GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HMG_box - HMG (high mobility group) box
Pfam: PF00505 (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: CL0114
Length: 69
Sequences: 3203
Seq/Len: 46.42
HH_delta: -0.093 (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
60_R64_E1.551153.030
48_A52_E1.406492.747
15_K38_M1.282392.505
15_K18_K1.215842.375
57_E60_R1.202972.350
43_S46_E1.063752.078
42_L46_E0.948951.853
12_C35_L0.890211.739
59_E63_K0.854411.669
37_Q41_N0.81781.597
34_I38_M0.807491.577
34_I37_Q0.801381.565
49_P53_E0.774151.512
14_E50_Y0.769621.503
9_M12_C0.726251.418
5_P57_E0.719551.405
53_E56_E0.708061.383
11_F42_L0.701281.370
53_E57_E0.689751.347
5_P9_M0.685131.338
5_P13_K0.68411.336
15_K35_L0.681381.331
10_L53_E0.679681.327
28_N32_S0.678091.324
60_R63_K0.662891.295
10_L57_E0.624961.221
58_K62_E0.610841.193
52_E56_E0.607881.187
44_E48_A0.577781.128
32_S36_A0.577531.128
51_K55_E0.573551.120
61_Y65_M0.57311.119
30_E33_K0.551251.077
44_E51_K0.550931.076
18_K22_E0.541721.058
12_C16_R0.53941.054
52_E55_E0.538951.053
12_C32_S0.534821.045
17_A21_E0.516181.008
56_E59_E0.514711.005
17_A20_K0.511240.999
38_M41_N0.508540.993
27_S30_E0.505790.988
7_A51_K0.492710.962
55_E59_E0.478850.935
8_F39_W0.468580.915
59_E62_E0.45880.896
14_E53_E0.439460.858
61_Y66_P0.433760.847
38_M42_L0.431890.844
1_P61_Y0.431690.843
54_A58_K0.430310.840
11_F38_M0.430120.840
48_A51_K0.425540.831
11_F50_Y0.416170.813
42_L49_P0.410320.801
6_N9_M0.407320.796
28_N35_L0.402150.785
8_F36_A0.400580.782
26_L30_E0.395530.773
9_M36_A0.390480.763
39_W47_K0.38830.758
11_F35_L0.381910.746
63_K66_P0.380490.743
5_P10_L0.371680.726
9_M13_K0.349990.684
36_A40_K0.347650.679
19_L31_I0.345440.675
7_A54_A0.338080.660
46_E49_P0.326930.639
13_K16_R0.325090.635
47_K51_K0.322550.630
9_M28_N0.316730.619
44_E47_K0.314710.615
9_M16_R0.308690.603
18_K21_E0.308350.602
63_K67_E0.306830.599
48_A55_E0.305320.596
11_F15_K0.30510.596
43_S49_P0.301620.589
37_Q40_K0.299950.586
16_R31_I0.299940.586
26_L34_I0.299720.585
6_N10_L0.299510.585
6_N28_N0.297850.582
19_L35_L0.297020.580
1_P6_N0.294530.575
15_K19_L0.290220.567
9_M32_S0.286940.560
19_L22_E0.280050.547
23_N26_L0.279190.545
57_E64_E0.277120.541
26_L31_I0.274890.537
3_R65_M0.273750.535
61_Y68_Y0.273520.534
62_E66_P0.270340.528
65_M68_Y0.270270.528
3_R9_M0.265940.519
13_K17_A0.263510.515
16_R36_A0.261450.511
56_E60_R0.260790.509
19_L38_M0.256550.501
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
2cs1A199.5-0.093
1k99A199.5-0.092
2co9A199.5-0.09
4euwA199.5-0.087
2crjA199.5-0.087
2e6oA199.5-0.083
2gzkA199.5-0.08
2lefA199.5-0.08
1cg7A199.5-0.08
2yrqA199.5-0.079

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