GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
REV - REV protein (anti-repression trans-activator protein)
Pfam: PF00424 (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: 91
Sequences: 1464
Seq/Len: 16.09
HH_delta: -0.003 (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
9_E12_R0.879243.792
51_R55_E0.621522.681
12_R16_I0.601642.595
13_A57_I0.536752.315
55_E59_S0.500652.159
56_R61_C0.492652.125
32_T51_R0.492272.123
30_E51_R0.424311.830
55_E61_C0.408121.760
45_A49_Q0.404711.746
16_I19_I0.401561.732
37_R81_T0.392811.694
19_I56_R0.377781.629
19_I23_S0.366011.579
26_Y45_A0.363041.566
45_A48_R0.357081.540
51_R54_S0.356941.540
8_E12_R0.354461.529
45_A52_A0.338011.458
9_E87_D0.329551.421
52_A56_R0.319981.380
62_L67_E0.317311.369
16_I61_C0.315391.360
19_I61_C0.288431.244
64_R67_E0.282931.220
77_L81_T0.278681.202
26_Y29_P0.277871.198
81_T85_L0.277141.195
82_L87_D0.274851.185
9_E28_S0.271751.172
78_E85_L0.268561.158
58_L61_C0.267241.153
12_R61_C0.267051.152
32_T35_A0.264271.140
86_E89_P0.254061.096
19_I52_A0.254051.096
16_I57_I0.253851.095
19_I49_Q0.251711.086
73_Q77_L0.251011.083
12_R18_K0.249851.078
55_E60_T0.248861.073
30_E37_R0.248131.070
53_L56_R0.244631.055
29_P35_A0.240231.036
82_L88_P0.239191.032
13_A61_C0.237111.023
1_M4_R0.234021.009
13_A19_I0.223070.962
70_V73_Q0.22080.952
48_R55_E0.220650.952
49_Q52_A0.217080.936
52_A55_E0.215990.932
30_E48_R0.214760.926
56_R59_S0.214020.923
18_K21_Y0.21360.921
49_Q57_I0.212620.917
29_P67_E0.209840.905
49_Q56_R0.20880.901
59_S67_E0.207130.893
36_R57_I0.204550.882
6_G64_R0.204070.880
67_E72_L0.203830.879
11_L18_K0.20320.876
77_L87_D0.198520.856
67_E71_P0.19380.836
28_S51_R0.193680.835
26_Y52_A0.192880.832
16_I60_T0.191670.827
45_A63_G0.188380.813
16_I37_R0.188080.811
2_A5_S0.18570.801
5_S55_E0.1850.798
82_L91_S0.184440.796
31_G36_R0.183720.792
85_L88_P0.18360.792
16_I90_T0.182590.788
22_Q70_V0.182410.787
76_P79_R0.182070.785
45_A61_C0.181210.782
30_E85_L0.180990.781
9_E88_P0.180870.780
16_I91_S0.180120.777
45_A53_L0.179490.774
26_Y81_T0.178580.770
84_C88_P0.17840.769
48_R51_R0.177110.764
59_S63_G0.176990.763
87_D90_T0.176240.760
16_I26_Y0.173720.749
84_C87_D0.171360.739
1_M5_S0.170950.737
26_Y61_C0.170870.737
26_Y56_R0.170740.736
16_I82_L0.168620.727
32_T48_R0.165490.714
8_E60_T0.164170.708
70_V78_E0.163070.703
12_R15_R0.163060.703
30_E39_R0.161980.699
9_E90_T0.160450.692
8_E15_R0.159590.688
85_L89_P0.159360.687
37_R90_T0.158290.683
88_P91_S0.157880.681
49_Q53_L0.156170.674
37_R45_A0.155410.670
59_S64_R0.152050.656
26_Y49_Q0.151930.655
65_P76_P0.150940.651
11_L19_I0.150430.649
28_S81_T0.150410.649
77_L91_S0.149640.645
8_E91_S0.148350.640
5_S12_R0.148110.639
45_A83_D0.147030.634
60_T85_L0.146620.632
6_G86_E0.14660.632
24_N68_E0.14650.632
45_A51_R0.145460.627
39_R77_L0.145440.627
54_S83_D0.145370.627
43_W46_R0.143740.620
51_R56_R0.143070.617
8_E39_R0.142480.615
19_I45_A0.141560.611
36_R79_R0.140680.607
7_D24_N0.139480.602
51_R85_L0.139080.600
47_Q75_P0.138630.598
19_I58_L0.137460.593
28_S37_R0.13710.591
13_A62_L0.135820.586
9_E82_L0.13580.586
33_R38_N0.135450.584
43_W50_I0.135410.584
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
2x7lM0.978100-0.003
3lphA0.74731000.225
1etfB0.285798.60.747
2hi3A0.637434.50.928
4egcA0.582432.10.929
1mh3A0.483532.10.929
1f15A0.703327.10.931
1k32A0.340719.50.935
1au7A0.516514.50.939
1mnmC0.494513.90.939

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