GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_Tnp_Tc5 - Tc5 transposase DNA-binding domain
Pfam: PF03221 (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: 66
Sequences: 1444
Seq/Len: 21.88
HH_delta: 0.085 (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
5_E56_F0.510722.060
24_R57_K0.501572.023
11_W30_K0.469651.895
28_R32_K0.457031.844
32_K48_A0.451451.821
12_I27_I0.443031.787
30_K33_E0.399731.613
6_K10_E0.377831.524
9_V13_K0.374931.513
5_E8_L0.364571.471
4_L30_K0.355071.432
53_L57_K0.343511.386
40_S45_E0.340531.374
9_V12_I0.335721.354
5_E59_R0.320441.293
14_R18_K0.318241.284
7_A10_E0.309681.249
50_K54_D0.298551.204
12_I62_I0.296641.197
35_A41_P0.286691.157
29_E33_E0.280311.131
15_M20_F0.270461.091
40_S43_P0.265631.072
35_A48_A0.261741.056
24_R53_L0.258651.043
28_R53_L0.256251.034
10_E13_K0.25381.024
12_I16_R0.253541.023
14_R17_R0.253021.021
9_V60_H0.250181.009
24_R28_R0.248741.003
24_R51_G0.247971.000
21_P49_S0.245580.991
23_T34_I0.245540.991
51_G55_R0.240920.972
50_K55_R0.237730.959
8_L30_K0.231260.933
43_P48_A0.230110.928
55_R61_G0.22770.919
18_K32_K0.221930.895
57_K63_K0.217270.876
5_E12_I0.215020.867
41_P44_P0.212920.859
28_R60_H0.211020.851
28_R48_A0.210070.847
4_L35_A0.209690.846
31_A52_W0.207880.839
55_R58_K0.206970.835
17_R41_P0.202760.818
21_P26_M0.202010.815
15_M28_R0.200680.810
4_L48_A0.199850.806
44_P47_K0.198940.803
3_E7_A0.19770.798
51_G54_D0.197190.795
11_W22_V0.196210.792
41_P45_E0.195490.789
50_K53_L0.195260.788
28_R50_K0.194890.786
26_M34_I0.192950.778
7_A33_E0.192540.777
17_R58_K0.192510.777
35_A46_F0.192370.776
27_I53_L0.191360.772
26_M30_K0.191010.771
14_R63_K0.188320.760
11_W51_G0.186910.754
26_M29_E0.186710.753
44_P58_K0.18580.750
24_R54_D0.184850.746
56_F60_H0.182240.735
16_R30_K0.181710.733
29_E42_G0.180620.729
32_K61_G0.179990.726
31_A55_R0.178930.722
34_I50_K0.177750.717
4_L19_G0.177660.717
16_R19_G0.176580.712
33_E44_P0.174910.706
51_G59_R0.17470.705
46_F49_S0.174530.704
56_F62_I0.174050.702
23_T26_M0.173490.700
30_K34_I0.17330.699
47_K54_D0.172930.698
21_P24_R0.171130.690
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
1iufA0.939499.30.085
1hlvA0.878899.30.104
1fexA0.80332.40.809
3u1uA0.560625.70.817
1bgxT122.20.823
2kfnA121.90.823
2bzeA0.590921.50.823
4dfkA121.20.824
3pv8A0.954518.80.829
1wymA0.939415.70.834

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