GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Dimer_Tnp_hAT - hAT family C-terminal dimerisation region
Pfam: PF05699 (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: 86
Sequences: 1246
Seq/Len: 14.49
HH_delta: 0.02 (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
61_G66_R0.532592.531
62_K67_N0.449862.137
30_S37_A0.438362.083
64_L76_V0.426392.026
54_E58_S0.409861.947
26_W40_A0.404831.924
25_W29_N0.348671.657
72_S75_N0.337741.605
62_K65_T0.332021.578
77_E83_K0.307151.459
41_R45_S0.305481.451
26_W36_L0.294061.397
37_A40_A0.288791.372
75_N78_A0.270681.286
57_F60_M0.268861.277
54_E57_F0.262991.250
58_S63_I0.25261.200
64_L69_N0.251011.193
42_K45_S0.248791.182
55_R68_R0.247061.174
60_M64_L0.235571.119
63_I79_L0.234341.113
27_K30_S0.229231.089
21_D24_E0.22811.084
22_P48_A0.224231.065
28_Q32_R0.223121.060
29_N33_F0.221871.054
64_L67_N0.220651.048
78_A81_F0.220381.047
71_L76_V0.218351.037
39_L42_K0.216231.027
50_S55_R0.215751.025
24_E28_Q0.215711.025
31_S38_K0.214161.018
80_L84_S0.2121.007
23_L41_R0.21121.003
65_T69_N0.206160.980
57_F68_R0.204170.970
42_K81_F0.203310.966
29_N32_R0.202820.964
60_M80_L0.201220.956
68_R71_L0.200370.952
21_D38_K0.200230.951
55_R58_S0.197430.938
58_S68_R0.197390.938
58_S61_G0.197130.937
27_K41_R0.19140.909
38_K41_R0.190570.905
57_F61_G0.188820.897
63_I80_L0.186850.888
52_S56_S0.185790.883
46_I69_N0.17910.851
36_L40_A0.178710.849
28_Q39_L0.178590.849
40_A44_L0.177970.846
50_S53_S0.177830.845
25_W40_A0.176310.838
54_E68_R0.173890.826
49_S80_L0.170640.811
62_K68_R0.170590.811
77_E81_F0.170350.809
49_S53_S0.170070.808
74_E83_K0.166960.793
34_P39_L0.166040.789
35_N59_A0.16540.786
27_K37_A0.164790.783
42_K78_A0.163640.778
47_P73_P0.162830.774
76_V84_S0.16280.774
39_L43_Y0.161890.769
27_K32_R0.160480.763
75_N82_L0.159390.757
28_Q31_S0.156930.746
20_M27_K0.156760.745
24_E35_N0.155690.740
51_A54_E0.155150.737
25_W81_F0.154940.736
27_K31_S0.154930.736
42_K47_P0.154530.734
71_L79_L0.154380.734
59_A62_K0.154020.732
24_E27_K0.151890.722
48_A80_L0.15080.717
29_N38_K0.150740.716
43_Y52_S0.150590.716
28_Q36_L0.148320.705
34_P74_E0.147270.700
50_S54_E0.147110.699
26_W44_L0.147020.699
53_S80_L0.146580.696
56_S80_L0.146210.695
59_A67_N0.146190.695
50_S60_M0.145930.693
74_E79_L0.145530.691
25_W64_L0.144650.687
74_E78_A0.143390.681
49_S79_L0.143120.680
47_P52_S0.142230.676
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
2bw3A0.953599.70.02
2fokA0.8605180.866
4inmV0.29079.10.882
1c4qA0.67448.50.884
2gagD0.53497.70.885
1r4pB0.69776.80.889
1ljrA16.10.891
2dr1A0.755860.891
3ombA0.34882.50.908
1ygpA0.98842.40.909

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