GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_23 - Homeodomain-like domain
Pfam: PF13384 (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: CL0123
Length: 50
Sequences: 41191
Seq/Len: 823.82
HH_delta: 0.037 (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
18_W26_R2.600351.916
20_I35_Y2.589011.908
19_S22_E2.49771.840
24_A34_V2.270141.673
18_W22_E2.243221.653
32_S35_Y2.227661.641
20_I38_I2.222221.637
6_R37_W2.185841.611
31_R35_Y2.0921.542
13_L26_R2.030571.496
21_R31_R1.994041.469
35_Y39_K1.679611.238
36_R40_R1.623121.196
21_R25_K1.605111.183
13_L23_I1.59331.174
14_L38_I1.572221.159
24_A31_R1.568221.156
32_S36_R1.556931.147
13_L18_W1.553351.145
33_T36_R1.529231.127
9_Q13_L1.463531.078
30_S33_T1.44751.067
6_R9_Q1.444991.065
22_E26_R1.394771.028
7_R11_I1.388721.023
20_I31_R1.36751.008
29_V33_T1.323150.975
11_I15_R1.238940.913
33_T37_W1.210730.892
29_V37_W1.186310.874
29_V34_V1.138030.839
23_I34_V1.130140.833
8_A12_R1.125040.829
12_R16_E1.057360.779
22_E25_K1.050590.774
10_I14_L1.041270.767
13_L27_L1.010520.745
9_Q12_R1.005940.741
36_R39_K1.005070.741
39_K42_R0.967380.713
20_I34_V0.941140.693
7_R37_W0.917650.676
7_R40_R0.909540.670
11_I41_Y0.875250.645
32_S39_K0.823860.607
30_S36_R0.81620.601
21_R35_Y0.803570.592
12_R15_R0.768780.566
20_I24_A0.768410.566
10_I27_L0.766410.565
23_I27_L0.765510.564
13_L16_E0.738140.544
6_R29_V0.724860.534
15_R41_Y0.719950.531
23_I38_I0.718730.530
10_I34_V0.70790.522
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
2k27A197.10.037
1k78A197.10.039
1pdnC1970.053
2jn6A1970.056
1u78A196.90.077
1tc3C0.9496.90.079
2elhA196.60.121
2lvsA196.60.121
3hotA0.9896.10.165
2jrtA196.10.17

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