GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CRAL_TRIO_N - CRALTRIO N-terminal domain
Pfam: PF03765 (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: 55
Sequences: 1426
Seq/Len: 25.93
HH_delta: 0.088 (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
44_D47_K0.938722.618
8_R31_D0.879552.453
40_A51_M0.825832.303
10_H49_F0.798262.226
41_R51_M0.75742.112
7_L34_L0.74482.077
5_K9_E0.665241.855
9_E12_S0.621321.733
3_K45_V0.600721.675
9_E13_E0.593191.654
7_L48_A0.568271.585
30_D33_F0.539411.504
50_K54_K0.533341.487
35_L43_F0.50151.398
4_L8_R0.449521.253
46_E49_F0.425321.186
47_K51_M0.414541.156
6_Q46_E0.367421.025
8_R34_L0.366611.022
7_L49_F0.354010.987
35_L39_R0.34010.948
6_Q9_E0.338190.943
3_K7_L0.331410.924
10_H53_K0.330860.923
33_F37_F0.329080.918
6_Q45_V0.324790.906
13_E53_K0.317140.884
47_K50_K0.315460.880
38_L43_F0.300150.837
36_R40_A0.296940.828
36_R41_R0.288120.803
36_R51_M0.284960.795
24_D27_E0.283060.789
28_D37_F0.274160.764
49_F53_K0.26680.744
48_A51_M0.2660.742
32_N36_R0.260250.726
4_L7_L0.260020.725
42_K50_K0.25950.724
39_R43_F0.248610.693
46_E50_K0.246520.687
13_E27_E0.245560.685
4_L32_N0.242860.677
11_L28_D0.232070.647
5_K23_D0.2320.647
25_E29_H0.228690.638
4_L35_L0.22230.620
4_L34_L0.222120.619
5_K42_K0.221520.618
33_F52_L0.220260.614
44_D53_K0.219460.612
37_F41_R0.21830.609
23_D26_K0.214060.597
4_L31_D0.211890.591
33_F36_R0.211650.590
6_Q12_S0.211320.589
10_H46_E0.211010.588
25_E28_D0.210020.586
33_F42_K0.208750.582
9_E26_K0.207840.580
30_D36_R0.205740.574
28_D33_F0.204790.571
45_V49_F0.202360.564
33_F54_K0.200810.560
25_E53_K0.197470.551
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
3hx3A0.854598.90.088
3q8gA0.836498.80.094
1olmA0.854598.70.134
1auaA0.836498.70.144
1r5lA0.890998.70.15
4fmmA198.30.256
1wglA0.727368.80.708
1ufzA0.745567.60.71
2dhyA0.727360.20.724
3zn0B0.781822.30.781

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