GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SAM_PNT - Sterile alpha motif (SAM)Pointed domain
Pfam: PF02198 (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: CL0003
Length: 84
Sequences: 1326
Seq/Len: 15.79
HH_delta: 0.171 (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
22_K47_N0.439822.220
57_T60_D0.399492.016
23_E44_S0.366161.848
20_W25_V0.363511.835
43_F48_M0.338621.709
17_P54_C0.313961.585
26_L44_S0.284281.435
21_T24_D0.281911.423
59_E62_R0.278321.405
15_K27_Q0.269851.362
77_L81_K0.263571.330
73_L77_L0.262931.327
29_L40_A0.261521.320
52_E55_S0.25341.279
16_D19_L0.251141.268
17_P20_W0.240581.214
47_N52_E0.23681.195
18_R51_R0.229131.157
49_N52_E0.228271.152
74_Y78_Q0.227441.148
30_R40_A0.22431.132
58_K62_R0.222481.123
38_L58_K0.2221.121
67_S77_L0.221981.120
22_K49_N0.218721.104
18_R81_K0.214691.084
36_F39_P0.214181.081
45_R51_R0.213911.080
17_P31_W0.213281.077
58_K74_Y0.20971.058
42_D45_R0.209471.057
20_W28_W0.208891.054
23_E27_Q0.208841.054
24_D63_R0.20721.046
46_F69_Y0.203161.025
74_Y81_K0.200561.012
17_P38_L0.200461.012
78_Q81_K0.199611.008
68_G71_D0.199571.007
31_W38_L0.197730.998
67_S73_L0.197390.996
46_F65_F0.197350.996
47_N69_Y0.196350.991
15_K24_D0.190770.963
20_W50_G0.188760.953
31_W41_I0.188690.952
30_R38_L0.185270.935
29_L43_F0.183950.929
18_R75_S0.18370.927
76_H79_L0.183430.926
30_R44_S0.181780.918
15_K19_L0.180140.909
37_D40_A0.177790.897
58_K63_R0.177240.895
15_K81_K0.174530.881
73_L76_H0.170890.863
30_R42_D0.169610.856
39_P61_F0.168380.850
31_W35_E0.166840.842
47_N57_T0.166180.839
22_K25_V0.164610.831
20_W24_D0.164450.830
30_R49_N0.164270.829
24_D51_R0.164090.828
52_E70_G0.161640.816
62_R71_D0.161290.814
34_R43_F0.160880.812
43_F56_L0.160860.812
42_D65_F0.160690.811
26_L51_R0.160580.811
61_F70_G0.159930.807
36_F70_G0.158040.798
25_V28_W0.156880.792
47_N68_G0.155470.785
62_R65_F0.15540.784
25_V53_L0.153410.774
52_E63_R0.153260.774
58_K75_S0.153150.773
61_F74_Y0.152070.768
60_D71_D0.150790.761
18_R66_P0.150150.758
42_D46_F0.149890.757
42_D67_S0.14980.756
26_L37_D0.149430.754
37_D41_I0.149090.753
16_D37_D0.145940.737
59_E63_R0.144170.728
18_R34_R0.14410.727
74_Y77_L0.144080.727
42_D55_S0.144060.727
24_D41_I0.1440.727
40_A43_F0.143730.725
61_F65_F0.143390.724
62_R74_Y0.142990.722
58_K79_L0.142880.721
29_L39_P0.142580.720
26_L29_L0.142010.717
49_N70_G0.140480.709
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
2jv3A199.50.171
1x66A199.50.175
2ytuA199.50.18
1sxeA199.50.189
2dkxA0.988199.50.191
1sxdA0.976299.40.229
2qb0B0.928699.40.24
1sv0A0.904899.40.245
2qarB0.928699.40.247
2e8pA0.988199.30.258

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