GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Flagellin_IN - Flagellin hook IN motif
Pfam: PF07196 (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. )
Length: 56
Sequences: 684
Seq/Len: 12.21
HH_delta: 0.545 (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
46_D49_R0.502372.534
27_A43_I0.491692.481
21_D25_D0.444352.242
21_D29_A0.389161.963
45_N48_G0.365841.846
40_T55_T0.321681.623
24_D28_D0.298051.504
43_I48_G0.269071.357
30_I52_L0.265151.338
17_V26_I0.263231.328
3_T12_T0.252781.275
17_V29_A0.248371.253
27_A50_L0.247881.251
4_I37_T0.244351.233
22_T25_D0.237011.196
3_T10_S0.233771.179
2_L6_G0.23011.161
30_I41_A0.22671.144
24_D43_I0.226041.140
17_V21_D0.216471.092
34_S39_V0.214271.081
16_S53_T0.213751.078
11_F35_S0.213421.077
25_D29_A0.210681.063
18_S21_D0.210231.061
43_I50_L0.203491.027
28_D53_T0.201241.015
27_A42_S0.200911.014
16_S19_A0.197510.996
28_D51_V0.194860.983
6_G12_T0.188620.952
30_I42_S0.185280.935
29_A42_S0.185140.934
20_G24_D0.179880.908
45_N54_S0.177420.895
42_S46_D0.176580.891
7_G24_D0.17650.890
9_G20_G0.171090.863
21_D26_I0.170390.860
23_L51_V0.16960.856
5_N55_T0.165890.837
21_D49_R0.163680.826
4_I12_T0.161390.814
31_N41_A0.160370.809
29_A53_T0.159330.804
2_L48_G0.159090.803
5_N54_S0.157490.795
4_I30_I0.156510.790
7_G26_I0.154730.781
44_D51_V0.154170.778
27_A52_L0.154160.778
2_L11_F0.14760.745
11_F36_N0.146510.739
31_N39_V0.146130.737
25_D42_S0.145290.733
7_G30_I0.145280.733
23_L48_G0.144910.731
36_N55_T0.142610.719
3_T7_G0.141470.714
15_I42_S0.141180.712
23_L43_I0.14070.710
4_I15_I0.136380.688
39_V53_T0.135790.685
5_N9_G0.135590.684
24_D51_V0.13540.683
30_I43_I0.134170.677
15_I18_S0.133420.673
36_N47_G0.133320.673
24_D39_V0.133090.671
35_S42_S0.132690.669
8_D11_F0.132430.668
2_L7_G0.132260.667
9_G37_T0.130570.659
37_T52_L0.12910.651
25_D38_G0.128470.648
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
3k8wA0.946495.50.545
4hwiB0.839362.10.714
3shqA0.839357.60.721
2lwpA0.839336.50.753
4a20A0.87534.40.756
1v86A0.839331.30.762
3m63B0.839330.80.763
1wggA0.839329.90.764
1y8xB0.892929.60.764
1v2yA0.910728.30.766
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