GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Trans_reg_C - Transcriptional regulatory protein C terminal
Pfam: PF00486 (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: 77
Sequences: 18384
Seq/Len: 238.75
HH_delta: -0.114 (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
27_R47_D2.970393.198
16_L33_A2.613852.814
15_E19_R2.548692.744
70_V76_R2.350252.531
44_N47_D2.180232.347
10_E56_K2.070872.230
9_K12_R2.010212.164
20_N23_R1.842381.984
68_E76_R1.776011.912
29_E33_A1.75651.891
26_S29_E1.719061.851
48_V51_S1.636111.762
49_H52_R1.60581.729
16_L30_L1.595941.718
16_L20_N1.525191.642
51_S55_K1.481161.595
16_L25_V1.45221.564
9_K35_W1.362871.467
8_P12_R1.346621.450
45_S49_H1.343341.446
21_P25_V1.329011.431
27_R43_D1.292761.392
24_V73_R1.226741.321
13_L49_H1.167481.257
60_A64_P1.095031.179
23_R29_E1.084891.168
12_R15_E1.082951.166
9_K49_H1.078341.161
7_T56_K1.064751.146
66_F77_L1.015151.093
25_V29_E0.987091.063
18_L77_L0.981761.057
20_N25_V0.972611.047
50_I75_Y0.967271.041
24_V70_V0.949741.023
20_N29_E0.947951.021
29_E32_E0.944051.016
48_V52_R0.933271.005
8_P73_R0.930941.002
13_L30_L0.90660.976
11_F15_E0.892360.961
16_L29_E0.890570.959
9_K34_L0.867850.934
58_E64_P0.866210.933
6_L53_L0.856080.922
7_T10_E0.846740.912
44_N51_S0.832010.896
17_L25_V0.820920.884
18_L21_P0.79210.853
16_L34_L0.778870.839
10_E52_R0.778830.839
15_E18_L0.771260.830
13_L50_I0.770870.830
58_E65_D0.768870.828
44_N48_V0.747910.805
14_L53_L0.745080.802
47_D71_R0.743570.801
59_D65_D0.733330.790
26_S73_R0.726960.783
28_E32_E0.707320.762
14_L18_L0.705890.760
54_R69_T0.690780.744
37_D40_D0.6650.716
52_R55_K0.662590.713
4_V56_K0.652610.703
27_R46_L0.651970.702
24_V76_R0.650090.700
42_S45_S0.647530.697
25_V46_L0.646840.696
27_R69_T0.63660.685
58_E66_F0.636250.685
24_V74_G0.636230.685
19_R33_A0.629720.678
37_D41_V0.61170.659
60_A66_F0.610240.657
27_R31_I0.608490.655
28_E43_D0.606930.653
39_E42_S0.604060.650
13_L17_L0.598030.644
16_L19_R0.594140.640
60_A65_D0.593840.639
47_D75_Y0.576260.620
41_V45_S0.573880.618
8_P72_G0.571340.615
59_D64_P0.568350.612
6_L56_K0.56290.606
46_L75_Y0.562260.605
47_D69_T0.555640.598
43_D47_D0.54570.588
2_Q5_K0.53950.581
25_V30_L0.539030.580
17_L77_L0.534110.575
34_L49_H0.530780.571
7_T52_R0.528770.569
30_L46_L0.527460.568
12_R16_L0.522480.563
73_R76_R0.516640.556
35_W49_H0.516230.556
53_L57_L0.515370.555
69_T74_G0.510890.550
50_I67_I0.510710.550
10_E49_H0.506630.545
37_D43_D0.505170.544
20_N33_A0.502430.541
22_G76_R0.498010.536
11_F18_L0.494170.532
47_D51_S0.489460.527
28_E31_I0.488290.526
31_I43_D0.469690.506
67_I70_V0.454690.490
45_S52_R0.452770.487
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
2zxjA199.7-0.114
2z9mA199.6-0.063
3q9vA0.98799.6-0.055
3zq7A199.6-0.054
2hwvA199.6-0.05
2k4jA199.6-0.048
1opcA199.6-0.046
3rjpA0.98799.6-0.039
2jzyA0.98799.5-0.033
2hqnA199.5-0.033

Page generated in 0.0356 seconds.