GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cys_rich_CPXG - Cysteine-rich CPXCG
Pfam: PF14255 (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: 52
Sequences: 254
Seq/Len: 4.88
HH_delta: 0.768 (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
12_I36_V0.387282.649
8_E29_V0.315092.155
5_Y34_I0.24281.661
26_D33_P0.237191.622
4_P34_I0.231561.584
26_D31_C0.221161.513
15_D19_G0.215091.471
44_E49_V0.205651.407
17_S21_Q0.198671.359
22_E37_Q0.19631.343
10_I28_Q0.195041.334
24_I35_E0.193951.327
29_V33_P0.191231.308
22_E35_E0.187871.285
12_I28_Q0.171861.175
13_L28_Q0.170321.165
1_I12_I0.168331.151
18_A23_Y0.165831.134
14_I40_V0.162961.115
37_Q48_S0.159051.088
39_T50_R0.156411.070
46_S49_V0.154161.054
47_V51_R0.151211.034
20_D39_T0.150111.027
3_C6_C0.147591.009
4_P13_L0.147381.008
41_D45_P0.147111.006
1_I34_I0.145820.997
7_G20_D0.143650.983
10_I34_I0.143240.980
24_I36_V0.14120.966
4_P10_I0.140670.962
7_G23_Y0.140320.960
7_G19_G0.140150.959
2_Q7_G0.138490.947
1_I9_P0.137450.940
7_G25_E0.137230.939
39_T48_S0.136220.932
9_P39_T0.13540.926
25_E33_P0.135270.925
2_Q9_P0.135210.925
20_D50_R0.13380.915
10_I29_V0.132960.909
20_D38_V0.13240.906
18_A21_Q0.132110.904
2_Q35_E0.131230.898
45_P51_R0.128160.877
15_D36_V0.125350.857
8_E25_E0.121510.831
9_P37_Q0.119660.818
16_P43_D0.119380.817
24_I33_P0.117390.803
37_Q46_S0.115940.793
37_Q50_R0.113150.774
11_E22_E0.112470.769
13_L36_V0.112050.766
24_I34_I0.111190.761
1_I4_P0.111040.759
5_Y43_D0.110010.752
15_D18_A0.110.752
20_D44_E0.109470.749
18_A38_V0.109210.747
13_L42_E0.107820.737
45_P49_V0.10760.736
2_Q11_E0.106130.726
5_Y8_E0.105530.722
16_P42_E0.103340.707
37_Q43_D0.102560.701
22_E41_D0.101070.691
46_S50_R0.100420.687
17_S40_V0.100170.685
26_D29_V0.099950.684
8_E32_R0.099490.680
41_D44_E0.099180.678
40_V44_E0.099030.677
2_Q48_S0.098680.675
1_I32_R0.096920.663
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
1wiiA0.961590.40.768
2fiyA0.961565.10.82
3na7A0.461561.50.824
4aybP0.865448.50.836
2kdxA0.788548.40.836
3k1lB0.384645.60.839
1yuzA0.5962450.84
4bbrM0.884642.60.842
1pqvS0.711538.40.846
3k7aM0.923137.20.846
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