GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TetR_C_6 - Bacterial transcriptional repressor
Pfam: PF13977 (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: CL0174
Length: 115
Sequences: 11455
Seq/Len: 99.61
HH_delta: 0.201 (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
55_A73_E1.457642.954
10_D103_R1.386692.810
4_R60_R1.279272.593
6_R107_R1.231262.495
59_R72_P1.123752.277
55_A59_R1.115562.261
4_R57_L1.03622.100
51_R77_R1.019952.067
59_R63_A0.947221.920
62_V72_P0.90951.843
59_R62_V0.905111.834
98_D101_R0.901361.827
78_M82_L0.842511.707
74_R104_A0.828051.678
81_A85_G0.822081.666
61_A65_G0.795611.612
67_R70_V0.778091.577
71_D74_R0.733921.487
61_A66_I0.726011.471
53_R56_E0.720851.461
6_R10_D0.71261.444
57_L61_A0.69251.403
77_R101_R0.682541.383
41_A45_E0.675091.368
58_L72_P0.673961.366
28_E31_A0.663871.345
28_E35_R0.651461.320
55_A72_P0.647551.312
3_E7_A0.635571.288
48_A52_S0.631071.279
51_R73_E0.622611.262
51_R55_A0.614971.246
36_D39_L0.614081.244
64_G67_R0.604971.226
52_S56_E0.591431.199
74_R101_R0.579981.175
72_P76_A0.576711.169
58_L79_L0.575811.167
19_D22_E0.569881.155
55_A76_A0.560231.135
103_R107_R0.556351.128
78_M109_F0.551121.117
104_A107_R0.548681.112
7_A10_D0.535781.086
70_V75_L0.530311.075
47_Y84_D0.516321.046
6_R103_R0.506711.027
28_E32_E0.506331.026
45_E49_R0.50611.026
74_R108_A0.504241.022
56_E60_R0.5011.015
42_L45_E0.496881.007
60_R63_A0.492750.999
100_E104_A0.490.993
37_P41_A0.488780.991
99_A103_R0.486210.985
12_L50_W0.480760.974
78_M81_A0.479010.971
57_L60_R0.474710.962
62_V70_V0.46840.949
9_L79_L0.467420.947
14_P99_A0.467250.947
101_R104_A0.465940.944
40_R44_R0.463190.939
62_V68_A0.46230.937
47_Y50_W0.448270.908
81_A84_D0.446690.905
54_L80_L0.444310.900
32_E35_R0.443490.899
24_R28_E0.442590.897
54_L76_A0.435110.882
68_A71_D0.433810.879
58_L62_V0.431570.875
3_E6_R0.429220.870
73_E77_R0.423820.859
10_D14_P0.423160.858
24_R27_L0.408390.828
12_L83_L0.407440.826
8_I54_L0.406590.824
32_E36_D0.406470.824
15_A18_E0.403130.817
52_S55_A0.403130.817
37_P40_R0.402550.816
84_D88_L0.399860.810
23_W28_E0.39970.810
89_Q92_L0.399110.809
20_P24_R0.397780.806
58_L75_L0.397340.805
26_W84_D0.396910.804
84_D87_W0.391940.794
46_A50_W0.391520.793
27_L30_W0.391310.793
49_R53_R0.390380.791
38_E42_L0.386540.783
24_R91_L0.386140.783
80_L84_D0.385410.781
12_L84_D0.384340.779
13_L100_E0.381870.774
71_D75_L0.38150.773
42_L46_A0.380270.771
95_D98_D0.380070.770
46_A49_R0.37870.767
50_W80_L0.377350.765
9_L83_L0.376540.763
105_I109_F0.375170.760
6_R9_L0.374420.759
77_R89_Q0.373020.756
38_E41_A0.371540.753
12_L80_L0.371460.753
9_L12_L0.370680.751
56_E59_R0.370060.750
39_L42_L0.369240.748
53_R57_L0.369070.748
81_A89_Q0.365110.740
23_W26_W0.361870.733
10_D100_E0.361510.733
10_D107_R0.361290.732
48_A51_R0.359860.729
102_A105_I0.359390.728
15_A19_D0.358390.726
26_W30_W0.355090.720
11_A14_P0.354990.719
23_W27_L0.354070.718
45_E48_A0.350320.710
51_R80_L0.349290.708
105_I108_A0.34820.706
84_D89_Q0.34640.702
26_W50_W0.342080.693
24_R32_E0.339810.689
6_R104_A0.338240.685
62_V71_D0.337240.683
85_G89_Q0.332270.673
104_A108_A0.331750.672
44_R47_Y0.328450.666
9_L13_L0.324620.658
61_A67_R0.322560.654
8_I57_L0.321320.651
74_R78_M0.320560.650
7_A11_A0.319270.647
103_R106_L0.31790.644
47_Y88_L0.317080.643
62_V67_R0.314550.637
75_L109_F0.313560.635
62_V66_I0.312860.634
97_F101_R0.311250.631
97_F102_A0.310290.629
5_L79_L0.310020.628
50_W53_R0.309160.627
75_L78_M0.308670.626
63_A72_P0.308420.625
58_L61_A0.308160.625
44_R48_A0.307630.623
82_L85_G0.307460.623
90_W93_D0.306840.622
52_S73_E0.306170.620
31_A34_R0.304990.618
47_Y51_R0.304820.618
59_R73_E0.300060.608
9_L106_L0.299330.607
87_W90_W0.298660.605
81_A86_L0.298410.605
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
2gfnA198.40.201
3e7qA198.30.221
2nx4A0.973998.20.253
4ichA198.20.258
2g3bA0.982698.10.261
4kwaA198.10.276
3crjA0.991398.10.278
3qbmA198.10.281
2hyjA0.9826980.284
3eupA197.90.305

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