GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TrmB - Sugar-specific transcriptional regulator TrmB
Pfam: PF01978 (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: 68
Sequences: 41971
Seq/Len: 617.22
HH_delta: -0.029 (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
47_E54_R2.47292.077
24_T27_E2.465352.070
16_A31_E2.392822.009
10_E45_S2.194951.843
10_E42_A2.163481.817
29_A36_R2.051121.722
10_E49_K1.895941.592
37_S40_Y1.78051.495
25_A40_Y1.705411.432
45_S49_K1.704461.431
36_R40_Y1.700261.428
9_N42_A1.646181.382
23_A31_E1.616031.357
27_E31_E1.605751.348
22_P55_E1.557251.308
11_A15_L1.431461.202
44_K47_E1.424371.196
16_A32_L1.412891.187
26_E36_R1.395851.172
9_N34_I1.392191.169
20_N23_A1.369791.150
29_A39_V1.361141.143
23_A27_E1.350181.134
40_Y44_K1.346721.131
12_K16_A1.337021.123
26_E30_E1.334841.121
44_K48_E1.288481.082
14_Y18_L1.254841.054
25_A36_R1.241281.042
16_A23_A1.221071.025
34_I39_V1.205391.012
38_T41_R1.165360.979
20_N31_E1.159450.974
9_N12_K1.139480.957
17_L23_A1.12040.941
37_S41_R1.091180.916
17_L52_V1.075650.903
27_E30_E1.063530.893
38_T42_A1.055650.887
47_E52_V1.051670.883
12_K15_L1.046980.879
35_S38_T1.04250.875
13_V42_A1.039530.873
13_V28_I1.02970.865
16_A19_K1.022560.859
39_V43_L1.010860.849
16_A20_N0.985310.827
25_A43_L0.964650.810
44_K54_R0.955940.803
28_I39_V0.947150.795
12_K32_L0.931520.782
41_R44_K0.928520.780
19_K23_A0.90540.760
13_V39_V0.885840.744
35_S41_R0.868790.730
41_R45_S0.840850.706
45_S48_E0.816320.686
42_A45_S0.812660.682
14_Y51_L0.804780.676
46_L51_L0.787420.661
34_I38_T0.782080.657
25_A39_V0.769410.646
32_L39_V0.761440.639
11_A14_Y0.728810.612
43_L52_V0.712420.598
15_L18_L0.707350.594
28_I43_L0.689730.579
26_E29_A0.682670.573
25_A37_S0.682180.573
43_L47_E0.675690.567
9_N38_T0.672170.564
26_E40_Y0.653870.549
12_K33_G0.647310.544
14_Y17_L0.640170.538
18_L42_A0.635170.533
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
3qphA198.8-0.029
1qgpA198.40.106
3tgnA0.985398.30.129
1hsjA198.30.137
4em2A198.30.139
3oopA198.30.139
3s2wA198.30.14
3hsrA198.20.142
4hblA198.20.147
2fxaA198.20.149

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