GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Hpt - Hpt domain
Pfam: PF01627 (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: 90
Sequences: 4121
Seq/Len: 45.79
HH_delta: 0.098 (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
44_G52_A1.072482.839
18_E81_E1.048442.776
28_D31_E0.855672.265
13_D35_L0.792882.099
43_A51_L0.719271.904
34_R38_R0.667891.768
16_Q35_L0.650981.723
6_F43_A0.646531.712
20_A31_E0.634971.681
17_L36_A0.581211.539
36_A58_L0.57191.514
36_A55_A0.569731.508
37_H41_G0.534731.416
36_A62_L0.533781.413
64_S69_E0.532631.410
40_K56_E0.530171.404
10_A39_L0.52821.398
83_M86_Q0.515661.365
37_H59_E0.50481.336
42_S45_N0.483791.281
32_L62_L0.479041.268
58_L76_L0.469581.243
16_Q20_A0.468961.241
7_L11_P0.467131.237
29_W65_G0.454071.202
41_G44_G0.448811.188
15_E81_E0.438011.160
77_L81_E0.429311.137
13_D16_Q0.427281.131
13_D38_R0.424741.124
10_A13_D0.419291.110
79_E82_A0.419131.110
10_A84_L0.414771.098
5_I9_E0.412861.093
33_R63_K0.406621.076
17_L35_L0.405511.074
37_H40_K0.40551.073
13_D42_S0.405431.073
54_L79_E0.39551.047
16_Q31_E0.387121.025
43_A55_A0.386741.024
4_D8_E0.385111.020
38_R42_S0.384261.017
6_F10_A0.38351.015
13_D45_N0.380281.007
49_P53_E0.37791.000
42_S46_L0.375390.994
20_A28_D0.372590.986
9_E13_D0.372130.985
30_E34_R0.369180.977
16_Q19_Q0.367530.973
20_A35_L0.366660.971
26_Q30_E0.3610.956
30_E33_R0.35270.934
12_E16_Q0.352520.933
40_K44_G0.351230.930
57_Q60_Q0.348760.923
39_L55_A0.347970.921
10_A14_L0.34780.921
5_I8_E0.340230.901
66_D69_E0.339010.897
3_L46_L0.336750.891
56_E60_Q0.330820.876
74_E78_D0.329510.872
19_Q26_Q0.326730.865
49_P52_A0.326190.864
17_L32_L0.325220.861
29_W66_D0.324060.858
14_L18_E0.312720.828
75_Q79_E0.307980.815
43_A52_A0.302360.800
12_E15_E0.302290.800
79_E83_M0.301860.799
75_Q82_A0.298090.789
13_D39_L0.291210.771
54_L57_Q0.29110.771
18_E74_E0.287770.762
30_E86_Q0.287690.762
26_Q68_P0.287370.761
20_A32_L0.284370.753
33_R66_D0.280480.743
15_E19_Q0.280430.742
14_L81_E0.273660.724
42_S52_A0.273420.724
54_L80_L0.272590.722
63_K67_K0.271280.718
5_I46_L0.270810.717
25_E67_K0.268450.711
41_G45_N0.268260.710
79_E86_Q0.266720.706
6_F34_R0.265260.702
11_P15_E0.262980.696
38_R45_N0.262580.695
21_L32_L0.262340.695
31_E35_L0.260.688
41_G48_A0.258730.685
53_E56_E0.254680.674
78_D82_A0.253940.672
7_L51_L0.253680.672
50_R83_M0.252940.670
29_W61_A0.252810.669
64_S75_Q0.2510.664
53_E75_Q0.250820.664
44_G59_E0.250440.663
29_W63_K0.250170.662
55_A80_L0.248390.658
9_E42_S0.247570.655
50_R86_Q0.247450.655
82_A86_Q0.246660.653
5_I42_S0.244650.648
51_L83_M0.237820.630
52_A56_E0.236670.627
29_W33_R0.233060.617
61_A66_D0.231670.613
9_E45_N0.231220.612
43_A46_L0.231190.612
2_L45_N0.226510.600
27_E53_E0.224280.594
33_R59_E0.224270.594
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
3us6A0.9333990.098
3myfA0.9667990.111
3iqtA0.9667990.115
4eukB0.9333990.126
2a0bA0.9667990.128
1yviA0.9333990.13
1sr2A0.9111990.135
1y6dA0.966798.90.146
1i5nA198.90.166
2r25A0.966798.90.167

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