0.199280.990
18_L24_I0.19920.989
93_N97_V0.199070.988
84_S88_I0.1980.983
112_I127_T0.197210.979
55_V104_L0.197080.979
57_R63_L0.195720.972
10_A13_P0.192950.958
2_T28_P0.189080.939
60_E107_V0.188160.934
51_V104_L0.18780.933
8_F124_I0.187180.929
30_L35_G0.182110.904
104_L110_V0.181460.901
29_S35_G0.179460.891
8_F15_L0.178990.889
3_G82_C0.17390.863
62_A121_P0.173670.862
46_A52_E0.170.844
3_G54_S0.169650.842
84_S113_N0.169520.842
4_C81_T0.168250.835
57_R106_E0.167580.832
66_L84_S0.166950.829
126_E129_L0.16420.815
5_T59_M0.161770.803
65_W104_L0.160540.797
75_A109_P0.160060.795
67_K109_P0.158580.787
116_G119_P0.158510.787
71_P108_V0.157260.781
8_F79_V0.156730.778
51_V63_L0.156360.776
64_E108_V0.156330.776
57_R83_A0.154490.767
97_V103_P0.153970.765
112_I123_W0.153910.764
25_R45_E0.153130.760
93_N114_I0.153110.760
85_F115_P0.1530.760
26_Y129_L0.152890.759
11_L125_L0.152830.759
47_D71_P0.151860.754
58_N97_V0.150490.747
3_G87_G0.149870.744
5_T12_E0.14960.743
52_E79_V0.148860.739
80_G118_P0.148380.737
81_T84_S0.148180.736
78_A104_L0.14810.735
63_L88_I0.147740.734
83_A107_V0.147510.732
93_N101_V0.147190.731
52_E55_V0.144980.720
66_L101_V0.144680.718
89_P93_N0.144650.718
4_C89_P0.14420.716
6_I10_A0.143970.715
62_A102_G0.143590.713
86_G113_N0.143380.712
127_T130_A0.14260.708
54_S97_V0.142440.707
31_M50_I0.142350.707
85_F126_E0.142040.705
64_E67_K0.141960.705
57_R60_E0.141690.704
31_M35_G0.141630.703
24_I28_P0.141530.703
105_L110_V0.141260.701
71_P74_K0.141060.700
81_T105_L0.14070.699
70_R101_V0.14040.697
18_L125_L0.140080.696
79_V123_W0.13970.694
66_L104_L0.13940.692
18_L129_L0.138860.689
3_G117_C0.13880.689
14_S125_L0.13850.688
66_L69_L0.137840.684
53_G80_G0.1370.680
62_A65_W0.136930.680
49_L52_E0.136890.680
105_L112_I0.136430.677
105_L108_V0.13640.677
102_G121_P0.136320.677
6_I120_H0.136140.676
56_P97_V0.135980.675
60_E101_V0.135780.674
17_D26_Y0.135590.673
55_V84_S0.135340.672
57_R88_I0.134910.670
14_S18_L0.134840.670
54_S101_V0.134670.669
27_H73_A0.13420.666
26_Y126_E0.134140.666
124_I128_L0.1340.665
50_I129_L0.13390.665
48_I75_A0.133890.665
51_V83_A0.133690.664
87_G125_L0.133340.662
61_E94_N0.133290.662
47_D108_V0.133120.661
50_I68_E0.132980.660
69_L73_A0.131970.655
5_T8_F0.131660.654
103_P110_V0.131510.653
74_K130_A0.131030.651
51_V110_V0.130050.646
7_S10_A0.12950.643
11_L30_L0.129330.642
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
3uqyS0.97711000.107
3rgwS0.97711000.115
3myrA0.97711000.116
1h2aS0.96951000.126
3ze9A0.97711000.13
2wpnA0.97711000.13
1wuiS0.96951000.131
3zfsB0.94661000.135
3ayxB0.97711000.14
1cc1S0.97711000.143

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