GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Arg_repressor_C - Arginine repressor C-terminal domain
Pfam: PF02863 (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. )
Length: 70
Sequences: 858
Seq/Len: 12.26
HH_delta: -0.022 (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
10_E55_R0.73743.248
13_D57_E0.64962.861
56_S59_D0.459712.025
32_I67_L0.410691.809
54_C60_A0.38731.706
25_A48_D0.356411.570
61_E65_E0.348931.537
54_C63_L0.346831.527
59_D62_E0.334651.474
23_G47_D0.318541.403
22_P47_D0.318121.401
33_D46_G0.317311.397
12_S41_F0.308651.359
6_V18_I0.308241.357
15_M53_I0.299231.318
39_E66_K0.298271.314
20_T46_G0.297681.311
22_P48_D0.289811.276
33_D43_T0.285761.258
5_S27_A0.285041.255
24_N27_A0.280471.235
45_A50_I0.267551.178
60_A64_E0.26521.168
16_V54_C0.264671.166
29_A45_A0.263751.162
17_V46_G0.26291.158
33_D42_G0.248041.092
66_K69_E0.246111.084
33_D48_D0.237311.045
13_D56_S0.23321.027
57_E60_A0.227121.000
22_P30_A0.226940.999
11_R60_A0.225420.993
30_A48_D0.225250.992
16_V64_E0.224380.988
20_T25_A0.221540.976
64_E68_K0.220480.971
5_S24_N0.217010.956
38_P62_E0.216780.955
2_L67_L0.214990.947
25_A33_D0.213630.941
32_I50_I0.213580.941
12_S54_C0.211160.930
62_E66_K0.208920.920
11_R61_E0.206840.911
46_G49_T0.206270.908
37_L40_I0.205430.905
57_E62_E0.203870.898
2_L63_L0.20340.896
11_R64_E0.202180.890
16_V60_A0.201710.888
58_E61_E0.199650.879
65_E68_K0.199270.878
12_S56_S0.198490.874
43_T46_G0.195380.860
11_R16_V0.194240.855
3_K36_N0.193980.854
9_V18_I0.192750.849
32_I40_I0.191990.846
20_T33_D0.19170.844
29_A33_D0.190850.841
17_V20_T0.189470.834
33_D49_T0.189160.833
58_E62_E0.188240.829
35_L70_L0.187540.826
20_T29_A0.18470.813
41_F46_G0.1830.806
62_E65_E0.182990.806
23_G41_F0.182450.804
40_I52_V0.180140.793
9_V64_E0.179520.791
18_I70_L0.177390.781
32_I44_I0.175440.773
29_A50_I0.175210.772
12_S60_A0.175030.771
26_Q50_I0.174630.769
43_T50_I0.173050.762
20_T28_V0.171580.756
17_V42_G0.169540.747
41_F55_R0.169520.747
2_L10_E0.169420.746
26_Q44_I0.167860.739
56_S60_A0.167630.738
20_T24_N0.165610.729
25_A46_G0.165580.729
50_I63_L0.163970.722
4_E30_A0.163780.721
26_Q30_A0.162360.715
27_A30_A0.162340.715
18_I52_V0.161190.710
31_A68_K0.160840.708
17_V33_D0.160430.707
58_E68_K0.159740.703
11_R34_Q0.159740.703
26_Q48_D0.159590.703
39_E62_E0.158930.700
23_G34_Q0.155650.685
17_V49_T0.15560.685
6_V27_A0.155430.685
17_V25_A0.152460.671
8_S70_L0.15210.670
32_I51_L0.151630.668
34_Q52_V0.1510.665
16_V59_D0.15090.665
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
3lapA199.9-0.022
1b4aA199.9-0.019
2p5mA199.8-0.016
2zfzA199.8-0.016
1b4bA199.8-0.006
3v4gA199.80.002
1xxaA199.80.016
1c4oA0.842965.60.836
2d7dA0.842965.30.836
3crvA0.857151.60.849

Page generated in 0.0457 seconds.