GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TFIID_20kDa - Transcription initiation factor TFIID subunit A
Pfam: PF03847 (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: CL0012
Length: 68
Sequences: 1689
Seq/Len: 24.84
HH_delta: 0.106 (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
50_S57_D0.527592.426
42_C53_L0.482232.217
41_A53_L0.459442.113
32_D36_D0.424371.951
6_Q18_L0.405281.864
45_A53_L0.399481.837
37_V61_H0.327131.504
47_H60_L0.303351.395
7_E10_K0.302461.391
48_R60_L0.29641.363
41_A61_H0.290611.336
40_F61_H0.286331.317
44_L47_H0.277641.277
18_L22_V0.276911.273
27_L31_D0.275381.266
36_D40_F0.271881.250
35_D38_V0.263231.210
60_L63_E0.256461.179
56_K59_Q0.249631.148
56_K60_L0.2471.136
46_K49_K0.24521.127
25_L28_E0.242821.117
8_L11_Q0.240371.105
41_A58_V0.239571.102
24_E27_L0.239391.101
21_D24_E0.232411.069
55_V59_Q0.229731.056
6_Q11_Q0.227131.044
37_V40_F0.224881.034
50_S53_L0.224121.031
21_D55_V0.21540.990
50_S61_H0.213330.981
34_V38_V0.212530.977
48_R57_D0.21060.968
35_D42_C0.206710.950
29_L32_D0.20360.936
44_L60_L0.197150.907
28_E32_D0.196970.906
34_V62_L0.194890.896
39_S43_R0.194390.894
13_D16_E0.193210.888
54_E57_D0.193130.888
14_P46_K0.192610.886
23_E30_A0.189660.872
31_D35_D0.189390.871
19_D22_V0.184830.850
24_E32_D0.181360.834
57_D60_L0.180870.832
28_E35_D0.180340.829
47_H63_E0.179980.828
32_D40_F0.179890.827
14_P24_E0.179350.825
37_V58_V0.179160.824
49_K60_L0.177920.818
40_F44_L0.174890.804
25_L29_L0.174330.802
24_E33_F0.173920.800
53_L57_D0.173690.799
20_P23_E0.173510.798
6_Q15_N0.172610.794
33_F36_D0.172260.792
9_V23_E0.172220.792
28_E56_K0.171730.790
20_P41_A0.171650.789
27_L35_D0.170780.785
21_D38_V0.168060.773
18_L36_D0.168020.773
21_D30_A0.167040.768
24_E48_R0.166260.764
47_H53_L0.165960.763
28_E34_V0.164750.758
5_L24_E0.163910.754
44_L61_H0.163840.753
39_S46_K0.163360.751
16_E39_S0.162490.747
17_K38_V0.160330.737
26_L29_L0.160280.737
31_D54_E0.160040.736
42_C45_A0.15990.735
20_P54_E0.159790.735
29_L35_D0.159620.734
29_L36_D0.158390.728
45_A54_E0.15680.721
30_A34_V0.155930.717
56_K63_E0.155290.714
34_V37_V0.155210.714
12_I15_N0.154820.712
16_E26_L0.154230.709
59_Q63_E0.153790.707
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
1h3oB199.30.106
1b67A0.955999.20.163
3b0cW199.20.17
1f1eA0.985399.10.195
1ku5A0.926599.10.195
3b0cT0.985399.10.195
1n1jA0.985399.10.208
1jfiB0.985399.10.21
1id3B0.9853990.22
1f1eA1990.232

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