GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MG1 - Alpha-2-macroglobulin MG1 domain
Pfam: PF11974 (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: CL0159
Length: 97
Sequences: 536
Seq/Len: 5.53
HH_delta: 0.703 (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
28_V31_A0.444563.313
4_L19_V0.442473.298
4_L28_V0.405633.023
47_G55_A0.386572.881
16_L54_F0.298042.221
8_A77_L0.285952.131
32_E69_R0.278032.072
3_D21_S0.25891.930
32_E48_K0.242121.805
19_V28_V0.227921.699
85_L90_F0.22481.675
33_V55_A0.210831.571
37_D40_N0.207391.546
79_L84_A0.20381.519
34_E69_R0.197031.468
31_A68_A0.194111.447
85_L91_D0.189351.411
32_E46_S0.186541.390
21_S24_T0.18331.366
19_V31_A0.182171.358
29_A51_A0.182051.357
6_L68_A0.178921.334
2_T18_W0.172511.286
19_V33_V0.167631.249
86_D89_R0.162871.214
30_G48_K0.160311.195
78_P82_G0.154611.152
18_W54_F0.153911.147
83_S89_R0.151541.129
66_V77_L0.148551.107
2_T75_S0.147941.103
73_D78_P0.145991.088
5_G22_L0.143361.068
35_L57_F0.143191.067
43_V72_G0.143021.066
7_T18_W0.142031.059
34_E76_F0.141151.052
20_T25_G0.13691.020
7_T20_T0.132240.986
5_G76_F0.132190.985
5_G54_F0.131460.980
9_K20_T0.129710.967
12_P62_K0.129540.965
29_A72_G0.129360.964
47_G75_S0.12880.960
21_S73_D0.127710.952
85_L88_S0.126790.945
5_G68_A0.123130.918
36_Y43_V0.1220.909
27_P73_D0.12030.897
11_G25_G0.119510.891
45_A61_K0.119340.889
36_Y67_I0.119080.888
18_W88_S0.118670.884
3_D23_S0.117310.874
33_V68_A0.116610.869
84_A87_L0.116310.867
21_S78_P0.116270.867
4_L14_G0.115970.864
81_W89_R0.115090.858
34_E43_V0.114930.857
66_V79_L0.113990.850
40_N76_F0.110560.824
23_S48_K0.110510.824
46_S69_R0.11020.821
77_L86_D0.110190.821
2_T73_D0.109530.816
22_L47_G0.108710.810
37_D74_F0.108180.806
10_Q33_V0.107080.798
49_T55_A0.106660.795
14_G62_K0.106260.792
21_S86_D0.106080.791
79_L85_L0.105990.790
37_D90_F0.105710.788
8_A15_L0.105160.784
6_L77_L0.104880.782
13_D60_T0.104880.782
6_L19_V0.104410.778
81_W84_A0.102880.767
35_L66_V0.102430.763
39_R76_F0.102270.762
6_L31_A0.101420.756
6_L84_A0.1010.753
9_K18_W0.100980.753
81_W88_S0.100830.751
50_D56_S0.100670.750
17_V82_G0.099980.745
82_G88_S0.099710.743
30_G49_T0.099690.743
43_V46_S0.099590.742
24_T61_K0.099430.741
2_T50_D0.098650.735
26_K51_A0.098550.735
69_R74_F0.098320.733
84_A89_R0.098290.733
48_K51_A0.098080.731
21_S28_V0.097920.730
30_G52_D0.097450.726
85_L89_R0.09740.726
35_L64_F0.096230.717
41_G63_P0.095560.712
34_E67_I0.095490.712
44_L82_G0.094580.705
69_R72_G0.094450.704
31_A69_R0.094140.702
44_L60_T0.093390.696
14_G40_N0.093190.695
83_S87_L0.0930.693
75_S85_L0.092860.692
16_L25_G0.092620.690
17_V33_V0.091930.685
33_V45_A0.091450.682
19_V69_R0.091390.681
27_P82_G0.091040.679
6_L22_L0.090870.677
22_L84_A0.090480.674
29_A49_T0.090420.674
27_P79_L0.090260.673
30_G72_G0.090220.672
79_L87_L0.090130.672
67_I74_F0.090040.671
50_D53_G0.089740.669
9_K76_F0.089310.666
32_E51_A0.089120.664
34_E82_G0.088980.663
17_V77_L0.08880.662
13_D61_K0.088550.660
33_V63_P0.088540.660
34_E78_P0.088520.660
17_V66_V0.088030.656
83_S90_F0.087820.655
29_A56_S0.087730.654
45_A57_F0.087390.651
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
3e8vA0.783597.30.703
3txaA0.762995.90.755
2g2nA0.835195.70.758
1oo2A0.814495.50.762
2ww8A0.927895.30.765
1f86A0.804195.30.765
3iwvA0.917594.80.772
2h0eA0.86694.80.773
3kptA0.876394.70.774
3qvaA0.886694.60.775
If you are interested in a protein containing this domain,
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