GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
WXG100 - Proteins of 100 residues with WXG
Pfam: PF06013 (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: CL0352
Length: 86
Sequences: 1943
Seq/Len: 22.59
HH_delta: 0.002 (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_Q75_R0.866333.716
10_R82_E0.691462.966
13_A71_S0.517182.218
13_A78_A0.439531.885
7_E11_A0.431541.851
24_Q68_E0.422321.812
10_R79_Q0.417131.789
46_A50_Q0.401681.723
16_L67_L0.400871.720
5_D8_Q0.395761.698
20_A71_S0.365051.566
49_F53_F0.359971.544
10_R78_A0.355291.524
24_Q64_N0.339711.457
6_P82_E0.337071.446
20_A64_N0.336111.442
61_R65_E0.324221.391
13_A75_R0.312581.341
17_Q71_S0.312031.338
79_Q83_Q0.303011.300
18_A22_E0.29771.277
30_L49_F0.294981.265
71_S75_R0.291371.250
41_W45_A0.280521.203
77_A81_Y0.278261.194
22_E25_S0.273951.175
66_A69_E0.266681.144
64_N68_E0.264531.135
28_Q32_S0.262311.125
10_R14_Q0.256681.101
47_D50_Q0.25081.076
42_Q46_A0.249411.070
8_Q11_A0.24691.059
14_Q18_A0.246321.057
42_Q62_Q0.244061.047
30_L41_W0.238471.023
78_A82_E0.237961.021
72_Q76_Q0.234331.005
6_P78_A0.233161.000
24_Q28_Q0.232220.996
32_S35_D0.229840.986
11_A26_Q0.229730.985
25_S32_S0.229380.984
72_Q75_R0.228310.979
27_L60_F0.225730.968
25_S65_E0.220760.947
16_L19_Q0.220150.944
75_R79_Q0.217820.934
31_E57_N0.215380.924
41_W49_F0.211880.909
9_L77_A0.209030.897
51_D55_E0.206940.888
13_A17_Q0.20620.885
38_Q50_Q0.206030.884
55_E59_A0.205280.881
30_L42_Q0.205080.880
15_Q18_A0.200190.859
31_E35_D0.19880.853
21_D25_S0.198740.853
52_K81_Y0.196820.844
68_E72_Q0.196220.842
21_D68_E0.193240.829
10_R75_R0.193190.829
18_A21_D0.191080.820
8_Q15_Q0.19090.819
26_Q29_Q0.188620.809
8_Q12_A0.187260.803
17_Q68_E0.186980.802
35_D39_A0.186510.800
12_A74_L0.185330.795
62_Q69_E0.185020.794
39_A42_Q0.184050.789
65_E69_E0.181950.780
56_W60_F0.181420.778
52_K55_E0.181090.777
76_Q79_Q0.180810.776
52_K59_A0.180110.773
11_A14_Q0.179520.770
47_D51_D0.179060.768
72_Q79_Q0.177690.762
49_F66_A0.175950.755
28_Q61_R0.175550.753
23_L63_L0.175420.752
12_A15_Q0.174110.747
24_Q61_R0.173710.745
74_L78_A0.172560.740
57_N61_R0.17240.740
21_D28_Q0.171890.737
80_N83_Q0.171150.734
30_L34_I0.170560.732
19_Q55_E0.169560.727
11_A18_A0.169530.727
6_P81_Y0.168990.725
11_A15_Q0.168090.721
62_Q65_E0.167550.719
66_A70_L0.167180.717
11_A68_E0.166940.716
9_L37_L0.166790.715
21_D24_Q0.163830.703
44_E47_D0.163060.699
12_A30_L0.162730.698
33_S36_S0.162370.696
30_L57_N0.159720.685
9_L32_S0.159590.685
57_N60_F0.159260.683
46_A56_W0.158820.681
19_Q22_E0.157750.677
37_L67_L0.157220.674
48_A52_K0.154350.662
6_P53_F0.154230.662
22_E33_S0.152940.656
9_L26_Q0.152720.655
43_G49_F0.152680.655
27_L64_N0.151160.648
77_A80_N0.149440.641
49_F70_L0.149430.641
65_E79_Q0.149050.639
16_L56_W0.148570.637
7_E76_Q0.148270.636
15_Q76_Q0.148260.636
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
4j42A199.20.002
3zbhA199.10.03
3favB199.10.034
3favA199.10.035
3gwkC199.10.039
2vs0A199.10.041
4ioeA199.10.057
3h6pC199.10.062
4i0xB1990.065
4i0xA0.9535990.103

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