GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gal_mutarotas_2 - Galactose mutarotase-like
Pfam: PF13802 (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: CL0103
Length: 68
Sequences: 1621
Seq/Len: 23.84
HH_delta: 0.066 (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
3_R15_N0.855893.257
45_F56_G0.824273.137
4_F46_F0.772922.942
25_N42_S0.730362.780
22_R66_F0.499291.900
45_F58_F0.45321.725
59_F65_T0.442521.684
20_R66_F0.434951.655
2_E53_K0.387611.475
22_R64_R0.379481.444
27_D40_Y0.374521.425
26_T38_P0.361941.378
46_F55_Y0.360081.370
24_W64_R0.35121.337
9_E41_K0.349231.329
23_L42_S0.347711.323
3_R13_P0.33141.261
7_L67_F0.318621.213
61_N65_T0.318461.212
11_F39_L0.301141.146
12_G16_R0.290291.105
9_E40_Y0.286031.089
23_L65_T0.280651.068
23_L67_F0.278081.058
51_S54_G0.274261.044
7_L21_Y0.271331.033
11_F31_Y0.268561.022
38_P64_R0.262040.997
47_I56_G0.261690.996
14_L44_P0.26160.996
2_E52_G0.259090.986
28_A37_D0.251960.959
26_T64_R0.251080.956
14_L17_R0.244410.930
52_G55_Y0.241730.920
16_R31_Y0.24050.915
28_A36_S0.237010.902
4_F51_S0.228830.871
24_W27_D0.227620.866
24_W63_S0.227310.865
12_G36_S0.221610.843
59_F63_S0.221530.843
8_G15_N0.21960.836
2_E51_S0.218370.831
11_F28_A0.21810.830
12_G21_Y0.214850.818
60_D63_S0.214110.815
17_R52_G0.213290.812
19_K66_F0.21210.807
46_F57_V0.207060.788
20_R29_F0.202670.771
2_E55_Y0.200840.764
59_F67_F0.199930.761
3_R46_F0.197280.751
21_Y29_F0.197050.750
10_R37_D0.195480.744
31_Y36_S0.192630.733
45_F60_D0.192550.733
25_N62_P0.192130.731
2_E37_D0.190510.725
26_T54_G0.188730.718
27_D30_G0.187540.714
43_I53_K0.186020.708
6_G9_E0.184110.701
15_N18_G0.183890.700
11_F40_Y0.182620.695
31_Y37_D0.181990.693
17_R23_L0.179030.681
5_Y38_P0.178920.681
41_K56_G0.178830.681
5_Y15_N0.176410.671
21_Y53_K0.174970.666
27_D41_K0.173840.662
10_R25_N0.171280.652
7_L16_R0.169860.646
5_Y17_R0.168910.643
28_A31_Y0.16790.639
12_G37_D0.16520.629
43_I55_Y0.163860.624
46_F67_F0.159650.608
4_F60_D0.159110.606
12_G25_N0.157820.601
63_S66_F0.155450.592
20_R30_G0.155150.590
9_E61_N0.155070.590
2_E18_G0.154870.589
47_I59_F0.154840.589
6_G44_P0.15430.587
10_R41_K0.154070.586
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
2g3mA0.985399.60.066
3nsxA0.970699.50.074
3lppA0.970699.50.082
4kmqA0.941299.50.093
4ba0A0.941299.50.102
3l4yA0.970699.50.11
3w37A0.970699.50.118
2f2hA0.897199.40.135
2x2hA199.40.141
4amwA199.40.141

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