GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MCE - mce related protein
Pfam: PF02470 (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: 81
Sequences: 4756
Seq/Len: 58.72
HH_delta: 0.809 (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
7_V47_L1.892713.942
8_Y44_R1.554233.237
32_T48_R1.439522.998
6_T44_R1.364482.842
20_P27_E1.340892.793
4_T46_T1.114132.321
6_T46_T1.0742.237
33_S46_T0.99152.065
5_V47_L0.964572.009
8_Y42_R0.837681.745
27_E30_K0.835031.739
15_L45_V0.832681.734
9_F45_V0.831031.731
22_R75_Y0.807641.682
66_R77_E0.776181.617
2_G48_R0.761171.585
61_S78_L0.759891.583
4_T48_R0.722841.506
21_V47_L0.713551.486
64_S79_I0.710871.481
32_T46_T0.700241.459
63_A78_L0.689811.437
22_R27_E0.670081.396
34_I45_V0.624381.301
23_Y28_V0.619461.290
4_T32_T0.619311.290
17_V33_S0.602371.255
5_V49_I0.572781.193
57_I61_S0.562751.172
39_D42_R0.554721.155
62_R79_I0.531361.107
47_L76_I0.522071.087
3_Y49_I0.498391.038
19_S74_K0.489941.020
18_G30_K0.486271.013
69_G73_E0.48141.003
68_S73_E0.475770.991
28_V49_I0.472120.983
12_A43_V0.466350.971
57_I78_L0.466250.971
22_R77_E0.461550.961
9_F65_I0.453770.945
58_P61_S0.452910.943
3_Y51_P0.45150.940
19_S31_V0.443710.924
15_L19_S0.442810.922
24_R43_V0.43970.916
7_V76_I0.418330.871
52_D56_R0.417220.869
2_G51_P0.41420.863
37_D44_R0.409210.852
23_Y57_I0.405580.845
37_D40_G0.395310.823
30_K48_R0.395130.823
7_V63_A0.389520.811
19_S73_E0.384980.802
10_D42_R0.384510.801
68_S75_Y0.384250.800
26_V43_V0.378290.788
63_A76_I0.368390.767
12_A34_I0.35110.731
13_G74_K0.348870.727
12_A69_G0.339580.707
67_S74_K0.337970.704
67_S73_E0.325490.678
19_S69_G0.324720.676
68_S71_L0.317180.661
17_V34_I0.310570.647
71_L74_K0.303960.633
70_L75_Y0.300790.627
16_S74_K0.299290.623
23_Y43_V0.296750.618
28_V78_L0.292380.609
31_V76_I0.290790.606
23_Y80_P0.28610.596
24_R79_I0.285240.594
72_G75_Y0.285170.594
13_G73_E0.282170.588
13_G68_S0.28020.584
31_V47_L0.277920.579
66_R74_K0.277910.579
11_D16_S0.274270.571
49_I78_L0.273990.571
20_P71_L0.273520.570
65_I74_K0.272260.567
50_D53_Y0.270490.563
12_A15_L0.270280.563
13_G67_S0.269180.561
33_S38_P0.268060.558
3_Y53_Y0.26760.557
15_L34_I0.267560.557
28_V53_Y0.267390.557
13_G65_I0.263090.548
27_E50_D0.260520.543
31_V45_V0.260510.543
9_F12_A0.25920.540
53_Y56_R0.259070.540
28_V57_I0.257030.535
7_V61_S0.25240.526
67_S72_G0.252270.525
8_Y37_D0.252180.525
20_P68_S0.248250.517
67_S70_L0.24270.506
39_D51_P0.238880.498
39_D44_R0.237920.496
51_P59_D0.234910.489
37_D46_T0.234520.488
14_G34_I0.233030.485
15_L71_L0.232810.485
61_S65_I0.231830.483
53_Y57_I0.231130.481
56_R60_D0.230040.479
66_R73_E0.229720.478
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
1yx2A0.925965.70.809
3ttgA0.901254.20.821
2j5uA0.9506490.826
1v5vA0.938347.40.828
3tfiA0.901245.20.83
3girA0.938344.40.831
2xyyA0.950639.40.835
2qf4A0.950638.80.836
2gagA0.938336.20.839
1pj5A0.925933.90.841
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