GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PepSY_TM_2 - PepSY-associated TM helix
Pfam: PF13703 (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: CL0490
Length: 88
Sequences: 1614
Seq/Len: 18.34
HH_delta: 0.858 (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
28_L76_L0.431872.163
22_I26_L0.409522.051
27_L79_A0.369561.851
7_R17_R0.363781.822
5_L10_L0.36231.815
3_Y7_R0.337221.689
4_N8_N0.303051.518
67_L71_F0.293821.472
25_L83_L0.290811.457
47_F51_P0.29081.457
59_R62_D0.28061.406
40_P48_S0.273151.368
31_L76_L0.270611.355
14_T18_W0.269261.349
20_V24_A0.268441.345
9_L16_G0.266111.333
52_K56_S0.264011.322
61_F65_R0.26361.320
28_L80_L0.261881.312
28_L79_A0.259911.302
33_S61_F0.252331.264
21_G25_L0.24711.238
31_L72_L0.245391.229
24_A83_L0.243741.221
32_I76_L0.24051.205
14_T19_I0.238721.196
25_L29_L0.237241.188
74_F78_I0.232171.163
62_D65_R0.229291.149
10_L78_I0.22561.130
7_R86_S0.224891.126
21_G26_L0.2221.112
46_F50_R0.221621.110
78_I85_F0.221091.107
40_P62_D0.218331.094
30_L60_W0.216491.084
83_L86_S0.21471.075
40_P44_R0.214091.072
8_N16_G0.20981.051
3_Y25_L0.207191.038
66_V70_W0.207181.038
35_L39_W0.206821.036
30_L39_W0.20521.028
52_K59_R0.203951.022
31_L79_A0.20111.007
34_G82_G0.200531.004
38_W42_R0.200441.004
47_F52_K0.198470.994
9_L20_V0.19820.993
1_F4_N0.195470.979
8_N12_G0.19470.975
3_Y78_I0.192790.966
17_R86_S0.190090.952
11_L14_T0.189370.949
46_F49_L0.188920.946
22_I25_L0.188590.945
20_V86_S0.187270.938
19_I23_L0.187220.938
79_A83_L0.184620.925
52_K62_D0.184350.923
62_D66_V0.183590.920
28_L33_S0.183070.917
10_L70_W0.183010.917
24_A85_F0.182190.913
45_W48_S0.1780.892
31_L62_D0.177390.889
71_F75_L0.174070.872
30_L33_S0.17390.871
18_W67_L0.173650.870
42_R46_F0.172720.865
27_L31_L0.172440.864
4_N17_R0.172320.863
26_L84_F0.171640.860
44_R47_F0.171630.860
22_I29_L0.171410.859
47_F50_R0.170850.856
4_N81_T0.170470.854
25_L78_I0.170150.852
29_L76_L0.170040.852
77_V80_L0.169080.847
38_W69_L0.168390.843
7_R21_G0.167040.837
30_L65_R0.165410.829
67_L77_V0.16540.828
1_F10_L0.163890.821
2_L71_F0.161540.809
51_P66_V0.159780.800
27_L86_S0.159710.800
1_F80_L0.15960.799
8_N81_T0.15940.798
3_Y85_F0.158040.792
31_L47_F0.157030.787
12_G21_G0.155950.781
49_L56_S0.155810.780
27_L81_T0.155620.780
11_L18_W0.15530.778
19_I76_L0.155180.777
32_I36_Y0.154990.776
36_Y65_R0.154610.774
21_G85_F0.153980.771
65_R85_F0.153920.771
10_L68_G0.153660.770
41_R45_W0.153660.770
49_L53_R0.152770.765
20_V27_L0.152260.763
63_L67_L0.151110.757
57_K60_W0.150760.755
41_R49_L0.150610.754
35_L76_L0.150080.752
48_S57_K0.147730.740
38_W41_R0.146950.736
72_L75_L0.146240.733
2_L78_I0.145340.728
8_N11_L0.145070.727
53_R65_R0.145050.727
48_S53_R0.14490.726
30_L37_L0.144640.725
32_I62_D0.144640.725
38_W82_G0.144040.721
35_L72_L0.143680.720
27_L75_L0.143560.719
49_L62_D0.143440.718
5_L12_G0.142970.716
45_W49_L0.141490.709
13_G18_W0.140320.703
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
2l2tA0.488628.40.858
2ks1B0.488618.90.869
4h44A0.647712.80.878
2jwaA0.4659100.883
1fgjA0.52277.70.889
2wdqC0.42056.90.891
1iijA0.39776.30.893
4he8J0.61366.30.893
3hb3B0.78416.10.894
1cd1A0.52275.50.896
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.063 seconds.