GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SNARE - SNARE domain
Pfam: PF05739 (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: CL0445
Length: 63
Sequences: 2200
Seq/Len: 34.92
HH_delta: -0.008 (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
17_K21_Q0.530141.990
24_G28_E0.509311.912
50_K54_K0.498531.871
4_E7_D0.427981.606
53_K56_K0.419731.575
36_R39_D0.413791.553
39_D43_R0.406371.525
37_I40_N0.403091.513
7_D10_E0.392311.473
5_E8_E0.357521.342
50_K53_K0.354941.332
44_A47_N0.353681.328
25_E28_E0.339791.275
12_S16_L0.335921.261
12_S15_E0.335321.259
22_D30_Q0.335061.258
31_N34_L0.333751.253
23_I54_K0.32811.232
25_E29_E0.318961.197
45_N49_K0.315511.184
32_E36_R0.309941.163
24_G27_V0.306851.152
52_N56_K0.297611.117
31_N35_D0.295681.110
3_D26_E0.294231.104
53_K57_K0.291581.094
9_L16_L0.278891.047
15_E18_Q0.277151.040
45_N48_L0.271671.020
20_F26_E0.263140.988
28_E32_E0.262850.987
32_E35_D0.260570.978
9_L60_K0.260370.977
35_D38_E0.25960.974
10_E44_A0.257350.966
22_D25_E0.251130.943
23_I27_V0.249670.937
51_G55_L0.248090.931
31_N55_L0.247130.928
8_E11_Q0.246140.924
35_D39_D0.242680.911
5_E40_N0.242660.911
16_L24_G0.240760.904
13_I33_M0.239980.901
3_D6_L0.239970.901
2_R19_M0.239650.900
33_M38_E0.239060.897
48_L51_G0.235440.884
7_D11_Q0.233130.875
2_R20_F0.229190.860
12_S52_N0.228630.858
4_E50_K0.228040.856
2_R12_S0.227660.855
56_K59_L0.227590.854
49_K57_K0.22660.851
46_E53_K0.225430.846
45_N52_N0.222230.834
21_Q25_E0.217210.815
42_D59_L0.217090.815
13_I21_Q0.21640.812
55_L58_A0.216150.811
3_D7_D0.216050.811
42_D46_E0.214850.806
2_R15_E0.213910.803
57_K60_K0.213490.801
51_G58_A0.212660.798
45_N59_L0.212630.798
6_L59_L0.210910.792
33_M40_N0.209740.787
14_Q18_Q0.209140.785
18_Q22_D0.207850.780
17_K56_K0.207140.777
46_E49_K0.207030.777
54_K57_K0.20690.777
6_L13_I0.206830.776
11_Q14_Q0.204590.768
36_R48_L0.20440.767
11_Q18_Q0.203710.765
43_R50_K0.202010.758
55_L59_L0.200640.753
23_I41_V0.200510.753
16_L19_M0.197920.743
51_G54_K0.19760.742
12_S39_D0.19750.741
18_Q23_I0.196760.739
33_M56_K0.196650.738
43_R46_E0.196630.738
15_E19_M0.194710.731
29_E54_K0.193630.727
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
3hd7B199-0.008
2xheB199-0.008
1dn1B1990.008
2npsB1990.014
3b5nB1990.015
1sfcB198.90.022
1jthB198.90.022
2npsD198.80.085
1l4aD0.968398.80.093
1n7sB0.952498.80.096

Page generated in 0.029 seconds.