GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MerR_1 - MerR HTH family regulatory protein
Pfam: PF13411 (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: 69
Sequences: 12270
Seq/Len: 177.83
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
39_S42_D2.39293.474
19_Y23_E1.954072.837
58_S61_E1.517632.203
15_S22_R1.35731.971
7_A14_P1.269861.844
48_E52_L1.254511.821
14_P18_R1.229411.785
4_K8_K1.165661.692
2_T5_E1.128641.639
2_T37_Y1.108691.610
21_E36_R1.064671.546
6_V46_L1.027121.491
5_E8_K0.982551.426
16_T20_Y0.957581.390
3_I18_R0.943711.370
63_K67_K0.93741.361
53_R59_L0.893311.297
50_K54_K0.876421.272
6_V43_V0.857371.245
48_E51_E0.846871.230
10_L43_V0.819451.190
45_R66_L0.814511.183
2_T35_Y0.812571.180
3_I7_A0.79891.160
23_E63_K0.789071.146
61_E64_K0.784571.139
9_L47_R0.763821.109
31_D34_G0.748871.087
31_D37_Y0.742611.078
4_K14_P0.73471.067
21_E38_Y0.730981.061
15_S19_Y0.726251.054
31_D35_Y0.719061.044
13_S16_T0.711151.032
29_P39_S0.70671.026
51_E55_Q0.691781.004
40_E44_E0.685130.995
6_V42_D0.674440.979
9_L43_V0.673090.977
7_A17_L0.672830.977
64_K67_K0.669190.972
42_D45_R0.667880.970
44_E47_R0.660260.959
16_T19_Y0.649720.943
5_E9_L0.641770.932
50_K53_R0.635360.922
10_L46_L0.634830.922
15_S18_R0.622410.904
47_R51_E0.601980.874
27_P45_R0.593160.861
3_I21_E0.590690.858
12_V16_T0.587890.854
47_R50_K0.586560.852
49_I62_I0.585610.850
9_L40_E0.582450.846
59_L63_K0.570210.828
48_E65_L0.564560.820
10_L50_K0.550750.800
52_L62_I0.548990.797
7_A10_L0.537170.780
38_Y42_D0.534750.776
21_E27_P0.533210.774
17_L38_Y0.530790.771
57_M61_E0.528040.767
6_V10_L0.527480.766
29_P42_D0.514010.746
60_E63_K0.511110.742
51_E54_K0.509110.739
41_E44_E0.508190.738
13_S19_Y0.49810.723
18_R21_E0.495080.719
52_L57_M0.485610.705
20_Y25_L0.484160.703
10_L17_L0.483420.702
10_L47_R0.481480.699
57_M65_L0.475690.691
45_R48_E0.47030.683
43_V47_R0.46770.679
17_L21_E0.458740.666
41_E45_R0.45330.658
52_L65_L0.451380.655
62_I66_L0.445790.647
53_R62_I0.438850.637
55_Q65_L0.43750.635
25_L49_I0.422550.613
6_V17_L0.420570.611
40_E47_R0.420160.610
55_Q61_E0.416060.604
49_I52_L0.410970.597
20_Y59_L0.387050.562
44_E51_E0.386560.561
28_P34_G0.385550.560
24_G27_P0.379030.550
6_V12_V0.372720.541
7_A13_S0.372270.540
27_P42_D0.367170.533
40_E43_V0.367170.533
53_R58_S0.357390.519
38_Y43_V0.353590.513
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
3qaoA199-0.009
3hh0A198.9-0
2dg6A198.90.004
3gp4A198.90.004
2zhgA198.90.01
1q06A198.90.02
2vz4A198.90.032
3gpvA198.90.033
1r8dA198.80.038
1r8eA198.80.04

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