GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_21 - HTH-like domain
Pfam: PF13276 (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: 60
Sequences: 3547
Seq/Len: 59.12
HH_delta: 0.521 (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
7_R50_M1.54942.836
9_L33_E1.166072.134
27_W31_R1.09562.005
39_S42_R1.085581.987
23_Y44_R1.041541.906
23_Y40_R1.000411.831
10_I26_I0.986411.805
7_R49_E0.953321.745
9_L12_E0.928231.699
13_I29_E0.915431.675
21_Y25_R0.893891.636
7_R46_L0.851991.559
38_V43_V0.829221.518
9_L36_I0.803121.470
13_I26_I0.762351.395
29_E32_R0.756981.385
44_R48_R0.749361.372
11_K15_K0.688751.261
42_R45_R0.664071.215
31_R37_R0.653411.196
14_F52_L0.632171.157
25_R29_E0.617421.130
26_I47_M0.614721.125
29_E33_E0.602471.103
17_S20_T0.5971.093
12_E16_E0.592781.085
27_W43_V0.582061.065
46_L50_M0.573981.051
4_E8_E0.562851.030
6_L38_V0.544670.997
11_K50_M0.542630.993
14_F19_P0.534270.978
15_K19_P0.515210.943
48_R53_R0.485890.889
28_A32_R0.466530.854
27_W40_R0.463270.848
41_K44_R0.45920.840
17_S21_Y0.458430.839
13_I21_Y0.434060.794
21_Y29_E0.432680.792
13_I16_E0.42960.786
5_A8_E0.42940.786
14_F26_I0.42690.781
38_V42_R0.425680.779
14_F47_M0.418850.767
5_A36_I0.412420.755
24_R44_R0.407680.746
40_R44_R0.406670.744
39_S45_R0.406250.744
14_F53_R0.40060.733
20_T25_R0.399070.730
16_E51_G0.394080.721
16_E19_P0.387570.709
11_K52_L0.387290.709
14_F17_S0.387270.709
44_R54_S0.376260.689
41_K45_R0.372660.682
10_I13_I0.36760.673
53_R56_R0.363520.665
14_F54_S0.362310.663
19_P53_R0.359150.657
21_Y26_I0.35250.645
17_S29_E0.349230.639
7_R11_K0.348490.638
28_A31_R0.346510.634
8_E15_K0.346110.633
6_L9_L0.345240.632
42_R46_L0.342460.627
30_L43_V0.335340.614
6_L13_I0.332740.609
10_I46_L0.329260.603
46_L49_E0.327720.600
23_Y43_V0.326630.598
13_I17_S0.324410.594
25_R28_A0.323010.591
8_E12_E0.320210.586
47_M52_L0.315930.578
30_L36_I0.315270.577
22_G25_R0.310630.569
53_R57_R0.309750.567
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
2ahqA0.983394.70.521
3hotA0.833392.10.567
1u78A0.988.60.598
1pdnC0.816786.90.609
4fcyA0.9833750.654
1k78A0.933367.80.671
3v4gA0.966761.30.684
1stzA0.933357.20.691
1b4aA0.966753.70.697
2o03A0.983352.40.7
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