GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TetR_C_8 - Transcriptional regulator C-terminal region
Pfam: PF14278 (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: 77
Sequences: 1318
Seq/Len: 17.12
HH_delta: 0.45 (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
63_F67_G0.803864.617
66_S70_G0.45742.627
10_Y18_Y0.386742.221
62_S74_W0.316521.818
66_S74_W0.299351.719
12_Y15_R0.278451.599
26_G30_F0.269041.545
11_I18_Y0.255521.467
67_G70_G0.254771.463
59_Y74_W0.245751.411
17_F21_L0.242011.390
65_V69_I0.239981.378
19_K23_S0.237281.363
35_K39_K0.234781.348
36_E39_K0.221251.271
31_Q41_W0.217861.251
67_G74_W0.213361.225
33_R37_L0.209691.204
12_Y72_I0.203161.167
13_E77_E0.203031.166
73_Q77_E0.198451.140
11_I72_I0.192721.107
34_L69_I0.19261.106
31_Q73_Q0.192071.103
42_I68_I0.188491.082
5_T9_E0.188071.080
52_D56_P0.186911.073
10_Y14_N0.183111.052
59_Y65_V0.18151.042
28_P64_I0.181341.041
10_Y67_G0.17831.024
60_L68_I0.177441.019
61_I65_V0.174911.005
71_V74_W0.174851.004
8_F63_F0.173490.996
60_L63_F0.172870.993
47_N50_S0.172050.988
60_L64_I0.171930.987
23_S26_G0.170360.978
11_I69_I0.169010.971
4_L38_I0.16820.966
43_T68_I0.165540.951
37_L40_E0.163730.940
58_E74_W0.163470.939
28_P37_L0.160190.920
35_K66_S0.159970.919
44_E59_Y0.159540.916
36_E71_V0.155740.894
18_Y21_L0.154930.890
36_E40_E0.154480.887
44_E52_D0.154110.885
21_L30_F0.15390.884
55_D58_E0.152930.878
59_Y75_W0.152830.878
50_S54_D0.151830.872
65_V68_I0.150130.862
52_D55_D0.148140.851
4_L8_F0.148030.850
35_K65_V0.145790.837
43_T50_S0.145760.837
49_N53_N0.145710.837
38_I68_I0.145380.835
41_W69_I0.144470.830
31_Q39_K0.144070.827
46_I52_D0.143380.823
6_E14_N0.142820.820
31_Q35_K0.142590.819
57_E61_I0.141880.815
36_E56_P0.141610.813
21_L29_N0.141340.812
47_N53_N0.141150.811
63_F71_V0.140880.809
30_F33_R0.140690.808
20_I24_P0.139820.803
13_E49_N0.138440.795
14_N17_F0.137760.791
43_T46_I0.136280.783
11_I14_N0.136060.781
34_L70_G0.135690.779
38_I77_E0.13550.778
40_E43_T0.134750.774
53_N57_E0.133640.767
20_I75_W0.133280.765
19_K40_E0.133010.764
30_F67_G0.132950.764
24_P31_Q0.132930.763
28_P33_R0.132850.763
40_E51_P0.132010.758
16_D72_I0.131350.754
45_Y48_E0.131070.753
68_I71_V0.131030.752
62_S70_G0.130940.752
35_K38_I0.130830.751
39_K62_S0.130810.751
4_L16_D0.130080.747
21_L75_W0.129320.743
11_I75_W0.129140.742
4_L29_N0.128380.737
23_S27_D0.128230.736
61_I70_G0.127950.735
7_I61_I0.127180.730
48_E54_D0.125630.721
4_L55_D0.12560.721
59_Y62_S0.125590.721
13_E51_P0.124680.716
51_P54_D0.124550.715
18_Y63_F0.124440.715
32_E58_E0.123980.712
24_P28_P0.122720.705
16_D20_I0.12260.704
9_E13_E0.121470.698
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
3kkcA0.98796.40.45
3o60A0.935195.60.49
2iu5A0.97492.10.567
4gfkA181.90.632
3qkxA0.98778.50.644
3aqtA0.98777.90.645
3lsjA177.40.646
3cjdA171.70.662
2iaiA166.20.674
3he0A0.987650.677

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