GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TetR_C_4 - YsiA-like protein C-terminal region
Pfam: PF08359 (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: 133
Sequences: 13938
Seq/Len: 104.8
HH_delta: 0.148 (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
25_K79_E1.611722.936
21_S24_E1.46652.671
74_E93_E1.439592.622
78_E82_E1.348562.456
78_E81_Q1.267792.309
78_E92_P1.230422.241
74_E78_E1.141322.079
21_S85_E1.108452.019
80_G85_E1.057281.926
98_F102_M1.0381.891
27_R124_E1.032351.880
80_G86_F1.006821.834
94_L125_E0.993741.810
79_E83_Q0.969581.766
101_G105_H0.960861.750
70_L97_R0.933291.700
31_E123_A0.924071.683
81_Q92_P0.92011.676
27_R127_M0.910761.659
25_K76_I0.90571.650
27_R31_E0.849931.548
22_P83_Q0.845811.541
23_E27_R0.828251.509
118_D121_D0.823851.501
31_E124_E0.801541.460
31_E120_E0.794771.448
76_I80_G0.745551.358
81_Q88_K0.742781.353
79_E82_E0.736621.342
77_I92_P0.726871.324
87_R90_L0.722811.317
70_L93_E0.717041.306
24_E28_A0.70681.287
91_D94_L0.700911.277
76_I79_E0.68531.248
28_A31_E0.674711.229
81_Q90_L0.664171.210
70_L74_E0.661981.206
73_I96_A0.659721.202
92_P96_A0.659541.201
71_R75_E0.644231.173
74_E92_P0.637751.162
81_Q89_D0.636511.159
22_P85_E0.624341.137
36_F40_N0.621411.132
123_A127_M0.60911.109
15_A32_A0.601011.095
20_S24_E0.5871.069
77_I99_I0.581391.059
35_D119_L0.579851.056
22_P76_I0.575111.048
74_E96_A0.563161.026
15_A28_A0.562851.025
55_N58_L0.561741.023
72_I75_E0.559571.019
24_E27_R0.552681.007
35_D39_E0.550171.002
90_L95_A0.548380.999
67_R71_R0.541280.986
23_E85_E0.539640.983
32_A35_D0.539490.983
22_P80_G0.533760.972
124_E128_D0.52710.960
33_H69_Y0.510970.931
19_E25_K0.510520.930
125_E128_D0.507240.924
30_I99_I0.504540.919
27_R128_D0.503830.918
20_S25_K0.503550.917
59_R63_N0.503060.916
68_E72_I0.501050.913
19_E28_A0.498480.908
30_I103_I0.498480.908
56_E59_R0.497720.907
28_A32_A0.495310.902
115_G118_D0.492320.897
93_E97_R0.4920.896
60_K64_E0.490220.893
98_F101_G0.488270.889
22_P86_F0.485080.884
120_E124_E0.480250.875
75_E79_E0.479020.873
77_I95_A0.4680.852
81_Q84_G0.466270.849
31_E35_D0.465960.849
77_I81_Q0.465930.849
33_H104_N0.465920.849
29_L76_I0.464340.846
25_K80_G0.46110.840
94_L98_F0.456850.832
33_H100_F0.45520.829
19_E24_E0.449960.820
91_D125_E0.448560.817
29_L73_I0.44320.807
88_K91_D0.440360.802
91_D95_A0.440110.802
109_D112_L0.438430.799
23_E128_D0.435390.793
64_E67_R0.431920.787
30_I123_A0.428580.781
22_P25_K0.427570.779
15_A18_D0.425950.776
71_R74_E0.425740.775
81_Q87_R0.422930.770
27_R30_I0.422170.769
35_D120_E0.420840.767
80_G84_G0.41980.765
65_I69_Y0.418830.763
30_I127_M0.4130.752
46_V50_E0.40820.744
104_N108_L0.405510.739
75_E78_E0.398450.726
35_D38_E0.398140.725
62_I66_R0.39610.721
87_R128_D0.395610.721
56_E60_K0.394390.718
77_I80_G0.392720.715
102_M106_T0.391980.714
34_L123_A0.389090.709
106_T122_I0.388410.707
66_R104_N0.388020.707
64_E68_E0.386750.704
33_H37_L0.385050.701
58_L61_K0.384310.700
110_W118_D0.383370.698
65_I68_E0.381790.695
94_L121_D0.378250.689
101_G104_N0.375480.684
81_Q91_D0.375410.684
42_D45_I0.373780.681
122_I126_L0.373250.680
23_E86_F0.370790.675
20_S28_A0.368480.671
54_S58_L0.368280.671
38_E119_L0.36770.670
100_F104_N0.366210.667
110_W113_N0.366020.667
105_H109_D0.365430.666
61_K64_E0.363530.662
40_N43_L0.359370.655
117_F121_D0.35850.653
102_M126_L0.35760.651
33_H107_V0.355620.648
120_E123_A0.355420.647
23_E127_M0.351660.641
67_R70_L0.351270.640
102_M105_H0.35020.638
18_D28_A0.348570.635
81_Q86_F0.347010.632
121_D124_E0.344110.627
117_F122_I0.338830.617
68_E71_R0.335450.611
71_R93_E0.333460.607
33_H103_I0.331920.605
36_F39_E0.331770.604
21_S83_Q0.331140.603
49_L53_Q0.330750.602
15_A19_E0.329670.600
31_E127_M0.32730.596
80_G83_Q0.327180.596
16_I72_I0.326930.595
123_A126_L0.325570.593
121_D125_E0.324460.591
66_R70_L0.322440.587
101_G109_D0.321950.586
54_S57_E0.321860.586
95_A99_I0.321810.586
29_L33_H0.321750.586
119_L122_I0.321740.586
94_L97_R0.317740.579
44_A104_N0.317640.579
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
1vi0A198.90.148
3anpC0.992598.70.214
4gfkA198.70.225
4gckA198.60.234
3nxcA198.60.236
3himA0.98598.60.241
2iaiA0.977498.60.248
3q0wA0.992598.60.248
3dewA0.992598.60.257
3kz9A198.50.261

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