GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MGS - MGS-like domain
Pfam: PF02142 (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: 95
Sequences: 3742
Seq/Len: 39.39
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
10_A32_E1.380933.650
23_A27_K1.069762.828
24_K28_E1.033732.732
25_F29_H1.025222.710
3_V25_F1.02282.703
81_K84_R0.960752.539
17_Y61_I0.835612.209
84_R88_E0.719161.901
3_V29_H0.709711.876
54_D58_N0.703121.858
23_A35_E0.657981.739
8_R12_L0.646311.708
20_E36_V0.608641.609
16_I31_I0.60781.607
46_P56_I0.607021.604
7_K11_E0.605741.601
8_R11_E0.605351.600
4_P7_K0.586471.550
17_Y39_K0.583831.543
45_S59_G0.573961.517
82_I85_A0.566971.499
64_V95_T0.54421.438
27_K36_V0.542481.434
27_K35_E0.490111.295
6_A26_L0.483111.277
80_Y84_R0.474121.253
64_V86_A0.466831.234
25_F28_E0.464191.227
53_M57_K0.46241.222
27_K32_E0.457081.208
3_V7_K0.448661.186
54_D57_K0.439491.162
17_Y35_E0.439371.161
68_P87_V0.436191.153
55_L58_N0.419641.109
5_L65_I0.410031.084
14_F63_L0.409851.083
15_E34_T0.408911.081
34_T39_K0.405431.072
75_E85_A0.395871.046
27_K39_K0.391091.034
6_A16_I0.387751.025
80_Y85_A0.373460.987
81_K85_A0.368850.975
53_M60_K0.364720.964
19_T22_T0.364290.963
56_I60_K0.362430.958
89_Y92_P0.347010.917
55_L60_K0.344250.910
2_I16_I0.340850.901
4_P8_R0.337050.891
73_D76_H0.335470.887
72_S76_H0.333080.880
7_K31_I0.330990.875
82_I95_T0.32570.861
37_V55_L0.323390.855
41_G89_Y0.322720.853
38_N47_D0.318940.843
24_K27_K0.3160.835
10_A16_I0.314740.832
68_P74_Q0.314020.830
15_E62_D0.312790.827
47_D52_I0.311050.822
2_I26_L0.310390.820
52_I55_L0.307620.813
69_Y76_H0.306670.811
23_A36_V0.303790.803
80_Y88_E0.300990.796
6_A31_I0.300190.793
70_P73_D0.297380.786
15_E35_E0.294570.779
18_A26_L0.291420.770
18_A23_A0.28860.763
13_G29_H0.288460.762
18_A94_F0.287620.760
7_K29_H0.286790.758
53_M81_K0.284250.751
23_A34_T0.283690.750
5_L67_T0.281930.745
69_Y79_G0.280170.741
53_M56_I0.278840.737
42_E45_S0.278320.736
45_S57_K0.275230.727
79_G84_R0.274310.725
74_Q85_A0.27290.721
46_P54_D0.270020.714
17_Y55_L0.269010.711
89_Y93_L0.266840.705
68_P89_Y0.263690.697
1_E4_P0.263510.697
69_Y89_Y0.256170.677
7_K28_E0.255990.677
56_I64_V0.255710.676
31_I34_T0.25460.673
26_L29_H0.247730.655
85_A89_Y0.247420.654
11_E83_R0.246680.652
9_L63_L0.245310.648
55_L59_G0.245040.648
42_E59_G0.242530.641
21_G25_F0.241640.639
14_F62_D0.239580.633
46_P55_L0.238570.631
64_V85_A0.237780.629
2_I22_T0.233860.618
16_I34_T0.231820.613
19_T52_I0.229820.607
56_I82_I0.229260.606
10_A13_G0.229030.605
17_Y62_D0.228650.604
71_F74_Q0.227740.602
42_E55_L0.226940.600
10_A27_K0.226280.598
43_G46_P0.225750.597
38_N41_G0.225560.596
20_E24_K0.225070.595
15_E60_K0.223440.591
68_P80_Y0.223190.590
37_V78_D0.222320.588
3_V28_E0.22170.586
63_L92_P0.221320.585
2_I5_L0.219520.580
6_A13_G0.218830.578
19_T82_I0.218820.578
70_P74_Q0.217420.575
86_A93_L0.216910.573
36_V89_Y0.216260.572
5_L86_A0.215740.570
20_E94_F0.214260.566
82_I86_A0.213680.565
80_Y87_V0.213010.563
57_K89_Y0.211730.560
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
2yvqA0.936899.80.093
1vmdA0.947499.80.093
1b93A0.947499.80.098
2xw6A0.947499.80.1
1a9xA0.915899.80.112
1g8mA199.40.359
1zczA0.989599.40.377
4ehiA0.989599.30.383
3zzmA0.989599.30.386
1t5oA0.884292.80.79

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