GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_CodY - CodY helix-turn-helix domain
Pfam: PF08222 (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: 61
Sequences: 34541
Seq/Len: 566.25
HH_delta: 0.132 (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
29_E36_S2.647982.514
6_V9_K2.273092.158
11_A18_R2.177682.067
50_N53_F2.049441.946
39_L47_K1.806021.714
7_A18_R1.766711.677
22_V26_R1.593551.513
27_K31_A1.504991.429
20_V23_N1.458331.384
20_V24_A1.445361.372
17_T20_V1.439391.366
7_A22_V1.435931.363
5_L9_K1.367461.298
11_A21_I1.366371.297
5_L13_R1.345751.278
9_K13_R1.326331.259
36_S46_I1.325311.258
18_R22_V1.278991.214
8_S18_R1.276061.211
8_S12_D1.272921.208
36_S44_T1.262181.198
24_A27_K1.25261.189
26_R29_E1.20761.146
26_R30_S1.199151.138
6_V45_Y1.193791.133
17_T23_N1.159471.101
27_K30_S1.115591.059
19_S22_V1.112751.056
35_E50_N1.101321.045
4_R37_R1.093861.038
19_S23_N1.080651.026
16_I20_V1.065861.012
9_K12_D1.056311.003
39_L45_Y1.053471.000
38_S46_I1.031990.980
23_N27_K0.967250.918
4_R47_K0.959360.911
4_R48_V0.937820.890
29_E34_I0.929940.883
16_I21_I0.929930.883
49_L53_F0.883710.839
23_N26_R0.873910.830
21_I25_L0.844490.802
7_A21_I0.843740.801
7_A25_L0.802820.762
8_S11_A0.776430.737
10_I25_L0.754180.716
35_E47_K0.745490.708
38_S43_G0.744530.707
29_E35_E0.737830.700
25_L34_I0.715920.680
39_L44_T0.714030.678
32_G52_Y0.705610.670
44_T47_K0.664550.631
14_V21_I0.663970.630
28_L33_V0.644980.612
15_G24_A0.636940.605
37_R48_V0.630790.599
31_A52_Y0.630670.599
10_I13_R0.626230.594
35_E48_V0.611410.580
28_L34_I0.592020.562
44_T48_V0.588620.559
33_V53_F0.583670.554
37_R47_K0.581190.552
24_A31_A0.562360.534
10_I21_I0.560880.532
11_A14_V0.555880.528
25_L29_E0.554810.527
26_R36_S0.549490.522
14_V17_T0.54220.515
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
3f6oA0.967298.20.132
3f6vA0.967298.20.136
1u2wA0.967298.20.139
3jthA0.967298.20.14
1hsjA198.10.145
3pqkA0.967298.10.147
3cuoA0.967298.10.148
2kkoA0.967298.10.152
4hblA198.10.154
4em2A198.10.154

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