GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytochrom_c3_2 - Cytochrome c3
Pfam: PF14537 (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: CL0317
Length: 80
Sequences: 1447
Seq/Len: 18.09
HH_delta: 0.208 (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
8_N11_D0.335182.121
14_G19_H0.295641.871
58_T61_D0.29161.846
75_C78_C0.283481.794
75_C79_H0.283481.794
16_H28_Q0.255261.616
38_D43_T0.238851.512
14_G56_K0.22211.406
39_M42_A0.211031.336
66_H74_T0.210721.334
59_C62_C0.20361.289
53_H57_L0.195171.235
69_S73_E0.189381.199
10_V16_H0.189121.197
73_E76_T0.187831.189
18_P21_D0.186941.183
37_E42_A0.185661.175
27_A30_L0.184061.165
49_P54_H0.181951.152
26_N30_L0.181741.150
40_A43_T0.181261.147
34_G37_E0.180641.143
30_L37_E0.179131.134
7_V11_D0.176551.117
35_D38_D0.175711.112
7_V20_K0.174881.107
61_D77_S0.174221.103
42_A47_N0.17391.101
30_L34_G0.173651.099
39_M43_T0.168971.069
55_G77_S0.16711.058
54_H57_L0.167081.057
34_G42_A0.166771.055
35_D80_E0.164851.043
51_S57_L0.16431.040
17_E35_D0.164261.040
10_V14_G0.161861.024
74_T77_S0.16171.023
48_N57_L0.160221.014
15_P65_P0.159921.012
27_A77_S0.157931.000
40_A58_T0.155730.986
73_E77_S0.154630.979
70_E73_E0.153860.974
47_N60_T0.153460.971
24_V35_D0.153330.970
14_G66_H0.1510.956
48_N53_H0.15070.954
53_H58_T0.150490.952
54_H58_T0.149960.949
6_G54_H0.149170.944
59_C63_H0.148240.938
52_A56_K0.145770.923
30_L39_M0.144310.913
65_P68_P0.142950.905
10_V15_P0.142520.902
70_E76_T0.142090.899
68_P77_S0.141630.896
10_V19_H0.140660.890
24_V28_Q0.140030.886
77_S80_E0.139610.884
15_P28_Q0.13940.882
25_S38_D0.138920.879
64_N67_D0.138790.878
17_E47_N0.136830.866
42_A52_A0.136610.865
76_T80_E0.136240.862
10_V20_K0.135810.860
11_D39_M0.135710.859
26_N31_S0.133770.847
27_A66_H0.133550.845
38_D61_D0.133170.843
57_L67_D0.132920.841
15_P19_H0.132860.841
43_T50_H0.132580.839
35_D67_D0.131240.831
47_N50_H0.130720.827
69_S77_S0.130580.826
23_Q70_E0.130320.825
8_N36_E0.129030.817
55_G58_T0.12720.805
56_K76_T0.125220.793
28_Q31_S0.124790.790
20_K34_G0.124430.788
51_S65_P0.124010.785
50_H53_H0.123860.784
40_A57_L0.123630.782
23_Q36_E0.123560.782
38_D41_A0.121870.771
31_S61_D0.121730.770
36_E41_A0.121730.770
49_P67_D0.121480.769
10_V40_A0.120610.763
17_E20_K0.120490.763
7_V52_A0.119920.759
18_P64_N0.119810.758
26_N60_T0.119120.754
70_E74_T0.118550.750
17_E60_T0.118050.747
26_N54_H0.118020.747
8_N38_D0.117670.745
64_N70_E0.117440.743
28_Q61_D0.117060.741
25_S67_D0.116850.740
26_N56_K0.116290.736
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
1y0pA0.9625990.208
1qo8A0.9598.90.232
2k3vA0.998.90.259
1m1qA0.998.80.262
1d4dA0.962598.60.325
2ozyA0.937598.60.33
3pmqA198.50.358
1fgjA198.40.384
2rdzA198.30.387
1ofwA0.998.30.391

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