GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
EB - EB module
Pfam: PF01683 (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: 256
Seq/Len: 4.92
HH_delta: 0.668 (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
23_E37_G0.224812.044
6_V27_Q0.214621.952
19_G38_R0.182051.655
1_C4_G0.173041.573
18_P31_G0.164741.498
45_Y48_V0.163811.489
13_V27_Q0.162991.482
18_P42_P0.157341.431
37_G49_G0.15121.375
20_E23_E0.149481.359
7_A32_S0.138011.255
25_D42_P0.134111.219
10_G42_P0.133851.217
19_G49_G0.123861.126
17_Q38_R0.123141.120
4_G36_N0.122721.116
33_V40_Q0.12231.112
24_S45_Y0.121671.106
14_P20_E0.120871.099
8_I13_V0.118321.076
35_V43_P0.117641.070
14_P23_E0.116231.057
21_S36_N0.115051.046
33_V36_N0.113531.032
5_Q10_G0.11291.027
4_G18_P0.112591.024
14_P25_D0.112371.022
10_G44_G0.111721.016
11_Q45_Y0.109680.997
17_Q40_Q0.107370.976
3_S35_V0.107170.974
37_G43_P0.106360.967
1_C5_Q0.105280.957
18_P30_G0.1040.946
4_G15_R0.103990.946
43_P46_V0.101970.927
21_S26_E0.098590.896
9_N23_E0.098440.895
11_Q29_I0.098240.893
5_Q14_P0.098230.893
16_V31_G0.098020.891
14_P40_Q0.096190.875
26_E30_G0.0960.873
40_Q45_Y0.095330.867
8_I44_G0.094880.863
14_P43_P0.094720.861
16_V20_E0.094280.857
11_Q49_G0.09280.844
32_S41_C0.092640.842
11_Q14_P0.092340.840
8_I49_G0.091930.836
31_G42_P0.091340.831
15_R18_P0.090260.821
26_E35_V0.089750.816
16_V30_G0.088210.802
33_V37_G0.087590.796
1_C20_E0.086980.791
29_I43_P0.086470.786
31_G45_Y0.085810.780
17_Q49_G0.085220.775
9_N25_D0.084770.771
19_G30_G0.084760.771
6_V15_R0.084380.767
17_Q42_P0.084060.764
24_S27_Q0.083260.757
32_S48_V0.083170.756
2_P25_D0.08310.756
8_I15_R0.083050.755
8_I40_Q0.082770.753
11_Q23_E0.082380.749
19_G23_E0.081450.741
8_I11_Q0.07990.727
16_V21_S0.079690.725
8_I46_V0.07650.696
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
1yo8A0.923191.30.668
1z1yA0.923190.60.674
2vj2A0.865486.70.695
1z1yA0.884686.70.695
3fcsB0.923186.70.695
2gy5A0.942386.70.695
2ygqA0.826984.20.705
2dduA0.961583.50.708
3g5cA0.961582.80.709
4d90A0.903881.20.714
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