GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
B-block_TFIIIC - B-block binding subunit of TFIIIC
Pfam: PF04182 (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: 75
Sequences: 32008
Seq/Len: 426.77
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
10_R27_L2.73262.369
49_V68_H2.503752.170
51_Q68_H2.289271.984
43_E50_K2.263181.962
18_G68_H2.208181.914
50_K65_N2.036641.765
20_T23_D2.01731.749
25_S32_P1.960251.699
4_Q41_K1.940841.682
4_Q38_R1.762891.528
53_V66_L1.659751.439
33_R37_Y1.574451.365
4_Q45_K1.570191.361
7_L38_R1.521481.319
53_V64_T1.510981.310
18_G66_L1.498541.299
33_R36_F1.485921.288
18_G51_Q1.473081.277
49_V70_K1.446971.254
19_I23_D1.43681.246
19_I27_L1.41371.225
20_T64_T1.403161.216
53_V60_K1.381351.197
41_K45_K1.312681.138
36_F40_K1.306741.133
10_R19_I1.303421.130
52_S65_N1.285331.114
12_A69_L1.284111.113
23_D26_K1.258631.091
22_S32_P1.258231.091
25_S35_I1.237581.073
22_S26_K1.225431.062
39_L67_L1.205421.045
40_K43_E1.186891.029
11_I48_I1.180381.023
10_R28_L1.178721.022
40_K44_K1.164511.009
6_C10_R1.160721.006
31_D34_S1.155791.002
32_P36_F1.139570.988
16_Y27_L1.138530.987
8_L47_L1.124870.975
34_S38_R1.117480.969
21_Q36_F1.092710.947
30_I35_I1.08430.940
23_D27_L1.079810.936
16_Y19_I1.07580.933
7_L35_I1.03960.901
51_Q66_L1.009540.875
21_Q67_L0.998420.865
34_S37_Y0.988880.857
38_R41_K0.974810.845
41_K44_K0.933840.810
8_L12_A0.928220.805
7_L24_L0.927750.804
43_E48_I0.908750.788
21_Q35_I0.886050.768
37_Y41_K0.885160.767
31_D37_Y0.877610.761
53_V61_G0.860930.746
10_R15_R0.846010.733
6_C9_E0.843980.732
9_E12_A0.838680.727
21_Q32_P0.829840.719
35_I39_L0.820730.711
37_Y40_K0.79910.693
40_K50_K0.792770.687
21_Q39_L0.785560.681
11_I19_I0.781780.678
61_G64_T0.780820.677
30_I34_S0.779190.675
9_E15_R0.759110.658
6_C28_L0.757180.656
52_S62_T0.750870.651
5_Y9_E0.74110.642
39_L48_I0.73290.635
7_L30_I0.72250.626
21_Q65_N0.710870.616
28_L35_I0.709740.615
60_K63_R0.706620.613
12_A15_R0.699020.606
10_R24_L0.689280.598
10_R16_Y0.688030.596
60_K64_T0.64520.559
46_G49_V0.640040.555
50_K67_L0.635440.551
4_Q34_S0.627130.544
15_R19_I0.61890.537
6_C38_R0.613880.532
24_L39_L0.607230.526
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
1hsjA0.933398.80.02
1p4xA0.933398.70.047
3nqoA0.933398.70.047
4em2A0.906798.70.048
1p4xA0.933398.70.05
3hsrA0.906798.70.052
3jw4A0.933398.70.054
4hblA0.906798.70.054
3k0lA0.906798.70.056
3echA0.906798.70.058

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