GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MDMPI_C - MDMPI C-terminal domain
Pfam: PF07398 (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: CL0311
Length: 82
Sequences: 520
Seq/Len: 6.34
HH_delta: 0.51 (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
53_T56_D0.31162.423
51_R72_E0.267852.083
37_H49_T0.25361.972
52_G71_L0.225171.751
2_L7_V0.218341.698
11_L54_A0.197851.539
33_T56_D0.194741.515
13_F63_G0.191231.487
8_D41_A0.186631.451
52_G57_L0.180861.407
14_F62_W0.180551.404
49_T74_D0.179321.395
3_A6_G0.169531.318
3_A9_E0.168231.308
6_G9_E0.165541.287
7_V54_A0.164871.282
6_G58_L0.162911.267
44_D49_T0.160671.250
34_V40_D0.156161.214
14_F17_R0.1541.198
33_T47_D0.153551.194
9_E62_W0.152791.188
2_L58_L0.14531.130
4_A8_D0.144421.123
6_G62_W0.143911.119
14_F61_L0.142451.108
50_V60_W0.141931.104
8_D12_D0.139511.085
66_P69_D0.139421.084
53_T57_L0.134521.046
31_G61_L0.13431.044
37_H44_D0.133221.036
4_A44_D0.130241.013
16_P62_W0.129541.007
47_D74_D0.128390.998
65_L69_D0.127430.991
13_F62_W0.125560.976
60_W71_L0.125540.976
32_R35_R0.12540.975
5_D9_E0.124540.969
47_D73_V0.124410.968
30_G33_T0.123350.959
14_F63_G0.122850.955
37_H51_R0.122840.955
38_A42_G0.122470.952
16_P63_G0.122410.952
11_L57_L0.11990.932
10_F63_G0.119660.931
7_V58_L0.119620.930
11_L19_A0.119460.929
36_L57_L0.118610.922
65_L76_D0.11850.922
19_A46_P0.117790.916
17_R20_G0.117140.911
75_G79_L0.116630.907
17_R42_G0.115150.896
34_V38_A0.114120.888
50_V63_G0.113760.885
3_A76_D0.113390.882
35_R49_T0.113380.882
10_F58_L0.11290.878
52_G61_L0.112670.876
6_G59_L0.111650.868
5_D8_D0.111650.868
12_D43_A0.110660.861
50_V66_P0.110470.859
4_A53_T0.109120.849
13_F17_R0.108770.846
54_A57_L0.108250.842
39_T53_T0.107780.838
41_A44_D0.107120.833
28_L45_W0.10650.828
5_D75_G0.105040.817
33_T73_V0.104820.815
68_D76_D0.104680.814
12_D50_V0.104640.814
30_G75_G0.104630.814
6_G67_P0.10460.813
39_T74_D0.104130.810
17_R34_V0.103930.808
68_D77_A0.103760.807
9_E52_G0.103650.806
73_V79_L0.102410.796
25_V37_H0.102290.796
36_L72_E0.10220.795
20_G26_L0.100950.785
73_V76_D0.100820.784
37_H78_A0.100650.783
18_R50_V0.09980.776
17_R62_W0.09980.776
41_A54_A0.099720.776
67_P71_L0.098870.769
43_A53_T0.098150.763
13_F65_L0.098050.763
20_G52_G0.097840.761
29_T41_A0.097460.758
67_P73_V0.0970.754
56_D65_L0.0970.754
48_V74_D0.096850.753
6_G18_R0.095350.742
53_T71_L0.095320.741
12_D55_S0.095060.739
3_A13_F0.094780.737
18_R55_S0.094490.735
60_W67_P0.094440.734
20_G47_D0.093340.726
42_G54_A0.093120.724
3_A77_A0.09280.722
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
2nsfA0.87897.40.51
2qztA119.60.819
1iktA0.9756150.828
1c44A114.80.828
3cnuA0.902480.846
2yheA16.30.854
2cfuA0.95125.20.858
3bkrA0.96344.50.863
1pz4A0.92683.50.869
3u2aA0.5612.50.878
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0284 seconds.