GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GerE - Bacterial regulatory proteins luxR family
Pfam: PF00196 (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: 58
Sequences: 37882
Seq/Len: 653.14
HH_delta: -0.042 (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
33_K36_K3.229152.166
19_M27_E3.21382.156
8_E45_K3.192972.142
22_K32_E2.884671.935
7_R38_H2.73581.835
14_L27_E2.437241.635
21_N36_K2.421891.625
21_N39_R2.303811.546
20_S23_E2.27091.523
14_L19_M2.173721.458
33_K40_R2.165981.453
32_E36_K2.129481.429
5_T8_E2.067721.387
33_K37_S2.057481.380
30_I38_H2.040881.369
19_M23_E2.037631.367
15_L39_R2.000311.342
37_S41_R1.982731.330
7_R10_E1.917521.286
34_T38_H1.895521.272
30_I35_V1.85211.242
37_S40_R1.824571.224
8_E38_H1.814761.217
21_N32_E1.731521.162
34_T37_S1.62661.091
14_L24_I1.622431.088
8_E41_R1.514631.016
31_S34_T1.497631.005
15_L42_I1.462210.981
22_K26_E1.419210.952
39_R43_M1.346370.903
9_L13_R1.333150.894
40_R44_K1.256040.843
7_R30_I1.249780.838
21_N35_V1.245520.836
38_H41_R1.183820.794
10_E28_L1.181850.793
11_V42_I1.175230.788
8_E42_I1.159470.778
24_I35_V1.154140.774
10_E13_R1.139370.764
30_I34_T1.089870.731
26_E29_G1.084020.727
4_L42_I1.050710.705
25_A32_E1.047060.702
6_E10_E1.041440.699
13_R17_Q0.993560.667
36_K40_R0.993220.666
7_R28_L0.987780.663
25_A35_V0.983280.660
24_I28_L0.966430.648
23_E27_E0.958990.643
11_V38_H0.956040.641
23_E26_E0.940240.631
14_L17_Q0.917130.615
41_R44_K0.910470.611
42_I46_L0.908230.609
15_L43_M0.902720.606
4_L46_L0.84290.565
36_K39_R0.807060.541
17_Q27_E0.791450.531
28_L38_H0.775460.520
22_K36_K0.764910.513
11_V39_R0.756820.508
12_L15_L0.747970.502
5_T45_K0.743670.499
5_T38_H0.736610.494
14_L28_L0.716810.481
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
3sztA198.3-0.042
3cloA198.3-0.024
3ulqB198.3-0.024
2q0oA198.3-0.023
3qp6A198.3-0.016
1l3lA198.3-0.013
2rnjA198.2-0.001
3c57A198.20.002
1p4wA198.20.002
1je8A198.20.005

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