GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GntR - Bacterial regulatory proteins gntR family
Pfam: PF00392 (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: 64
Sequences: 28587
Seq/Len: 446.67
HH_delta: -0.126 (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
6_Y47_R3.167092.766
12_A17_R2.951212.577
19_P22_D2.726152.381
27_E38_R2.608972.278
8_Q12_A2.437512.129
10_R51_E2.290122.000
49_E56_R2.286671.997
6_Y51_E2.267061.980
26_S29_E2.167141.892
6_Y10_R2.063861.802
27_E42_R1.774621.550
5_I36_V1.706981.491
57_R60_R1.621681.416
42_R46_R1.562451.364
28_R32_E1.543241.348
10_R14_L1.511051.320
46_R49_E1.498271.308
29_E33_R1.48171.294
11_Q15_S1.474631.288
12_A16_G1.457131.272
46_R50_A1.431531.250
12_A33_R1.379791.205
47_R50_A1.366171.193
37_S40_T1.362551.190
5_I34_Y1.35551.184
31_A38_R1.348521.178
8_Q34_Y1.339131.169
10_R53_L1.317231.150
4_Q8_Q1.307651.142
47_R51_E1.24791.090
8_Q11_Q1.247041.089
43_E47_R1.24221.085
30_L45_L1.231671.076
40_T43_E1.191351.040
27_E45_L1.126410.984
43_E46_R1.116440.975
30_L41_V1.103260.963
46_R56_R1.101290.962
39_T42_R1.062860.928
49_E54_I1.054810.921
12_A18_L1.028090.898
18_L22_D1.022170.893
23_R61_G1.009030.881
29_E32_E1.002270.875
39_T43_E0.971040.848
36_V41_V0.96550.843
12_A15_S0.932470.814
31_A41_V0.91910.803
45_L54_I0.910060.795
28_R31_A0.870870.760
28_R38_R0.863680.754
14_L53_L0.843580.737
42_R49_E0.825460.721
23_R57_R0.824140.720
27_E56_R0.814360.711
36_V40_T0.774080.676
21_G55_E0.770770.673
38_R42_R0.759850.664
23_R26_S0.74470.650
27_E39_T0.729570.637
7_D11_Q0.719220.628
16_G33_R0.689460.602
57_R61_G0.675310.590
42_R56_R0.649740.567
40_T44_A0.642820.561
5_I44_A0.640770.560
4_Q7_D0.623240.544
23_R60_R0.623230.544
9_L36_V0.621430.543
44_A48_L0.60840.531
42_R45_L0.603350.527
41_V45_L0.592030.517
8_Q17_R0.586050.512
48_L54_I0.580070.507
34_Y41_V0.567090.495
17_R33_R0.563490.492
26_S59_G0.558790.488
7_D10_R0.558170.487
24_L33_R0.552020.482
16_G20_P0.550230.480
8_Q33_R0.548550.479
16_G24_L0.542390.474
44_A47_R0.534740.467
13_I21_G0.526470.460
11_Q14_L0.510460.446
56_R60_R0.502530.439
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
4hamA198.8-0.126
1hw1A198.8-0.117
3eetA198.8-0.105
3edpA198.7-0.103
3bwgA198.7-0.089
2wv0A198.7-0.086
2ra5A198.7-0.085
2di3A198.7-0.082
3ic7A198.7-0.081
4h0eA198.7-0.081

Page generated in 0.0406 seconds.