GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TFIIB - Transcription factor TFIIB repeat
Pfam: PF00382 (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: CL0065
Length: 71
Sequences: 1980
Seq/Len: 27.89
HH_delta: -0.012 (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_C44_I0.878883.565
17_R51_N0.654442.655
5_C15_R0.611742.482
56_T59_E0.499562.027
11_P53_V0.457711.857
55_R59_E0.381451.547
58_K62_E0.348841.415
4_I63_A0.346951.408
21_I43_C0.337551.369
33_G41_A0.334751.358
14_V47_A0.33331.352
47_A51_N0.315161.279
17_R50_L0.312931.270
22_Y43_C0.308991.254
48_C54_P0.30241.227
20_E24_K0.302091.226
3_R6_S0.295481.199
17_R20_E0.295191.198
8_L40_A0.288291.170
41_A60_I0.287111.165
5_C12_E0.282491.146
4_I44_I0.27841.129
15_R62_E0.276291.121
24_K28_R0.273261.109
14_V53_V0.269471.093
34_R39_I0.268231.088
3_R36_P0.260141.055
25_A30_L0.25781.046
24_K49_R0.257431.044
38_S42_A0.2571.043
19_K23_K0.254511.033
8_L63_A0.25361.029
2_P19_K0.253081.027
7_K12_E0.25011.015
32_K35_S0.246641.001
44_I64_A0.24641.000
10_L44_I0.243360.987
22_Y31_L0.237240.962
2_P58_K0.235350.955
31_L46_L0.234170.950
20_E23_K0.231810.940
35_S38_S0.230530.935
32_K36_P0.227020.921
21_I26_Q0.22560.915
40_A64_A0.222120.901
60_I63_A0.219270.890
10_L48_C0.219180.889
2_P15_R0.217860.884
55_R58_K0.217860.884
18_A47_A0.213470.866
52_G55_R0.210850.855
26_Q30_L0.208560.846
13_D19_K0.204160.828
47_A54_P0.203760.827
15_R18_A0.201940.819
12_E15_R0.200590.814
18_A44_I0.197250.800
45_Y49_R0.197240.800
22_Y49_R0.196590.798
4_I64_A0.195160.792
12_E16_E0.194450.789
57_L60_I0.193880.787
3_R38_S0.192360.780
12_E46_L0.191590.777
46_L49_R0.191450.777
41_A64_A0.18960.769
25_A29_G0.187570.761
57_L61_A0.187170.759
17_R24_K0.186550.757
21_I35_S0.186390.756
9_G40_A0.1860.755
45_Y50_L0.185110.751
6_S62_E0.184840.750
6_S9_G0.182180.739
43_C47_A0.181850.738
10_L55_R0.181790.737
54_P57_L0.179990.730
16_E19_K0.176730.717
45_Y57_L0.176090.714
34_R57_L0.175980.714
35_S39_I0.175010.710
42_A46_L0.174680.709
26_Q35_S0.174360.707
36_P46_L0.171890.697
49_R57_L0.170840.693
13_D16_E0.170650.692
17_R21_I0.16970.688
2_P5_C0.169490.688
14_V54_P0.167590.680
21_I50_L0.166570.676
10_L53_V0.165820.673
3_R65_G0.165750.672
30_L33_G0.160920.653
59_E63_A0.160780.652
29_G32_K0.160290.650
5_C8_L0.159130.646
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
4bbrM199.5-0.012
3k7aM199.50.016
1aisB199.50.017
1c9bA199.50.037
4bbrM199.40.084
1aisB199.30.125
3k7aM199.30.137
1c9bA199.10.191
1zp2A199.10.206
1jkwA1990.239

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