GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2404 - Putative integral membrane protein conserved region (DUF2404)
Pfam: PF10296 (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: 91
Sequences: 701
Seq/Len: 7.7
HH_delta: 0.856 (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
34_L38_L0.306372.551
57_N74_D0.294752.454
9_F12_R0.243272.026
19_D23_E0.178461.486
59_R74_D0.174361.452
44_T86_E0.173861.448
62_D66_D0.164461.369
24_K28_K0.163381.360
20_K24_K0.160551.337
60_I72_E0.159041.324
80_G83_L0.158691.321
29_L39_D0.156761.305
19_D47_D0.150951.257
22_K26_Q0.149171.242
61_P72_E0.146471.220
27_K33_K0.144721.205
33_K75_V0.144691.205
64_D74_D0.144481.203
56_S74_D0.144161.200
82_S85_L0.143531.195
21_I47_D0.14321.192
33_K50_D0.140951.174
50_D75_V0.138361.152
59_R72_E0.136771.139
29_L41_I0.136541.137
11_F85_L0.135651.130
31_K36_S0.135571.129
50_D80_G0.13451.120
72_E76_S0.133521.112
11_F77_Y0.131811.098
55_I75_V0.128251.068
17_F39_D0.127631.063
13_R18_R0.126731.055
63_L79_G0.126091.050
16_A55_I0.124831.039
30_N87_T0.123961.032
59_R62_D0.123191.026
16_A73_F0.122161.017
20_K47_D0.12151.012
69_L72_E0.118750.989
45_E50_D0.118590.988
23_E48_L0.116940.974
20_K25_L0.116850.973
11_F17_F0.116750.972
39_D87_T0.115030.958
9_F18_R0.115020.958
64_D67_G0.114640.955
41_I60_I0.114490.953
10_D45_E0.114330.952
28_K31_K0.113130.942
40_E44_T0.113080.942
50_D83_L0.110620.921
16_A20_K0.11060.921
34_L66_D0.109220.909
33_K64_D0.109180.909
9_F46_L0.108990.908
39_D78_S0.107650.896
13_R75_V0.107150.892
54_I85_L0.107020.891
11_F33_K0.106760.889
12_R17_F0.106590.888
58_V67_G0.106110.884
57_N75_V0.105930.882
77_Y81_F0.105610.879
47_D54_I0.105540.879
52_P81_F0.10550.879
55_I64_D0.104730.872
15_E19_D0.104710.872
10_D43_V0.103270.860
12_R75_V0.103270.860
26_Q30_N0.10290.857
30_N55_I0.102550.854
13_R26_Q0.102350.852
61_P73_F0.10230.852
28_K34_L0.102140.851
13_R55_I0.101880.848
78_S83_L0.101830.848
10_D52_P0.101610.846
58_V71_I0.101490.845
11_F16_A0.101280.843
59_R78_S0.101020.841
26_Q77_Y0.100720.839
16_A21_I0.100490.837
13_R80_G0.100230.835
38_L41_I0.098630.821
60_I78_S0.098030.816
58_V72_E0.097950.816
30_N76_S0.097860.815
24_K53_P0.097850.815
79_G83_L0.097070.808
30_N43_V0.097060.808
36_S46_L0.097040.808
24_K77_Y0.097020.808
35_P81_F0.097010.808
58_V69_L0.096790.806
18_R38_L0.095870.798
44_T84_T0.095740.797
54_I69_L0.095620.796
21_I24_K0.095270.793
62_D65_P0.095210.793
22_K64_D0.095080.792
56_S76_S0.094740.789
27_K66_D0.094480.787
35_P86_E0.094040.783
37_F75_V0.093860.782
35_P39_D0.093770.781
20_K45_E0.093170.776
22_K74_D0.093140.776
15_E37_F0.093110.775
17_F80_G0.092840.773
13_R40_E0.092810.773
29_L35_P0.092440.770
65_P82_S0.092370.769
18_R81_F0.092330.769
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
2obdA0.956420.856
1ewfA0.956300.866
2ag4A0.60448.20.895
2k60A0.85717.20.898
3bwtA0.50556.80.898
1qwzA0.91216.80.899
3bu8A0.93415.70.902
2wwq50.65935.40.903
3rwnA0.46155.10.904
2dyjA0.857150.904
If you are interested in a protein containing this domain,
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