GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MHC_II_beta - Class II histocompatibility antigen beta domain
Pfam: PF00969 (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: CL0343
Length: 75
Sequences: 6634
Seq/Len: 88.45
HH_delta: -0.036 (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
45_N48_Y1.617493.164
62_A65_T1.422912.783
55_F58_Q1.190572.329
16_E59_R1.181082.310
55_F59_R1.125942.203
24_E27_R1.081562.116
62_A66_Y1.074362.102
41_L45_N1.024482.004
58_Q62_A1.013971.983
45_N49_W0.945391.849
25_F45_N0.911531.783
6_S10_E0.882161.726
46_A50_N0.864231.691
26_V49_W0.848011.659
27_R38_Y0.847891.659
58_Q61_A0.84221.647
59_R62_A0.814941.594
43_E47_E0.790911.547
6_S22_K0.726771.422
61_A65_T0.708431.386
20_Y25_F0.700411.370
52_Q55_F0.673151.317
13_R31_D0.640211.252
44_K47_E0.639861.252
25_F41_L0.631651.236
47_E51_S0.60161.177
40_E43_E0.600891.175
48_Y52_Q0.595421.165
16_E35_F0.577581.130
26_V45_N0.520641.018
22_K25_F0.517611.013
44_K48_Y0.512141.002
30_S33_G0.496760.972
18_Y25_F0.489230.957
34_K47_E0.472950.925
60_R64_D0.462070.904
37_G44_K0.457430.895
26_V48_Y0.457180.894
30_S39_T0.448650.878
2_E6_S0.443790.868
58_Q65_T0.439460.860
14_F62_A0.435480.852
64_D68_R0.432940.847
26_V41_L0.429870.841
5_F12_V0.428830.839
19_I22_K0.425730.833
52_Q56_L0.420510.823
23_E39_T0.418830.819
59_R63_V0.409490.801
35_F59_R0.405260.793
6_S13_R0.404150.791
25_F48_Y0.394670.772
50_N56_L0.388910.761
57_E60_R0.387180.757
18_Y49_W0.381390.746
42_G46_A0.380.743
16_E19_I0.373550.731
28_F56_L0.373480.731
9_T68_R0.369840.723
49_W55_F0.363770.712
22_K32_V0.359570.703
8_G68_R0.357510.699
53_K56_L0.355880.696
33_G60_R0.355220.695
19_I24_E0.352940.690
11_R31_D0.348280.681
48_Y51_S0.346920.679
53_K57_E0.344290.673
44_K49_W0.339750.665
56_L59_R0.339620.664
30_S64_D0.329460.644
37_G41_L0.328990.644
41_L44_K0.325920.638
14_F66_Y0.325220.636
34_K53_K0.325120.636
39_T44_K0.322360.631
24_E38_Y0.321570.629
15_L40_E0.32110.628
18_Y45_N0.31670.620
61_A64_D0.312930.612
46_A61_A0.309350.605
2_E68_R0.304290.595
28_F35_F0.304280.595
40_E44_K0.301850.590
18_Y35_F0.300270.587
15_L36_V0.300030.587
6_S11_R0.293450.574
61_A66_Y0.291160.570
11_R53_K0.288150.564
2_E15_L0.287680.563
54_E58_Q0.286140.560
63_V66_Y0.281760.551
33_G57_E0.273530.535
16_E55_F0.273180.534
23_E41_L0.273020.534
40_E53_K0.272370.533
4_Y22_K0.27130.531
4_Y10_E0.270060.528
65_T68_R0.269190.527
27_R34_K0.268430.525
18_Y59_R0.265850.520
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
3dbxA0.986799.5-0.036
3usaD199.5-0.035
4ah2B199.5-0.034
4d8pB199.5-0.031
4g59A0.973399.5-0.026
4gupA0.986799.5-0.022
3m17A0.986799.5-0.013
3fruA0.986799.4-0.011
3p73A0.986799.4-0.009
1kcgC0.986799.4-0.001

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