GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HupF_HypC - HupFHypC family
Pfam: PF01455 (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: 68
Sequences: 832
Seq/Len: 12.24
HH_delta: -0.009 (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
57_E61_E0.626612.469
9_V38_V0.609482.402
20_V27_R0.592082.333
7_G23_F0.559652.205
19_A32_L0.524352.066
61_E65_D0.515212.030
58_E62_E0.500641.973
42_D54_K0.455151.794
11_E20_V0.438321.727
53_E59_E0.41881.650
62_E65_D0.410651.618
63_T67_L0.404211.593
20_V29_E0.392691.548
8_R43_Y0.378851.493
8_R22_D0.367021.446
7_G21_V0.361611.425
9_V19_A0.352891.391
10_V27_R0.343811.355
39_K42_D0.3431.352
31_S34_L0.336591.326
47_H52_I0.327881.292
30_V51_A0.317531.251
24_G68_E0.315551.244
7_G46_V0.309991.222
31_S50_F0.309871.221
22_D25_G0.298451.176
17_G33_A0.291981.151
35_V51_A0.273741.079
4_A52_I0.271921.072
12_V40_V0.271771.071
60_A64_L0.26041.026
8_R57_E0.257361.014
26_V48_A0.254171.002
22_D27_R0.246110.970
2_C6_P0.245080.966
37_D54_K0.243980.961
48_A51_A0.243820.961
26_V47_H0.238230.939
48_A53_E0.237560.936
32_L38_V0.228160.899
35_V54_K0.22530.888
23_F46_V0.221890.874
38_V42_D0.219760.866
36_P54_K0.219730.866
29_E35_V0.218110.860
45_L56_D0.214960.847
23_F28_R0.213040.840
38_V54_K0.211480.833
9_V44_V0.211470.833
55_I66_L0.208180.820
59_E62_E0.205930.812
13_D29_E0.205410.809
8_R13_D0.202860.799
30_V33_A0.201680.795
56_D59_E0.201250.793
28_R67_L0.200190.789
21_V30_V0.197720.779
7_G24_G0.196090.773
39_K54_K0.196080.773
13_D36_P0.195890.772
43_Y52_I0.19520.769
64_L68_E0.194380.766
30_V46_V0.189960.749
62_E66_L0.189590.747
17_G34_L0.188840.744
3_L50_F0.187210.738
43_Y60_A0.184070.725
13_D40_V0.181720.716
40_V58_E0.180020.709
45_L55_I0.179850.709
8_R41_G0.178880.705
20_V54_K0.17860.704
13_D16_G0.175410.691
16_G36_P0.175070.690
32_L36_P0.174850.689
30_V55_I0.173890.685
12_V39_K0.173870.685
12_V17_G0.169850.669
18_M29_E0.16980.669
35_V38_V0.169350.667
62_E67_L0.168560.664
48_A52_I0.167720.661
25_G60_A0.166370.656
3_L28_R0.164220.647
7_G22_D0.163760.645
27_R58_E0.157490.621
13_D62_E0.155770.614
10_V22_D0.155620.613
5_I53_E0.154310.608
54_K61_E0.153740.606
55_I64_L0.153670.606
21_V47_H0.153650.606
45_L50_F0.153110.603
4_A53_E0.152910.603
18_M33_A0.151280.596
28_R52_I0.150960.595
17_G32_L0.150570.593
59_E63_T0.148020.583
27_R64_L0.14760.582
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
3d3rA199.9-0.009
2z1cA0.970699.90.008
2ot2A0.970699.90.016
3pqiA0.985381.10.833
2rcnA0.970645.30.868
2wfwA0.955940.60.871
2yv5A0.970634.20.876
2vz8A0.941228.70.881
2ztdA0.970619.60.889
2ftcK0.397119.30.89

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