GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
EXOSC1 - Exosome component EXOSC1CSL4
Pfam: PF10447 (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: CL0021
Length: 82
Sequences: 1873
Seq/Len: 22.84
HH_delta: 0.142 (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
9_I76_R1.260424.307
10_A22_V1.13233.869
7_I76_R0.692132.365
18_R21_K0.67572.309
20_A69_F0.621952.125
18_R49_I0.571281.952
11_R74_I0.560211.914
8_V77_A0.544991.862
25_L74_I0.539431.843
7_I78_R0.510731.745
19_Q49_I0.471911.612
23_E47_Q0.443781.516
9_I74_I0.438541.498
11_R25_L0.422531.444
3_K6_D0.420711.437
22_V50_I0.379751.298
12_V69_F0.36881.260
10_A75_V0.362491.239
12_V22_V0.344551.177
16_N49_I0.341521.167
54_D80_I0.322681.103
55_V65_M0.316891.083
20_A50_I0.315511.078
11_R23_E0.309781.058
56_R60_K0.308121.053
15_V71_P0.297051.015
57_A60_K0.295131.008
3_K79_V0.292510.999
12_V20_A0.289260.988
55_V69_F0.28530.975
69_F73_D0.284460.972
16_N21_K0.283440.968
25_L45_P0.282420.965
4_V80_I0.271830.929
21_K47_Q0.26070.891
51_R54_D0.256180.875
14_R71_P0.25270.863
7_I74_I0.252420.862
50_I75_V0.25070.857
9_I25_L0.247280.845
60_K68_C0.237690.812
6_D9_I0.237330.811
60_K67_D0.236850.809
57_A67_D0.234660.802
16_N19_Q0.227160.776
21_K49_I0.226830.775
62_K65_M0.226390.774
24_I46_F0.224440.767
54_D57_A0.219860.751
10_A79_V0.219410.750
13_T23_E0.214640.733
8_V16_N0.214440.733
47_Q77_A0.209290.715
46_F51_R0.208860.714
65_M69_F0.207680.710
10_A50_I0.206130.704
44_E69_F0.199390.681
17_P62_K0.198610.679
6_D44_E0.195570.668
26_C44_E0.192850.659
56_R80_I0.190740.652
11_R71_P0.189760.648
59_E65_M0.186790.638
15_V46_F0.186350.637
55_V75_V0.185350.633
52_K78_R0.184610.631
4_V7_I0.181870.621
55_V71_P0.179870.615
14_R46_F0.179530.613
48_G51_R0.178860.611
23_E68_C0.17880.611
55_V60_K0.177440.606
66_Y71_P0.176330.602
54_D78_R0.175310.599
70_R73_D0.174970.598
23_E44_E0.17470.597
3_K8_V0.173980.594
4_V53_Q0.173660.593
26_C60_K0.170950.584
57_A61_D0.17080.584
58_T65_M0.169940.581
48_G77_A0.167070.571
50_I54_D0.166690.570
11_R45_P0.164230.561
61_D70_R0.163980.560
8_V79_V0.161370.551
44_E57_A0.161210.551
57_A73_D0.160640.549
25_L81_S0.159360.544
50_I77_A0.159290.544
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
4ifdI199.50.142
2nn6I0.87899.40.21
1kl9A0.780599.30.256
3m7nA0.865999.20.263
4aidA0.756199.20.269
2je6I0.780599.20.277
2a19A0.780599.20.278
1q8kA0.780599.20.288
3aevA0.780599.20.291
3cdiA0.756199.20.293

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