GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_13 - HTH DNA binding domain
Pfam: PF11972 (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: 54
Sequences: 27371
Seq/Len: 506.87
HH_delta: 0.197 (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_L22_E2.654442.453
15_S18_M2.431352.246
28_Q31_Q2.285532.112
16_A31_Q1.816981.679
20_A27_P1.628171.504
7_L11_R1.60631.484
3_R7_L1.516091.401
4_L30_A1.490241.377
26_T29_A1.482391.370
25_V30_A1.479911.367
7_L23_L1.468381.357
14_V22_E1.467591.356
27_P31_Q1.452731.342
31_Q35_A1.43181.323
11_R14_V1.421011.313
8_L14_V1.412091.305
7_L14_V1.410841.304
45_R48_Y1.397611.291
4_L19_V1.349471.247
25_V29_A1.321881.221
17_P27_P1.314041.214
17_P21_K1.312851.213
28_Q32_R1.308181.209
20_A30_A1.288111.190
29_A32_R1.281271.184
5_I39_L1.240121.146
4_L33_L1.2271.134
11_R22_E1.225791.133
18_M22_E1.130181.044
7_L10_S1.073270.992
23_L30_A1.067080.986
5_I9_L1.054890.975
19_V30_A1.028030.950
14_V18_M1.022410.945
3_R6_D1.021050.943
19_V34_I0.983660.909
26_T32_R0.928980.858
16_A27_P0.891780.824
18_M21_K0.888390.821
29_A33_L0.886040.819
16_A34_I0.850640.786
6_D9_L0.836250.773
40_R43_T0.827930.765
3_R23_L0.799040.738
4_L23_L0.795720.735
8_L40_R0.790510.730
11_R18_M0.759080.701
34_I40_R0.756190.699
16_A20_A0.753510.696
8_L13_L0.739660.683
32_R35_A0.730180.675
7_L19_V0.716580.662
28_Q33_L0.708870.655
16_A30_A0.705980.652
15_S48_Y0.698720.646
44_G48_Y0.697060.644
17_P20_A0.672710.622
26_T33_L0.669630.619
6_D37_L0.657620.608
39_L43_T0.635550.587
32_R36_E0.612950.566
13_L43_T0.596670.551
19_V33_L0.589540.545
19_V22_E0.586460.542
44_G47_R0.58090.537
17_P48_Y0.573140.530
20_A25_V0.551920.510
42_I45_R0.548340.507
6_D10_S0.539410.498
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
1u2wA197.40.197
3f6vA0.981597.30.219
3cuoA197.30.223
2wteA0.96397.20.24
2oqgA0.981597.10.241
1ub9A197.10.243
3jthA0.981597.10.244
2jscA0.981597.10.249
3pqkA0.981597.10.252
2kkoA0.9815970.255

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