GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cna_B - Cna protein B-type domain
Pfam: PF05738 (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: CL0287
Length: 70
Sequences: 3852
Seq/Len: 55.03
HH_delta: -0.028 (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
38_T60_T1.281132.518
8_L31_F1.201262.361
9_Y40_T1.115852.193
5_T45_K1.114692.191
24_D28_K1.031342.027
9_Y42_K1.017922.001
2_A25_E1.014571.994
21_V31_F0.989681.945
6_F43_E0.982931.932
7_E44_T0.955651.878
7_E42_K0.904041.777
21_V29_Y0.900291.769
10_D14_N0.8521.675
5_T22_T0.818431.609
4_A43_E0.719191.414
38_T58_E0.714611.405
3_G22_T0.684271.345
40_T56_P0.683741.344
6_F29_Y0.682261.341
10_D13_G0.669921.317
62_T65_G0.668021.313
5_T44_T0.647841.273
45_K48_D0.592381.164
41_L59_F0.592221.164
40_T58_E0.584031.148
11_E40_T0.576381.133
34_L39_Y0.571351.123
23_T27_G0.569491.119
13_G16_V0.559151.099
29_Y43_E0.549631.080
11_E38_T0.545831.073
44_T52_L0.545181.072
8_L34_L0.526731.035
10_D35_P0.523941.030
12_D38_T0.476240.936
8_L39_Y0.460890.906
23_T29_Y0.456820.898
15_E18_E0.453830.892
6_F23_T0.45290.890
36_P63_E0.44920.883
8_L41_L0.446690.878
11_E58_E0.445280.875
10_D15_E0.426720.839
4_A23_T0.426490.838
43_E53_D0.41380.813
7_E18_E0.406030.798
17_I21_V0.405620.797
29_Y41_L0.403440.793
61_I65_G0.39360.774
8_L50_Y0.389480.766
1_L43_E0.388230.763
2_A23_T0.383560.754
31_F41_L0.37580.739
5_T18_E0.365270.718
4_A49_G0.359590.707
9_Y13_G0.356490.701
9_Y16_V0.356460.701
24_D27_G0.34570.679
42_K52_L0.343710.676
53_D56_P0.343090.674
44_T48_D0.340690.670
6_F53_D0.339560.667
1_L4_A0.336980.662
11_E14_N0.336730.662
10_D16_V0.334930.658
4_A50_Y0.329250.647
9_Y15_E0.327530.644
3_G48_D0.323680.636
39_Y61_I0.322520.634
10_D17_I0.319940.629
1_L50_Y0.313730.617
33_N51_Q0.310570.610
34_L37_G0.307570.605
6_F21_V0.305270.600
2_A24_D0.300260.590
1_L23_T0.29410.578
36_P61_I0.293430.577
12_D15_E0.286220.563
36_P62_T0.279050.548
1_L45_K0.276950.544
61_I64_D0.272290.535
52_L55_T0.272220.535
17_I32_K0.264210.519
15_E30_T0.262590.516
42_K54_D0.261980.515
52_L56_P0.259480.510
3_G43_E0.259380.510
32_K62_T0.251330.494
18_E21_V0.249440.490
30_T33_N0.247780.487
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
3txaA0.985799.3-0.028
2ww8A0.985799.20.009
2pz4A199.10.061
3kptA0.9857990.107
2ww8A198.90.116
2x5pA0.928698.90.116
3kptA198.90.12
3hr6A198.90.138
3uxfA198.90.147
2x9xA198.80.157

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