GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Big_3_4 - Bacterial Ig-like domain (group 3)
Pfam: PF13754 (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: CL0159
Length: 54
Sequences: 1024
Seq/Len: 18.96
HH_delta: 0.18 (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_D13_N1.041464.619
34_D38_N0.896753.977
18_V21_L0.528572.344
6_T16_F0.477962.120
23_D26_Y0.421081.868
33_T39_T0.369481.639
23_D51_T0.35361.568
31_T39_T0.35011.553
8_V13_N0.348741.547
22_A26_Y0.348531.546
26_Y49_I0.328761.458
8_V32_A0.3221.428
14_W47_F0.308321.367
50_D54_P0.305361.354
27_T44_S0.303671.347
50_D53_A0.277981.233
31_T41_T0.276111.225
28_I45_V0.251521.116
26_Y47_F0.240791.068
16_F28_I0.225030.998
21_L29_T0.218530.969
14_W49_I0.215270.955
29_T44_S0.214050.949
25_T41_T0.212820.944
13_N43_S0.203290.902
18_V28_I0.200550.889
33_T45_V0.197380.875
48_T53_A0.191130.848
7_T25_T0.186340.826
10_S15_S0.185790.824
10_S35_A0.177510.787
43_S46_T0.177230.786
23_D52_T0.176640.783
43_S47_F0.175560.779
32_A40_S0.173740.771
7_T22_A0.172850.767
8_V25_T0.172450.765
10_S42_S0.172040.763
31_T40_S0.17070.757
24_G47_F0.168260.746
30_V46_T0.168120.746
14_W36_A0.165330.733
17_T39_T0.164610.730
24_G49_I0.16260.721
35_A40_S0.162480.721
15_S27_T0.160880.714
23_D48_T0.159610.708
18_V42_S0.157110.697
35_A41_T0.155980.692
16_F20_A0.155610.690
28_I47_F0.153590.681
24_G28_I0.151350.671
26_Y39_T0.150260.666
22_A35_A0.145590.646
41_T46_T0.145370.645
40_S43_S0.144990.643
32_A44_S0.144280.640
15_S29_T0.142950.634
25_T48_T0.141920.629
39_T43_S0.141830.629
39_T45_V0.141530.628
23_D29_T0.141520.628
8_V28_I0.138980.616
29_T41_T0.137050.608
21_L35_A0.135420.601
20_A45_V0.133910.594
14_W45_V0.133670.593
29_T42_S0.133660.593
12_G16_F0.13240.587
6_T23_D0.131720.584
19_P45_V0.12970.575
7_T11_D0.128760.571
31_T46_T0.127830.567
35_A38_N0.12650.561
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
2yn5A1990.18
2yn5A0.981598.80.241
3pddA0.96397.80.456
3pddA0.944497.20.534
3pe9A0.944495.80.61
1xf1A194.40.645
3arxA0.981591.10.682
4hmeA0.96390.10.688
4a2lA0.981589.90.689
4hu2A0.925989.80.69

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