GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2231 - Predicted membrane protein (DUF2231)
Pfam: PF09990 (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: 104
Sequences: 591
Seq/Len: 5.68
HH_delta: 0.847 (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
54_F83_G0.295662.659
47_G90_T0.192641.733
10_V62_W0.182831.644
46_L90_T0.172621.553
23_G43_H0.17171.544
91_G95_G0.171411.542
50_A90_T0.17021.531
61_R80_S0.166221.495
39_V93_L0.163671.472
30_V36_A0.163011.466
55_L62_W0.160571.444
6_F10_V0.156261.405
76_G80_S0.154741.392
16_A51_L0.15451.390
27_L40_A0.153561.381
11_L14_L0.152691.373
7_W77_L0.149361.343
20_V51_L0.141571.273
26_D40_A0.140311.262
12_G87_L0.140221.261
14_L18_V0.139471.254
25_V98_V0.136921.232
61_R76_G0.128281.154
27_L61_R0.127541.147
47_G50_A0.126841.141
21_L49_V0.126651.139
68_D76_G0.126631.139
27_L30_V0.124961.124
26_D45_I0.124121.116
40_A47_G0.122441.101
54_F87_L0.122361.101
43_H47_G0.120141.081
13_L55_L0.119921.079
64_W79_L0.118891.069
53_L78_A0.11871.068
24_F48_L0.118621.067
14_L63_L0.118251.064
55_L63_L0.118221.063
34_P54_F0.117591.058
14_L85_V0.11751.057
21_L74_P0.1171.052
12_G97_L0.116481.048
38_R47_G0.115361.038
14_L72_V0.114991.034
30_V34_P0.114961.034
17_I63_L0.114181.027
9_L14_L0.114141.027
81_L88_L0.114111.026
81_L85_V0.11411.026
37_H53_L0.112951.016
75_F78_A0.112721.014
62_W77_L0.112611.013
29_T50_A0.112071.008
20_V47_G0.111271.001
78_A98_V0.109660.986
72_V76_G0.10940.984
12_G16_A0.109130.982
51_L84_V0.109130.982
15_G36_A0.108970.980
18_V22_T0.108940.980
70_R79_L0.106470.958
27_L41_W0.106260.956
35_P77_L0.105640.950
25_V44_A0.105150.946
56_L78_A0.105110.945
63_L66_R0.104540.940
25_V29_T0.104090.936
22_T95_G0.103210.928
55_L66_R0.103130.928
52_G56_L0.102150.919
9_L50_A0.101840.916
43_H94_G0.101250.911
24_F44_A0.100920.908
36_A85_V0.100480.904
8_L76_G0.100160.901
27_L44_A0.098420.885
16_A19_A0.098280.884
20_V24_F0.097530.877
86_L90_T0.097450.877
25_V85_V0.097390.876
27_L80_S0.097180.874
22_T66_R0.09690.872
65_R68_D0.09680.871
54_F61_R0.096490.868
3_D6_F0.094830.853
91_G94_G0.094280.848
17_I20_V0.094220.847
75_F88_L0.094060.846
11_L66_R0.093730.843
17_I48_L0.093030.837
4_A76_G0.092660.833
37_H85_V0.092120.829
5_A8_L0.092030.828
25_V87_L0.091210.820
23_G94_G0.091160.820
26_D30_V0.090870.817
22_T77_L0.090320.812
8_L98_V0.090160.811
33_G86_L0.090150.811
4_A51_L0.090040.810
53_L71_A0.089930.809
68_D71_A0.089710.807
66_R81_L0.089150.802
30_V90_T0.089090.801
17_I77_L0.089040.801
77_L89_V0.088790.799
38_R42_L0.088260.794
50_A86_L0.088180.793
67_R78_A0.088120.793
62_W79_L0.087980.791
86_L89_V0.087630.788
62_W65_R0.087370.786
20_V50_A0.086870.781
52_G82_L0.086860.781
37_H98_V0.086740.780
36_A84_V0.086640.779
70_R81_L0.08660.779
29_T34_P0.086570.779
19_A87_L0.08650.778
67_R71_A0.08620.775
82_L86_L0.085560.770
12_G54_F0.085540.769
11_L70_R0.08550.769
8_L12_G0.085280.767
34_P41_W0.085180.766
55_L64_W0.085050.765
6_F81_L0.085020.765
28_L43_H0.084960.764
46_L80_S0.084860.763
29_T87_L0.084810.763
23_G26_D0.084310.758
26_D47_G0.084080.756
19_A23_G0.084020.756
20_V48_L0.083880.754
69_P77_L0.083210.748
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
3ayfA0.961538.80.847
3o0rB0.8942190.868
4ev6A0.62517.60.87
4gd3A0.942315.90.872
4i0uA0.62515.50.872
2iubA0.615415.20.873
1fftA0.971290.885
2yevA17.30.889
1fftC0.99046.20.892
3mk7A0.90385.90.893
If you are interested in a protein containing this domain,
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