GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TfoX_C - TfoX C-terminal domain
Pfam: PF04994 (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: CL0198
Length: 81
Sequences: 2390
Seq/Len: 29.51
HH_delta: 0.156 (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_K16_E1.241313.136
20_A25_H1.11412.814
22_V41_R0.853612.156
39_Y52_N0.827242.090
6_K20_A0.823282.080
53_L57_L0.8032.029
25_H29_D0.76041.921
9_P57_L0.755771.909
8_L27_V0.743571.878
24_I33_L0.721381.822
14_K17_R0.713651.803
17_R21_K0.684261.729
35_A52_N0.669591.692
33_L37_E0.653061.650
24_I30_L0.651231.645
28_E32_E0.649651.641
55_Y59_G0.63371.601
26_T29_D0.611661.545
35_A55_Y0.555241.403
3_N7_D0.540731.366
56_A61_I0.519591.313
16_E20_A0.503151.271
31_R58_E0.496531.254
51_L55_Y0.471021.190
22_V42_L0.46861.184
2_S27_V0.465441.176
4_R7_D0.441561.115
19_L54_L0.439441.110
35_A56_A0.426141.077
37_E41_R0.424681.073
52_N56_A0.416121.051
37_E40_L0.405171.024
18_M21_K0.400121.011
35_A39_Y0.396771.002
31_R59_G0.393430.994
43_K51_L0.383490.969
5_L24_I0.380830.962
17_R20_A0.366840.927
2_S28_E0.361250.913
34_G59_G0.328630.830
8_L57_L0.324270.819
29_D32_E0.319530.807
34_G37_E0.309460.782
33_L38_A0.308080.778
4_R25_H0.305860.773
13_P45_S0.303780.767
28_E31_R0.302150.763
7_D14_K0.286720.724
38_A42_L0.278010.702
12_G66_W0.277910.702
30_L58_E0.274340.693
11_I19_L0.272930.689
41_R45_S0.272520.688
62_Q65_H0.267240.675
9_P45_S0.266780.674
34_G39_Y0.266340.673
9_P27_V0.265660.671
56_A63_G0.264630.669
36_V40_L0.264180.667
62_Q66_W0.262010.662
15_S42_L0.260590.658
18_M41_R0.257260.650
30_L38_A0.256220.647
2_S26_T0.254740.644
39_Y56_A0.253110.639
58_E62_Q0.252630.638
51_L58_E0.249630.631
8_L31_R0.248880.629
27_V31_R0.247370.625
56_A59_G0.246870.624
13_P64_I0.246160.622
33_L41_R0.240660.608
45_S53_L0.238770.603
5_L16_E0.236490.597
18_M42_L0.236060.596
32_E63_G0.23560.595
9_P64_I0.23220.587
11_I54_L0.230740.583
8_L34_G0.229710.580
22_V37_E0.223040.563
27_V58_E0.219650.555
54_L57_L0.219220.554
36_V52_N0.217650.550
14_K18_M0.217170.549
27_V45_S0.217020.548
2_S63_G0.216550.547
9_P53_L0.211130.533
5_L26_T0.210110.531
24_I31_R0.208670.527
14_K37_E0.205640.519
51_L62_Q0.202940.513
5_L39_Y0.202740.512
10_N64_I0.201520.509
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
3bqsA199.40.156
3mabA199.40.167
3gqcA0.925999.20.262
4irkB0.913699.20.264
4dezA0.925999.20.269
3osnA0.925999.20.273
4f4yA0.901299.20.273
3bq0A0.913699.20.281
1jx4A0.913699.20.281
4ecqA0.913699.10.298

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