GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_20 - Helix-turn-helix domain
Pfam: PF12840 (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: 51866
Seq/Len: 850.26
HH_delta: -0.019 (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_L33_E3.476822.528
12_R44_H2.885412.098
26_T29_E2.660231.934
31_A38_Q2.568131.867
12_R47_K2.430081.767
49_E56_V2.417511.758
38_Q42_S2.02681.474
25_M33_E2.007541.460
27_V42_S1.9341.406
39_S42_S1.893581.377
42_S46_K1.84721.343
28_S32_E1.841391.339
28_S38_Q1.818971.323
11_T44_H1.795261.305
47_K51_A1.768571.286
18_L25_M1.72041.251
25_M29_E1.714341.246
24_P57_E1.675041.218
12_R51_A1.661771.208
14_R18_L1.628411.184
37_S40_T1.611961.172
16_L53_L1.561961.136
29_E33_E1.548131.126
39_S43_Y1.524471.108
40_T43_Y1.476081.073
36_I40_T1.457811.060
31_A41_V1.451961.056
18_L34_L1.436491.044
11_T14_R1.393431.013
22_N25_M1.309850.952
46_K50_E1.300960.946
13_L17_R1.295540.942
46_K49_E1.293690.941
11_T36_I1.284970.934
27_V45_L1.261940.918
29_E32_E1.245340.905
36_I41_V1.24350.904
27_V38_Q1.234410.898
15_I44_H1.231940.896
15_I41_V1.207280.878
19_L25_M1.190970.866
14_R17_R1.188230.864
43_Y47_K1.177180.856
19_L54_I1.123230.817
49_E54_I1.119260.814
14_R34_L1.079220.785
18_L21_S1.063570.773
34_L41_V1.032380.751
22_N33_E1.030140.749
44_H47_K1.024440.745
15_I30_L1.006240.732
27_V41_V0.97720.711
30_L45_L0.971270.706
40_T44_H0.96990.705
45_L54_I0.955640.695
43_Y46_K0.950220.691
21_S25_M0.946860.688
47_K50_E0.943820.686
18_L22_N0.90350.657
37_S43_Y0.897530.653
28_S42_S0.888510.646
27_V31_A0.871480.634
30_L41_V0.86690.630
46_K56_V0.824440.599
17_R21_S0.81710.594
28_S31_A0.798030.580
16_L20_A0.728710.530
18_L30_L0.728150.529
48_L53_L0.724250.527
19_L24_P0.716040.521
42_S58_R0.70130.510
17_R20_A0.664720.483
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
3f6vA0.983698.3-0.019
1u2wA198.3-0.007
3f6oA0.983698.3-0.006
3jthA0.983698.3-0.004
4g6qA0.983698.20.025
3pqkA0.983698.20.026
2oqgA0.983698.20.031
3cuoA198.10.034
1r1uA0.983698.10.035
2jscA0.983698.10.035

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