GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BMFP - Membrane fusogenic activity
Pfam: PF04380 (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: 79
Sequences: 458
Seq/Len: 5.8
HH_delta: 0.828 (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
59_L62_T0.333542.235
55_Q59_L0.293871.969
29_I33_I0.289741.941
65_K70_E0.2871.923
64_E68_A0.269441.805
58_V62_T0.261891.755
72_R77_E0.260631.746
41_L46_L0.259191.737
70_E74_A0.257141.723
40_A44_L0.251321.684
26_R30_E0.237741.593
73_L76_L0.230431.544
26_R56_K0.211891.420
15_I33_I0.210691.412
47_V52_F0.205981.380
6_K9_D0.201971.353
60_A64_E0.201861.353
58_V61_R0.199091.334
3_D6_K0.191951.286
72_R76_L0.188611.264
52_F62_T0.183761.231
75_A78_A0.183241.228
55_Q62_T0.179961.206
62_T66_L0.179071.200
38_Q42_S0.178071.193
71_A75_A0.173921.165
25_P29_I0.172651.157
49_R53_D0.172231.154
2_Q6_K0.172071.153
75_A79_Q0.166551.116
62_T65_K0.163871.098
34_R38_Q0.163611.096
52_F63_R0.163011.092
53_D57_A0.162041.086
58_V63_R0.160781.077
55_Q58_V0.157961.058
58_V66_L0.157291.054
34_R45_D0.156811.051
42_S73_L0.155261.040
28_E31_K0.153721.030
26_R34_R0.147480.988
19_L34_R0.146550.982
54_A57_A0.146060.979
7_I79_Q0.144580.969
14_Q32_N0.144070.965
33_I37_L0.143450.961
41_L61_R0.143320.960
30_E76_L0.142910.958
52_F55_Q0.142340.954
58_V65_K0.142340.954
24_G71_A0.141580.949
43_K79_Q0.139690.936
32_N35_A0.139150.932
15_I20_P0.138150.926
55_Q65_K0.138110.925
13_K72_R0.135410.907
53_D58_V0.135350.907
73_L77_E0.13340.894
12_A36_R0.131660.882
33_I42_S0.131480.881
2_Q7_I0.131280.880
53_D61_R0.130110.872
17_E23_Q0.128960.864
15_I19_L0.128870.864
69_L76_L0.127020.851
43_K59_L0.126340.847
68_A71_A0.122730.822
36_R48_T0.120690.809
9_D40_A0.120040.804
53_D56_K0.120.804
14_Q41_L0.118660.795
11_L64_E0.117660.788
24_G28_E0.117220.785
21_A24_G0.116520.781
28_E54_A0.115870.776
21_A28_E0.115850.776
17_E22_A0.115730.775
45_D58_V0.115570.774
74_A79_Q0.115470.774
49_R61_R0.114760.769
9_D26_R0.113850.763
13_K17_E0.113540.761
4_P38_Q0.11330.759
16_S56_K0.112870.756
8_F57_A0.112410.753
41_L53_D0.111770.749
50_E76_L0.111390.746
29_I61_R0.111260.746
57_A72_R0.111160.745
10_D56_K0.111150.745
60_A71_A0.110940.743
18_A25_P0.110160.738
28_E43_K0.109820.736
71_A78_A0.109370.733
49_R63_R0.109290.732
21_A25_P0.108650.728
35_A39_S0.108520.727
52_F65_K0.10830.726
48_T51_E0.108020.724
29_I68_A0.107640.721
53_D68_A0.106950.717
56_K60_A0.106810.716
17_E21_A0.10680.716
3_D20_P0.106650.715
63_R67_E0.106380.713
19_L58_V0.106010.710
23_Q32_N0.105560.707
66_L70_E0.104290.699
56_K78_A0.103970.697
49_R52_F0.103360.693
21_A27_E0.103360.693
7_I11_L0.102630.688
45_D51_E0.102620.688
47_V55_Q0.102320.686
15_I69_L0.102090.684
15_I66_L0.101860.683
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
4gifA0.4557720.828
1dipA0.468469.70.831
1go4E0.51966.50.834
3p8qA0.8861640.837
2yy0A0.607662.70.838
3hrnA0.44362.50.838
3qneA0.9873610.84
3te3A0.455751.20.848
3vkgA0.924150.50.849
1lwuB0.683550.20.85
If you are interested in a protein containing this domain,
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