GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Sec20 - Sec20
Pfam: PF03908 (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: 92
Sequences: 1013
Seq/Len: 11.01
HH_delta: 0.461 (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_R0.313292.107
80_F84_V0.2911.957
74_F78_L0.261421.758
77_F80_F0.256041.722
53_K56_R0.254571.712
71_I75_F0.247431.664
24_S28_L0.244531.645
52_L55_S0.226041.520
20_E23_R0.22561.517
8_E11_R0.218241.468
13_T16_M0.2121.426
33_E84_V0.20871.404
79_F83_V0.205711.384
15_Q19_Q0.203421.368
12_R15_Q0.202751.364
14_R18_A0.197981.332
81_L85_L0.192061.292
10_L13_T0.189881.277
19_Q59_L0.187861.264
39_R43_D0.183611.235
61_K71_I0.173071.164
77_F81_L0.172251.159
27_T30_T0.171431.153
32_E40_S0.171071.151
22_E29_Q0.170811.149
21_V36_A0.170361.146
41_T48_Q0.169571.141
35_S41_T0.166881.122
75_F79_F0.16491.109
32_E36_A0.162131.090
40_S56_R0.159261.071
16_M20_E0.157431.059
20_E34_S0.15571.047
12_R78_L0.152661.027
44_E65_R0.151911.022
47_G50_S0.151251.017
13_T23_R0.1511.016
29_Q32_E0.149491.005
39_R46_D0.149371.005
53_K65_R0.148951.002
25_E29_Q0.148370.998
46_D60_K0.148240.997
60_K63_E0.147690.993
27_T74_F0.147590.993
73_I77_F0.146880.988
69_D72_L0.14620.983
55_S66_D0.145390.978
40_S44_E0.144870.974
10_L17_M0.142190.956
21_V25_E0.142170.956
13_T20_E0.141520.952
36_A40_S0.140560.945
11_R14_R0.139410.938
51_L73_I0.138660.933
22_E26_L0.138060.929
8_E12_R0.137680.926
80_F83_V0.13760.926
8_E17_M0.136190.916
51_L82_L0.136140.916
68_T74_F0.135780.913
82_L85_L0.135760.913
39_R50_S0.134490.905
35_S65_R0.133470.898
30_T64_R0.132450.891
78_L82_L0.132120.889
36_A55_S0.132040.888
57_K68_T0.131850.887
42_N55_S0.130360.877
58_L73_I0.130120.875
56_R63_E0.128960.867
65_R72_L0.126510.851
43_D57_K0.126130.848
22_E41_T0.126070.848
22_E59_L0.125830.846
68_T72_L0.125520.844
79_F84_V0.125380.843
31_L45_Y0.124140.835
20_E45_Y0.123720.832
16_M25_E0.123520.831
24_S86_Y0.122950.827
42_N48_Q0.122030.821
32_E44_E0.121650.818
63_E67_K0.12140.817
66_D70_R0.121360.816
58_L66_D0.119840.806
60_K71_I0.119670.805
29_Q47_G0.119650.805
11_R54_K0.119570.804
69_D76_A0.119560.804
50_S58_L0.118950.800
46_D78_L0.11860.798
27_T33_E0.118430.797
22_E25_E0.117730.792
62_L69_D0.117540.791
19_Q86_Y0.117420.790
56_R60_K0.117120.788
26_L29_Q0.116970.787
33_E37_T0.116850.786
30_T34_S0.116350.783
16_M22_E0.116090.781
17_M20_E0.1160.780
36_A42_N0.115860.779
76_A80_F0.115560.777
72_L75_F0.11530.776
46_D49_S0.114590.771
22_E57_K0.114590.771
47_G57_K0.114350.769
78_L86_Y0.114210.768
9_S69_D0.114190.768
21_V80_F0.1140.767
23_R47_G0.113890.766
17_M54_K0.113110.761
10_L19_Q0.11280.759
10_L14_R0.11270.758
8_E33_E0.112630.758
19_Q23_R0.112560.757
22_E27_T0.112040.754
60_K72_L0.111960.753
77_F83_V0.111120.747
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
2npsC0.760998.50.461
1gl2C0.695798.20.514
1n7sC0.695797.80.569
2kogA197.10.635
1nhlA0.587970.643
1l4aC0.695796.90.647
3b5nC0.717496.10.68
3hd7B196.10.681
3hd7A0.967495.80.69
1sfcD0.717494.90.709

Page generated in 0.0518 seconds.