GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cmc1 - Cytochrome c oxidase biogenesis protein Cmc1 like
Pfam: PF08583 (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: CL0351
Length: 69
Sequences: 312
Seq/Len: 4.52
HH_delta: 0.8 (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
21_A24_H0.210951.985
18_E22_E0.180931.702
2_H5_L0.179371.688
64_L67_R0.175041.647
19_A41_A0.173781.635
6_K9_A0.168391.584
30_K33_G0.161641.521
2_H24_H0.14891.401
24_H36_R0.139291.311
6_K10_H0.138431.303
22_E26_D0.13571.277
15_D43_N0.135641.276
4_Q8_E0.135451.274
36_R46_L0.132481.247
12_K15_D0.130331.226
41_A44_E0.129521.219
27_R30_K0.127351.198
57_N61_A0.124161.168
59_E62_E0.123911.166
10_H17_I0.123321.160
19_A37_E0.122851.156
26_D30_K0.122021.148
55_F60_K0.121571.144
46_L50_R0.120281.132
5_L46_L0.119471.124
7_E37_E0.114961.082
24_H39_K0.113711.070
20_F36_R0.113031.064
61_A65_K0.112361.057
22_E51_N0.110821.043
12_K49_E0.1081.016
29_F34_K0.107961.016
10_H31_F0.107941.016
24_H33_G0.106441.002
49_E52_D0.105890.996
12_K54_R0.105290.991
9_A17_I0.105130.989
16_E49_E0.104620.984
48_E51_N0.104310.981
21_A36_R0.104290.981
34_K41_A0.104190.980
36_R39_K0.103780.976
22_E53_E0.101240.953
20_F55_F0.10070.948
54_R58_R0.100690.947
13_C17_I0.099920.940
40_K44_E0.099580.937
25_K48_E0.098950.931
18_E37_E0.098670.928
4_Q10_H0.098640.928
26_D34_K0.098570.927
32_V39_K0.09740.916
22_E58_R0.097350.916
38_E58_R0.097320.916
12_K48_E0.097180.914
4_Q16_E0.096940.912
20_F33_G0.096490.908
25_K50_R0.095330.897
31_F41_A0.095150.895
22_E25_K0.094590.890
15_D19_A0.094530.889
21_A26_D0.094380.888
20_F24_H0.094270.887
44_E67_R0.094260.887
18_E51_N0.09420.886
8_E12_K0.094190.886
33_G49_E0.093740.882
60_K63_Y0.09270.872
60_K64_L0.09090.855
39_K47_K0.090850.855
20_F39_K0.090740.854
29_F33_G0.090050.847
15_D48_E0.088130.829
40_K65_K0.087420.823
25_K46_L0.086930.818
33_G47_K0.086780.817
18_E46_L0.086730.816
6_K12_K0.085520.805
60_K67_R0.084610.796
15_D41_A0.084110.791
52_D55_F0.083920.790
55_F63_Y0.083320.784
37_E60_K0.082510.776
19_A40_K0.081490.767
52_D63_Y0.080660.759
31_F59_E0.080630.759
12_K67_R0.079490.748
5_L57_N0.079340.747
16_E57_N0.079140.745
2_H31_F0.078780.741
14_A54_R0.078740.741
20_F63_Y0.078710.741
42_M47_K0.078030.734
4_Q42_M0.077750.732
19_A65_K0.077690.731
11_K14_A0.077470.729
22_E38_E0.077250.727
12_K66_E0.077220.727
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
1ei0A0.550760.70.8
1hp8A0.898632.20.83
2lqlA0.97130.10.833
2l0yB0.391323.70.841
2zxtA0.985513.10.857
1u96A0.4783130.858
3cx5F0.855110.10.864
1pp9H0.85514.80.882
3tguH0.85514.50.883
3payA0.521730.892
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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