GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
COX2 - Cytochrome C oxidase subunit II periplasmic domain
Pfam: PF00116 (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: CL0026
Length: 120
Sequences: 4246
Seq/Len: 35.38
HH_delta: -0.018 (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_V48_L1.266133.442
60_L80_A1.10112.994
50_L92_P1.074222.920
6_T61_T0.953982.594
8_H13_Q0.936072.545
92_P119_V0.924262.513
52_A95_P0.880462.394
102_C106_C0.773132.102
52_A119_V0.744092.023
58_F90_F0.701061.906
74_L92_P0.677681.842
47_E118_I0.668391.817
4_K15_E0.664061.805
29_I38_D0.655481.782
78_M88_V0.632221.719
30_P33_D0.624941.699
60_L78_M0.617881.680
97_T116_K0.596931.623
106_C110_H0.591021.607
55_P91_T0.580361.578
77_K104_E0.57861.573
8_H63_E0.553611.505
47_E116_K0.550821.498
70_W103_A0.546251.485
50_L117_V0.52991.441
5_V58_F0.520241.414
56_V92_P0.516051.403
2_T57_R0.510191.387
102_C110_H0.50541.374
79_D104_E0.502521.366
7_G80_A0.498121.354
55_P89_T0.481651.309
100_G115_G0.479121.303
53_G91_T0.472031.283
67_H102_C0.462121.256
68_S77_K0.460561.252
58_F88_V0.455421.238
97_T118_I0.449951.223
29_I33_D0.444411.208
49_V118_I0.440431.197
4_K59_H0.439511.195
8_H11_Y0.43821.191
76_I88_V0.423751.152
51_P56_V0.420571.143
57_R87_S0.414351.126
110_H113_M0.405451.102
66_I80_A0.404571.100
74_L117_V0.398331.083
6_T15_E0.394131.072
71_I74_L0.392971.068
101_Q114_P0.390321.061
109_G112_F0.387511.054
67_H106_C0.379971.033
54_Q81_I0.375921.022
44_T116_K0.375511.021
68_S104_E0.374991.019
99_Y116_K0.372311.012
26_S44_T0.366480.996
2_T59_H0.364940.992
47_E97_T0.363770.989
64_D67_H0.361580.983
106_C113_M0.359480.977
13_Q25_D0.356390.969
14_Y115_G0.355880.968
95_P119_V0.355540.967
3_V58_F0.355220.966
50_L119_V0.350990.954
9_Q65_V0.349970.951
56_V90_F0.342120.930
60_L88_V0.338250.920
29_I88_V0.33820.919
44_T47_E0.327710.891
102_C113_M0.320550.871
59_H85_T0.319780.869
29_I98_Y0.315510.858
68_S103_A0.310670.845
75_G100_G0.310260.844
99_Y114_P0.310210.843
48_L117_V0.308470.839
3_V50_L0.305840.831
43_E47_E0.305430.830
62_S66_I0.301580.820
2_T18_D0.300280.816
23_S27_Y0.299060.813
9_Q64_D0.298060.810
87_S94_K0.296180.805
50_L56_V0.294850.802
50_L90_F0.293610.798
14_Y48_L0.293170.797
88_V91_T0.290510.790
20_D53_G0.289380.787
62_S69_F0.28810.783
29_I32_D0.286780.780
16_Y38_D0.285030.775
82_P94_K0.284360.773
77_K103_A0.283340.770
19_F23_S0.278990.758
75_G90_F0.278450.757
11_Y45_D0.27810.756
5_V63_E0.274630.747
55_P88_V0.273980.745
16_Y48_L0.272330.740
107_G110_H0.271820.739
10_W65_V0.270150.734
33_D38_D0.269820.734
17_P21_E0.26520.721
52_A62_S0.262620.714
71_I98_Y0.262330.713
71_I117_V0.262320.713
66_I81_I0.261560.711
78_M86_N0.261020.710
6_T13_Q0.260490.708
21_E32_D0.259090.704
67_H110_H0.258610.703
55_P93_D0.257890.701
3_V16_Y0.256090.696
75_G86_N0.255740.695
3_V22_I0.252610.687
4_K61_T0.250060.680
68_S71_I0.249620.679
21_E55_P0.248930.677
1_V54_Q0.247530.673
20_D52_A0.246560.670
88_V92_P0.244880.666
116_K119_V0.244690.665
38_D43_E0.244650.665
21_E89_T0.244540.665
17_P20_D0.242050.658
55_P78_M0.241420.656
43_E118_I0.240570.654
105_Y108_A0.240180.653
105_Y109_G0.238420.648
23_S29_I0.237860.647
30_P81_I0.236270.642
78_M81_I0.234570.638
74_L98_Y0.234370.637
92_P117_V0.233960.636
53_G93_D0.233370.634
70_W111_S0.232910.633
21_E38_D0.231270.629
25_D33_D0.230020.625
20_D32_D0.229980.625
22_I48_L0.229490.624
108_A111_S0.228550.621
74_L119_V0.22750.619
20_D38_D0.227440.618
30_P39_F0.226810.617
43_E116_K0.226480.616
30_P38_D0.225510.613
48_L58_F0.225280.612
5_V60_L0.223780.608
38_D54_Q0.222280.604
5_V38_D0.22180.603
26_S48_L0.22140.602
38_D93_D0.221010.601
65_V104_E0.22090.601
54_Q91_T0.220620.600
59_H87_S0.220330.599
104_E110_H0.219330.596
55_P59_H0.219320.596
20_D78_M0.218960.595
107_G113_M0.217770.592
1_V56_V0.217360.591
27_Y33_D0.217180.590
48_L80_A0.216750.589
19_F22_I0.21580.587
11_Y109_G0.215630.586
28_M41_L0.215610.586
64_D82_P0.215140.585
41_L112_F0.215120.585
41_L109_G0.215030.585
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
1v54B1100-0.018
3hb3B0.9917100-0.001
2gsmB0.99171000.026
1fftB0.8251000.087
2yevB0.8251000.093
1cyxA0.8251000.118
3s8fB0.74171000.329
2cuaA0.741799.90.372
3sbqA0.741799.90.442
1fwxA0.891799.80.554

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