GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Conotoxin - Conotoxin
Pfam: PF02950 (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: CL0083
Length: 75
Sequences: 351
Seq/Len: 4.68
HH_delta: 0.768 (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
51_T55_S0.223651.739
51_T63_E0.199191.549
11_V15_T0.194491.512
52_P55_S0.174171.354
45_K48_R0.170611.327
9_V37_D0.168021.306
63_E66_S0.163831.274
67_G70_N0.163771.273
55_S63_E0.161181.253
66_S70_N0.160111.245
38_R42_A0.159671.242
54_G68_S0.159231.238
62_S67_G0.15771.226
8_I12_L0.156251.215
54_G67_G0.155991.213
51_T56_Y0.153731.195
59_K66_S0.150071.167
61_N67_G0.14711.144
26_Q39_R0.146631.140
55_S62_S0.145671.133
18_A21_D0.145451.131
40_S44_S0.144781.126
18_A27_P0.143181.113
50_C57_C0.142941.111
29_D41_S0.136871.064
53_P56_Y0.135671.055
49_R70_N0.13561.054
15_T20_A0.133051.035
56_Y63_E0.13261.031
63_E68_S0.131421.022
26_Q32_A0.13111.019
56_Y59_K0.130981.018
22_L26_Q0.129821.009
6_V11_V0.129821.009
5_C19_T0.128771.001
33_R39_R0.128621.000
14_L45_K0.127950.995
59_K63_E0.126630.985
61_N66_S0.12650.984
8_I22_L0.125330.975
60_R68_S0.125180.973
63_E67_G0.125040.972
10_A20_A0.12480.970
17_L21_D0.124010.964
8_I15_T0.123940.964
5_C8_I0.122810.955
9_V15_T0.122090.949
19_T28_A0.120060.934
8_I11_V0.119940.933
61_N68_S0.119390.928
62_S68_S0.119210.927
60_R70_N0.119180.927
15_T19_T0.11850.921
12_L40_S0.118160.919
46_L49_R0.118160.919
27_P33_R0.117350.912
53_P61_N0.115390.897
49_R62_S0.115190.896
59_K67_G0.114890.893
56_Y62_S0.114720.892
6_V15_T0.114320.889
62_S66_S0.114130.887
9_V29_D0.113970.886
28_A40_S0.113440.882
51_T60_R0.113030.879
8_I19_T0.112850.877
25_D28_A0.112370.874
52_P70_N0.11180.869
21_D26_Q0.111650.868
15_T37_D0.111650.868
10_A14_L0.110960.863
5_C64_C0.11010.856
38_R41_S0.109710.853
26_Q33_R0.10840.843
49_R60_R0.107650.837
5_C29_D0.106950.832
32_A36_R0.103830.807
13_L55_S0.103670.806
29_D33_R0.10350.805
49_R67_G0.103440.804
37_D46_L0.103060.801
44_S48_R0.102740.799
8_I20_A0.102620.798
27_P37_D0.101330.788
18_A25_D0.099880.777
54_G60_R0.099620.775
49_R59_K0.099050.770
45_K63_E0.098540.766
36_R43_N0.097870.761
11_V34_R0.096320.749
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
1hvwA0.333390.80.768
1fu3A0.3690.30.771
1yz2A0.333389.10.776
1f3kA0.333388.90.777
1omcA0.333387.90.781
1fygA0.346787.40.782
1cnnA0.3467850.789
2m36A0.346783.30.793
1v4qA0.346782.70.795
1v5aA0.346779.30.802
If you are interested in a protein containing this domain,
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