GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Toprim_C_rpt - Topoisomerase C-terminal repeat
Pfam: PF13368 (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: 61
Sequences: 1125
Seq/Len: 18.44
HH_delta: 0.852 (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
31_E40_E1.444174.183
43_E47_E0.755662.189
6_K21_G0.730332.116
8_I38_L0.729322.113
32_D35_E0.659081.909
40_E43_E0.577791.674
19_K24_N0.576481.670
10_K24_N0.57051.653
37_T40_E0.542931.573
10_K19_K0.523891.518
25_A48_K0.521331.510
42_V46_A0.517891.500
38_L42_V0.49441.432
25_A44_L0.492531.427
2_P42_V0.462291.339
23_K48_K0.44611.292
31_E35_E0.427821.239
39_E43_E0.420981.219
23_K49_K0.413881.199
8_I45_L0.388721.126
20_H49_K0.387771.123
28_P31_E0.381061.104
6_K22_K0.380941.103
20_H45_L0.369541.070
12_G17_Y0.36641.061
7_P21_G0.348691.010
14_F17_Y0.328160.951
19_K22_K0.326440.946
8_I18_V0.319640.926
8_I42_V0.312820.906
14_F29_K0.306860.889
11_N50_K0.286680.830
18_V25_A0.284010.823
3_E42_V0.283060.820
11_N24_N0.282210.817
10_K26_S0.27520.797
26_S48_K0.272680.790
6_K19_K0.267590.775
5_G41_A0.255070.739
8_I41_A0.254130.736
47_E50_K0.250410.725
28_P43_E0.249640.723
2_P7_P0.248680.720
46_A49_K0.24780.718
2_P33_P0.243460.705
27_L31_E0.242830.703
9_V18_V0.242740.703
13_R16_P0.23940.693
10_K17_Y0.238240.690
25_A45_L0.237110.687
5_G16_P0.225690.654
39_E42_V0.224080.649
43_E46_A0.223870.648
28_P32_D0.212480.615
24_N34_E0.211990.614
8_I39_E0.209090.606
32_D40_E0.207520.601
30_D36_I0.205990.597
10_K14_F0.204270.592
29_K33_P0.20320.589
36_I40_E0.200260.580
35_E39_E0.197370.572
16_P33_P0.196510.569
13_R29_K0.195060.565
2_P5_G0.19430.563
14_F28_P0.193690.561
16_P36_I0.189860.550
14_F30_D0.189780.550
5_G11_N0.18830.545
18_V45_L0.186660.541
9_V36_I0.185530.537
9_V16_P0.185040.536
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
3ml1A0.983631.50.852
2napA0.967228.70.855
2vpzA0.983623.90.859
3i9v30.983620.40.863
2e7zA0.983620.40.864
1g8kA0.983619.40.865
3bboD0.950816.30.87
1gyhA0.37714.50.872
4ghnA0.770514.20.873
1ti6A0.983611.50.878
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