GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GPW_gp25 - Gene 25-like lysozyme
Pfam: PF04965 (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. )
Length: 99
Sequences: 1331
Seq/Len: 13.44
HH_delta: 0.064 (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
10_I89_L0.533853.006
14_L57_I0.487512.745
57_I64_L0.476482.683
4_V12_Q0.36732.068
16_M31_Y0.347141.955
64_L87_G0.341951.926
30_D59_R0.303791.711
13_S17_L0.291451.641
17_L63_R0.288851.627
13_S63_R0.280871.582
68_S86_S0.278681.569
13_S61_E0.273431.540
23_G29_P0.271191.527
17_L60_F0.269851.520
50_R54_R0.258571.456
8_E11_R0.257991.453
14_L17_L0.252471.422
17_L61_E0.247811.395
18_L57_I0.245741.384
21_R24_E0.23081.300
65_K88_T0.230771.300
10_I64_L0.225731.271
9_S16_M0.222181.251
17_L31_Y0.220321.241
25_R28_R0.218331.229
24_E38_F0.217771.226
65_K90_R0.217681.226
48_A52_E0.216141.217
53_I69_V0.214131.206
17_L56_A0.211141.189
54_R58_Q0.211031.188
18_L53_I0.210491.185
69_V85_I0.206321.162
66_V69_V0.205711.158
10_I57_I0.204851.154
47_Q50_R0.197191.110
70_E86_S0.194261.094
36_L52_E0.192431.084
26_P31_Y0.192031.081
67_V88_T0.191751.080
20_T25_R0.191111.076
53_I83_F0.18981.069
28_R60_F0.188531.062
44_D62_P0.18761.056
25_R56_A0.186261.049
15_E19_N0.185091.042
46_R71_V0.18451.039
44_D47_Q0.184221.037
72_E84_T0.183611.034
25_R38_F0.178331.004
7_R93_P0.176770.995
66_V85_I0.175040.986
52_E55_E0.170620.961
29_P38_F0.168420.948
10_I61_E0.168240.947
13_S25_R0.165780.934
33_L58_Q0.163970.923
72_E75_D0.163360.920
88_T92_T0.154860.872
4_V8_E0.154690.871
30_D60_F0.154190.868
71_V83_F0.153810.866
74_D78_D0.15310.862
49_I68_S0.150410.847
13_S16_M0.150130.845
57_I85_I0.147870.833
88_T91_D0.14550.819
9_S89_L0.145070.817
73_E82_T0.145020.817
11_R15_E0.144390.813
34_P86_S0.143250.807
41_I45_T0.143230.807
50_R69_V0.143220.807
46_R50_R0.142190.801
75_D78_D0.141320.796
9_S13_S0.140690.792
46_R65_K0.140270.790
45_T49_I0.140090.789
28_R40_P0.139840.787
46_R81_L0.13960.786
11_R90_R0.139080.783
7_R11_R0.138210.778
14_L18_L0.138130.778
43_P47_Q0.136250.767
49_I81_L0.135710.764
29_P51_R0.135460.763
4_V70_E0.134190.756
70_E84_T0.133910.754
10_I81_L0.133160.750
34_P81_L0.13260.747
33_L78_D0.132170.744
50_R67_V0.132160.744
77_E80_K0.131430.740
7_R89_L0.131170.739
61_E85_I0.1310.738
59_R82_T0.130990.738
56_A60_F0.130930.737
30_D93_P0.130810.737
65_K78_D0.130740.736
37_I59_R0.129820.731
48_A51_R0.129820.731
41_I46_R0.12850.724
30_D71_V0.128450.723
57_I66_V0.128310.723
61_E64_L0.127990.721
28_R31_Y0.127370.717
27_S93_P0.126810.714
67_V70_E0.12680.714
88_T93_P0.126680.713
51_R54_R0.124930.704
21_R69_V0.124840.703
60_F63_R0.124750.703
9_S87_G0.124670.702
9_S79_G0.124560.701
68_S84_T0.124310.700
22_P33_L0.123950.698
35_D62_P0.123590.696
40_P45_T0.123520.696
39_E65_K0.122980.693
19_N53_I0.122750.691
8_E52_E0.122730.691
34_P38_F0.122580.690
44_D70_E0.122320.689
70_E77_E0.121880.686
19_N81_L0.120850.681
21_R33_L0.120510.679
83_F92_T0.120010.676
33_L45_T0.119860.675
7_R33_L0.119790.675
49_I52_E0.118710.668
12_Q61_E0.118580.668
8_E75_D0.118190.666
46_R49_I0.118070.665
38_F87_G0.117950.664
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
2ia7A199.70.064
2vycA0.919216.30.875
2kxoA0.838411.40.883
2lpmA0.575810.70.884
4hhuA0.55567.20.893
3ku7A0.71727.20.893
2p62A0.888970.893
2fekA0.646570.893
4hw9A0.90916.70.894
3n0rA0.65666.20.895

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