GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
V-SNARE_C - Snare region anchored in the vesicle membrane C-terminus
Pfam: PF12352 (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: CL0147
Length: 66
Sequences: 844
Seq/Len: 12.79
HH_delta: 0.051 (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
9_S12_R0.313141.809
40_R44_K0.298451.724
8_D11_Q0.294441.701
20_T23_I0.289331.671
60_K63_S0.256871.484
53_P56_N0.243761.408
52_L55_S0.241131.393
35_R45_L0.224051.294
14_H18_D0.223221.289
36_E40_R0.222371.284
16_M25_A0.221091.277
30_D33_S0.215351.244
53_P58_L0.209021.207
12_R15_R0.207841.200
19_E59_L0.206171.191
21_E25_A0.204551.181
6_E53_P0.202741.171
39_K43_D0.202591.170
35_R39_K0.201321.163
58_L63_S0.199711.154
16_M20_T0.195641.130
16_M19_E0.192281.111
17_A63_S0.191331.105
24_G51_N0.185931.074
24_G28_L0.184791.067
27_T33_S0.183031.057
34_Q38_L0.181441.048
19_E22_E0.181211.047
4_L8_D0.177771.027
15_R19_E0.177091.023
49_D52_L0.176361.019
13_S16_M0.176281.018
26_A29_E0.17180.992
18_D21_E0.171690.992
22_E59_L0.171530.991
22_E26_A0.171460.990
10_L24_G0.169910.981
48_I51_N0.169340.978
38_L49_D0.169190.977
46_D60_K0.168840.975
39_K50_S0.168640.974
58_L62_I0.166350.961
35_R50_S0.165590.956
5_R23_I0.165230.954
8_D46_D0.164590.951
18_D29_E0.164020.947
35_R42_R0.163740.946
41_V45_L0.163370.944
40_R56_N0.16140.932
22_E44_K0.159720.923
31_L49_D0.159330.920
56_N60_K0.157250.908
50_S56_N0.15690.906
7_S37_Q0.156840.906
54_K63_S0.154940.895
27_T37_Q0.154750.894
39_K42_R0.153990.889
8_D12_R0.153730.888
32_R44_K0.152030.878
55_S58_L0.151980.878
41_V46_D0.151430.875
13_S23_I0.150740.871
9_S38_L0.150360.868
35_R41_V0.150190.867
17_A43_D0.149880.866
10_L14_H0.149490.863
30_D34_Q0.148750.859
29_E59_L0.147770.854
51_N55_S0.147740.853
28_L45_L0.147680.853
49_D53_P0.147420.851
9_S13_S0.143220.827
19_E23_I0.143090.826
47_D50_S0.142890.825
12_R62_I0.14230.822
59_L62_I0.140310.810
15_R20_T0.138370.799
13_S20_T0.138130.798
61_R64_R0.138130.798
22_E48_I0.137150.792
57_S61_R0.135650.784
22_E25_A0.13550.783
14_H64_R0.135140.781
33_S37_Q0.132240.764
38_L41_V0.132180.763
55_S64_R0.131980.762
10_L56_N0.131590.760
39_K46_D0.13140.759
28_L53_P0.131320.758
29_E61_R0.130190.752
6_E59_L0.1290.745
6_E21_E0.128460.742
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
2npsC199.20.051
1gl2C0.969799.10.077
1n7sC0.969798.80.185
1nhlA0.818298.40.304
1l4aC0.969798.20.341
3b5nC197.80.419
1l4aD0.9848870.684
2npsD186.40.687
1gl2D0.969783.70.698
3b5nD0.939482.90.7

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