GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ank_2 - Ankyrin repeats (3 copies)
Pfam: PF12796 (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: CL0465
Length: 89
Sequences: 47477
Seq/Len: 533.45
HH_delta: -0.112 (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
13_L41_I2.641152.266
42_V74_I2.594252.226
43_K77_L2.484772.132
14_K44_L2.432.085
15_F19_K2.256051.936
44_L48_N2.188211.877
9_N12_I2.188051.877
8_G38_N2.170481.862
77_L81_H2.029491.741
27_N56_D2.003731.719
37_G71_N1.982251.701
39_L77_L1.959941.682
10_L44_L1.933161.659
39_L73_E1.828861.569
10_L40_E1.802211.546
12_I15_F1.758761.509
60_N68_E1.712231.469
27_N35_E1.661431.425
31_H65_Y1.604611.377
30_L42_V1.602441.375
60_N65_Y1.554561.334
10_L41_I1.534431.317
63_L75_V1.506381.292
17_L44_L1.500841.288
72_L76_K1.448981.243
64_H67_A1.4321.229
2_H32_Y1.425891.223
46_L77_L1.423791.222
39_L74_I1.400641.202
21_A24_N1.395651.197
27_N32_Y1.38311.187
10_L14_K1.356551.164
33_A42_V1.306191.121
39_L43_K1.302621.118
66_A75_V1.284661.102
31_H64_H1.280211.098
71_N74_I1.279921.098
38_N41_I1.266711.087
60_N64_H1.263471.084
3_I7_N1.249181.072
56_D60_N1.242351.066
4_A13_L1.222961.049
6_Q32_Y1.215851.043
4_A12_I1.21571.043
31_H62_A1.183391.015
63_L79_L1.181441.014
35_E65_Y1.178851.011
46_L81_H1.168591.003
61_T64_H1.160720.996
76_K80_E1.159710.995
5_A29_A1.135540.974
43_K47_E1.133830.973
67_A75_V1.133250.972
79_L85_V1.115720.957
47_E81_H1.108710.951
44_L47_E1.080490.927
65_Y68_E1.077770.925
6_Q36_N1.07180.920
35_E69_N1.062980.912
64_H79_L1.058130.908
34_A62_A1.042370.894
18_E48_N1.035630.889
51_D54_S1.032380.886
28_T31_H1.032120.886
46_L52_I1.024270.879
1_L13_L1.023530.878
53_N84_D1.009530.866
67_A70_G0.999720.858
34_A37_G0.997950.856
2_H29_A0.993860.853
20_G23_I0.991010.850
67_A79_L0.980250.841
14_K18_E0.975760.837
77_L80_E0.972040.834
5_A41_I0.969140.832
15_F18_E0.965320.828
32_Y36_N0.964430.827
63_L67_A0.956990.821
32_Y35_E0.951650.816
34_A74_I0.94970.815
22_D25_L0.935290.802
32_Y65_Y0.935030.802
17_L23_I0.932090.800
5_A36_N0.928690.797
17_L48_N0.927210.796
55_Q59_G0.920130.789
34_A42_V0.919890.789
53_N83_A0.9150.785
2_H31_H0.913750.784
5_A13_L0.913180.783
5_A8_G0.898590.771
65_Y69_N0.88920.763
56_D65_Y0.888420.762
55_Q61_T0.879540.755
26_G57_K0.876470.752
27_N31_H0.87350.749
2_H64_H0.86970.746
31_H54_S0.86210.740
12_I16_L0.859450.737
29_A45_L0.841740.722
27_N65_Y0.83410.716
6_Q35_E0.804890.691
24_N51_D0.791850.679
35_E68_E0.776590.666
30_L46_L0.774940.665
34_A69_N0.772560.663
73_E76_K0.772020.662
27_N60_N0.756360.649
3_I6_Q0.749520.643
74_I77_L0.746150.640
41_I44_L0.729350.626
28_T54_S0.728240.625
34_A71_N0.722260.620
16_L21_A0.707480.607
9_N15_F0.70550.605
24_N50_A0.687750.590
62_A78_L0.685220.588
3_I9_N0.680820.584
8_G36_N0.670650.575
5_A38_N0.665330.571
20_G24_N0.665220.571
14_K48_N0.664220.570
13_L44_L0.663680.569
24_N54_S0.654670.562
13_L17_L0.649160.557
39_L71_N0.649130.557
56_D59_G0.648740.557
43_K81_H0.648510.556
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
3lvqE199.4-0.112
1oy3D199.4-0.092
4gpmA199.4-0.089
3lvqE199.4-0.081
4gpmA199.3-0.073
1ycsB199.3-0.072
1n11A199.3-0.07
1n11A199.3-0.067
3keaA199.3-0.065
3jueA199.3-0.063

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