GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_1 - Bacterial regulatory helix-turn-helix protein lysR family
Pfam: PF00126 (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: 60
Sequences: 51560
Seq/Len: 859.33
HH_delta: -0.048 (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
9_A22_E3.647712.695
13_T22_E3.496852.584
6_Y33_Q2.879982.128
15_S18_A2.588621.913
9_A13_T2.459351.817
3_Q40_E2.422761.790
3_Q36_Q2.398391.772
47_E54_R2.211541.634
8_L12_E2.2041.628
18_A21_E2.179661.610
3_Q33_Q2.165871.600
26_S29_A2.107421.557
49_S54_R2.012421.487
25_I29_A2.008151.484
11_A55_L1.994291.473
7_F11_A1.889891.396
9_A12_E1.760961.301
31_S35_K1.693351.251
38_E48_R1.602921.184
17_S27_Q1.543791.141
16_I34_I1.54071.138
13_T18_A1.535461.134
9_A23_L1.523661.126
28_S31_S1.495591.105
11_A60_E1.48711.099
32_R36_Q1.441721.065
35_K39_E1.42791.055
44_P47_E1.406481.039
6_Y30_V1.401891.036
20_A27_Q1.341990.992
5_R9_A1.329560.982
57_E60_E1.316120.972
32_R35_K1.308560.967
33_Q36_Q1.307660.966
14_G54_R1.292980.955
20_A30_V1.254170.927
7_F45_L1.252030.925
35_K38_E1.242820.918
17_S21_E1.238510.915
5_R8_L1.229220.908
12_E22_E1.209430.894
18_A22_E1.206620.891
6_Y25_I1.188410.878
9_A19_A1.177380.870
55_L59_G1.170220.865
56_T59_G1.167270.862
3_Q6_Y1.148960.849
16_I53_L1.102860.815
44_P58_A1.093910.808
29_A33_Q1.081080.799
28_S32_R1.027840.759
19_A30_V1.021340.755
36_Q39_E1.018750.753
7_F37_L1.016440.751
6_Y23_L1.014620.750
26_S32_R1.003470.741
11_A14_G0.982450.726
13_T19_A0.964410.713
36_Q40_E0.963310.712
14_G60_E0.960790.710
29_A32_R0.944970.698
10_V19_A0.935940.692
47_E56_T0.903390.667
21_E24_G0.885310.654
38_E46_F0.876030.647
34_I38_E0.873290.645
7_F46_F0.861490.637
34_I53_L0.835740.617
25_I30_V0.81370.601
27_Q31_S0.806420.596
23_L30_V0.79930.591
54_R60_E0.789990.584
10_V46_F0.775730.573
46_F53_L0.75360.557
49_S52_G0.73640.544
55_L60_E0.732110.541
7_F55_L0.730970.540
31_S53_L0.706870.522
3_Q32_R0.706580.522
10_V34_I0.688920.509
16_I30_V0.676010.499
35_K48_R0.67320.497
4_L8_L0.670810.496
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
2h9bA198.8-0.048
2h98A198.8-0.048
2esnA198.8-0.046
1ixcA198.8-0.046
1uthA198.8-0.045
3szpA198.7-0.041
3fxqA198.7-0.04
3hhgA198.7-0.04
1al3A198.7-0.027
3fzvA198.7-0.023

Page generated in 0.0311 seconds.