GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HHH_5 - Helix-hairpin-helix domain
Pfam: PF14520 (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: CL0198
Length: 60
Sequences: 13315
Seq/Len: 221.92
HH_delta: -0.006 (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
17_R50_T1.957442.385
36_D39_E1.93492.358
8_L18_A1.802492.197
37_P52_E1.702392.075
37_P55_I1.662612.026
41_A48_E1.510941.841
41_A51_A1.465541.786
48_E52_E1.449141.766
51_A55_I1.396591.702
27_K31_D1.335591.628
37_P41_A1.258511.534
28_T31_D1.25071.524
26_I35_A1.235791.506
12_G53_K1.172681.429
52_E56_E1.119021.364
47_G50_T1.084611.322
24_A43_I1.060831.293
17_R20_K1.049111.278
39_E42_E0.993771.211
16_K20_K0.989011.205
24_A42_E0.92511.127
37_P48_E0.918471.119
20_K43_I0.878541.071
30_E34_N0.873421.064
5_D8_L0.872931.064
17_R46_I0.868511.058
16_K19_E0.868431.058
20_K23_E0.837191.020
33_A58_A0.797050.971
14_G17_R0.789180.962
40_L51_A0.783410.955
5_D9_S0.770810.939
11_P57_A0.75060.915
53_K57_A0.741370.903
6_D9_S0.736610.898
31_D34_N0.716750.873
20_K45_G0.713990.870
6_D33_A0.706710.861
15_P19_E0.704150.858
22_Y27_K0.699080.852
38_E41_A0.688760.839
19_E23_E0.685880.836
46_I50_T0.673180.820
44_P47_G0.638920.779
20_K44_P0.638220.778
13_I18_A0.636540.776
26_I30_E0.632980.771
12_G49_K0.629860.768
50_T53_K0.626240.763
10_I57_A0.625670.762
8_L33_A0.60820.741
26_I31_D0.607950.741
31_D35_A0.602450.734
13_I17_R0.59570.726
29_L33_A0.583320.711
53_K56_E0.559790.682
46_I54_I0.556750.678
32_L58_A0.554390.676
49_K52_E0.553750.675
30_E33_A0.553730.675
55_I58_A0.553220.674
49_K53_K0.539170.657
46_I51_A0.530040.646
23_E27_K0.525520.640
18_A22_Y0.524890.640
21_L43_I0.513460.626
19_E22_Y0.512530.625
11_P53_K0.509940.621
26_I32_L0.504210.614
7_L18_A0.499010.608
35_A39_E0.495120.603
37_P51_A0.493530.601
43_I46_I0.487340.594
34_N38_E0.484210.590
51_A54_I0.481130.586
24_A44_P0.477870.582
20_K24_A0.474350.578
13_I20_K0.471490.575
24_A28_T0.468520.571
36_D55_I0.465140.567
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
3sgiA0.983398.1-0.006
2owoA0.983397.90.042
3c65A0.966797.90.044
4glxA0.983397.90.044
1dgsA0.983397.80.07
1cukA0.983397.80.082
1ixrA0.983397.80.084
1vq8Y197.80.087
1kftA0.983397.70.096
4glxA197.70.102

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