GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ClpS - ATP-dependent Clp protease adaptor protein ClpS
Pfam: PF02617 (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: 82
Sequences: 1054
Seq/Len: 12.85
HH_delta: -0.001 (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
64_A82_I0.860773.636
43_E47_E0.665822.812
12_W81_T0.640832.707
9_V60_A0.58522.472
32_C40_I0.563492.380
40_I50_A0.549432.321
8_R51_V0.489072.066
32_C36_Q0.488082.062
29_V70_A0.480692.030
33_S36_Q0.469931.985
19_F41_A0.444791.879
10_V49_R0.422191.783
27_R34_E0.405691.714
29_V66_K0.383751.621
68_Q79_R0.379791.604
43_E50_A0.337131.424
59_E62_E0.318531.345
42_M46_R0.317981.343
10_V51_V0.290241.226
11_L78_L0.288451.218
11_L44_V0.280641.185
41_A45_H0.271261.146
56_S59_E0.264611.118
13_N45_H0.258241.091
19_F45_H0.257151.086
58_E61_E0.257071.086
53_G63_Y0.256451.083
25_V70_A0.256291.083
64_A81_T0.253011.069
23_I41_A0.24951.054
12_W57_R0.242371.024
15_E18_T0.241851.022
67_L80_A0.239491.012
24_D28_R0.238381.007
42_M45_H0.235420.994
11_L26_L0.232140.981
12_W79_R0.228290.964
24_D70_A0.227470.961
24_D27_R0.222950.942
8_R54_T0.222730.941
28_R70_A0.222630.940
36_Q39_Q0.220450.931
17_H21_Q0.218950.925
11_L82_I0.216440.914
44_V78_L0.214920.908
18_T79_R0.212560.898
9_V63_Y0.207140.875
19_F42_M0.204290.863
66_K70_A0.202230.854
65_E69_R0.201370.851
4_P56_S0.199810.844
21_Q70_A0.195970.828
64_A68_Q0.194820.823
34_E46_R0.188760.797
52_V67_L0.187570.792
58_E62_E0.187410.792
34_E38_R0.187280.791
34_E39_Q0.185170.782
30_F63_Y0.184850.781
7_Y57_R0.181110.765
59_E63_Y0.180070.761
4_P58_E0.179140.757
52_V80_A0.17860.754
20_E36_Q0.175340.741
29_V67_L0.172650.729
30_F60_A0.172270.728
35_E42_M0.171630.725
17_H55_G0.171320.724
38_R42_M0.170390.720
4_P59_E0.170330.719
35_E39_Q0.169580.716
15_E21_Q0.169230.715
18_T44_V0.168480.712
24_D69_R0.167790.709
9_V50_A0.167250.706
23_I38_R0.162710.687
3_E36_Q0.162170.685
20_E24_D0.161670.683
3_E47_E0.160880.680
24_D47_E0.160680.679
35_E56_S0.159660.674
12_W49_R0.158150.668
5_D65_E0.157760.666
21_Q59_E0.156280.660
18_T68_Q0.156110.659
37_A41_A0.155470.657
5_D82_I0.155020.655
17_H71_G0.153610.649
3_E12_W0.152160.643
27_R33_S0.152130.643
53_G59_E0.151640.640
51_V65_E0.150710.637
28_R31_G0.148870.629
51_V81_T0.148860.629
65_E79_R0.14820.626
20_E23_I0.145840.616
3_E69_R0.14540.614
10_V82_I0.145310.614
71_G80_A0.143670.607
3_E39_Q0.143640.607
17_H25_V0.143160.605
8_R15_E0.142260.601
47_E69_R0.140670.594
46_R57_R0.140510.593
19_F23_I0.140170.592
14_D45_H0.139070.587
21_Q63_Y0.137780.582
31_G43_E0.137710.582
19_F44_V0.136940.578
9_V71_G0.135070.571
21_Q25_V0.1350.570
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
2w9rA199.9-0.001
3dnjA199.90.006
3o1fA0.951299.80.044
4kcze0.841571.60.837
2zjq50.865971.20.838
2j01L0.865971.20.838
1dd3A0.914667.70.842
1ctfA0.87867.40.842
2ftcE0.890257.90.851
2giaA0.707353.70.854

Page generated in 0.0332 seconds.