GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cpn10 - Chaperonin 10 Kd subunit
Pfam: PF00166 (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: CL0296
Length: 93
Sequences: 1821
Seq/Len: 19.58
HH_delta: -0.061 (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
12_K79_E1.295164.417
12_K38_K1.250434.264
9_V89_I0.976063.329
48_N52_E0.8182.790
75_K80_K0.720922.459
47_Y53_E0.714252.436
36_Q63_K0.671742.291
58_V89_I0.656892.240
13_K66_F0.558711.905
2_I91_A0.549621.874
40_V81_Y0.497461.697
37_G66_F0.49011.671
59_K62_D0.473171.614
57_D86_E0.466721.592
48_N54_V0.440091.501
56_M86_E0.438891.497
38_K60_V0.437011.490
14_I63_K0.425241.450
44_P57_D0.419071.429
69_Y85_R0.414241.413
73_E80_K0.408961.395
38_K61_G0.405871.384
18_E31_K0.405541.383
41_A60_V0.400751.367
14_I38_K0.41.364
38_K63_K0.383741.309
19_K25_I0.376091.283
12_K81_Y0.36471.244
67_P70_A0.364081.242
66_F82_L0.362941.238
10_L83_I0.361911.234
11_V37_G0.360211.228
7_D85_R0.355221.211
35_N72_T0.353061.204
11_V84_V0.350911.197
28_E31_K0.348791.190
46_R87_D0.335611.145
3_K92_V0.317191.082
42_V56_M0.3141.071
2_I10_L0.308571.052
64_V89_I0.305661.042
44_P53_E0.304281.038
20_T23_G0.300491.025
34_P68_K0.294251.004
67_P90_L0.28620.976
12_K15_E0.283570.967
53_E57_D0.283050.965
85_R88_D0.280320.956
6_G26_L0.269470.919
76_F81_Y0.269080.918
36_Q91_A0.264750.903
66_F84_V0.257380.878
42_V60_V0.256310.874
58_V92_V0.252690.862
44_P48_N0.251350.857
14_I36_Q0.247930.846
45_G56_M0.247570.844
47_Y57_D0.244380.833
47_Y51_G0.242950.829
13_K37_G0.241350.823
36_Q93_I0.241070.822
35_N68_K0.239030.815
67_P84_V0.238320.813
45_G55_P0.237610.810
14_I37_G0.232370.792
7_D43_G0.230640.787
83_I90_L0.2270.774
6_G57_D0.226940.774
47_Y50_N0.226620.773
68_K73_E0.225580.769
31_K83_I0.225460.769
44_P56_M0.224830.767
31_K73_E0.221240.755
39_V58_V0.219620.749
87_D91_A0.219240.748
67_P88_D0.218480.745
5_L58_V0.216850.740
73_E81_Y0.214580.732
17_E20_T0.214540.732
24_I75_K0.214090.730
69_Y72_T0.213020.726
47_Y54_V0.210330.717
70_A82_L0.210170.717
48_N53_E0.208820.712
24_I86_E0.208540.711
21_A29_S0.208060.710
37_G84_V0.206860.705
44_P47_Y0.206160.703
15_E79_E0.204640.698
29_S35_N0.20370.695
17_E78_G0.20240.690
8_R67_P0.202220.690
37_G82_L0.201550.687
6_G88_D0.200220.683
43_G83_I0.19950.680
68_K71_G0.197160.672
57_D75_K0.195670.667
84_V90_L0.194340.663
67_P85_R0.193270.659
46_R85_R0.190610.650
32_E68_K0.190350.649
44_P92_V0.190080.648
72_T88_D0.188880.644
68_K88_D0.188590.643
23_G64_V0.187190.638
38_K79_E0.185630.633
49_E87_D0.18460.630
7_D45_G0.183030.624
26_L67_P0.182340.622
46_R50_N0.182050.621
11_V65_L0.180910.617
7_D86_E0.179220.611
6_G86_E0.177890.607
8_R85_R0.175960.600
86_E89_I0.175670.599
34_P88_D0.174230.594
3_K57_D0.174160.594
11_V82_L0.173090.590
10_L81_Y0.171650.585
58_V86_E0.171030.583
10_L65_L0.170880.583
32_E75_K0.170160.580
65_L90_L0.167730.572
2_I83_I0.166950.569
46_R56_M0.164420.561
3_K31_K0.162360.554
59_K92_V0.161740.552
11_V27_P0.161470.551
15_E52_E0.160460.547
15_E29_S0.160330.547
46_R86_E0.160280.547
9_V56_M0.158070.539
46_R53_E0.157590.537
18_E28_E0.156940.535
52_E55_P0.156770.535
37_G56_M0.156260.533
35_N93_I0.154730.528
22_S35_N0.154360.526
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
3nx6A1100-0.061
1we3O1100-0.06
1p3hA1100-0.058
1pcqO1100-0.055
1g31A0.924799.90.149
4a2cA0.892565.10.866
3pi7A0.881759.80.87
3slkA0.82858.70.871
4dupA0.838758.60.871
3jv7A0.892556.80.873

Page generated in 0.0222 seconds.