GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
V4R - V4R domain
Pfam: PF02830 (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: CL0210
Length: 62
Sequences: 660
Seq/Len: 10.65
HH_delta: 0.113 (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
22_C56_C0.460252.695
48_C56_C0.452782.652
8_C11_C0.419682.458
47_K57_E0.375632.200
43_V60_I0.325261.905
45_E56_C0.322331.888
22_C48_C0.320921.879
45_E48_C0.31081.820
20_P51_M0.301741.767
48_C52_G0.277861.627
47_K55_H0.266381.560
33_F60_I0.238271.395
47_K53_D0.223171.307
38_G41_V0.202991.189
19_E23_W0.201981.183
22_C45_E0.198721.164
46_T59_V0.197221.155
21_V50_A0.18881.106
35_A38_G0.188541.104
40_E43_V0.180061.054
45_E50_A0.178671.046
44_E59_V0.178581.046
17_S21_V0.176621.034
22_C52_G0.176551.034
5_V25_T0.175771.029
24_F28_Y0.173211.014
40_E44_E0.173171.014
32_F36_L0.17191.007
33_F43_V0.169560.993
15_G21_V0.164470.963
26_A30_A0.16050.940
5_V11_C0.159040.931
38_G59_V0.156810.918
10_E25_T0.156790.918
9_F31_G0.155770.912
7_D10_E0.153610.900
52_G56_C0.153480.899
36_L50_A0.153030.896
29_L33_F0.151940.890
48_C53_D0.151230.886
12_A21_V0.150640.882
29_L60_I0.150020.879
3_I8_C0.148990.873
46_T57_E0.148870.872
9_F24_F0.14840.869
6_E55_H0.147570.864
33_F37_F0.141420.828
33_F58_F0.141190.827
45_E52_G0.1410.826
34_S51_M0.137550.806
20_P34_S0.135610.794
12_A25_T0.13470.789
18_D55_H0.134150.786
4_S57_E0.132340.775
50_A56_C0.132170.774
12_A37_F0.13210.774
30_A43_V0.13180.772
5_V12_A0.131620.771
26_A44_E0.130450.764
19_E35_A0.130150.762
29_L39_K0.128740.754
16_N37_F0.127780.748
10_E14_L0.127110.744
18_D53_D0.126530.741
15_G33_F0.126460.741
20_P50_A0.125340.734
8_C29_L0.124740.731
43_V58_F0.1240.726
23_W26_A0.122550.718
6_E59_V0.121930.714
23_W60_I0.12190.714
6_E57_E0.121440.711
7_D49_Q0.120910.708
44_E55_H0.120360.705
25_T32_F0.120120.703
13_G18_D0.118960.697
9_F14_L0.117590.689
20_P24_F0.1170.685
10_E24_F0.11650.682
17_S34_S0.116070.680
20_P45_E0.115280.675
42_E61_R0.114690.672
39_K51_M0.114640.671
6_E38_G0.114390.670
9_F35_A0.11420.669
18_D51_M0.11420.669
8_C24_F0.113990.668
3_I27_G0.112660.660
8_C25_T0.112520.659
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
2osoA0.967799.30.113
3tfgA0.9677980.465
2kiiA0.967797.80.487
3sj5A0.967795.90.628
3njcA0.9677920.693
1sz7A0.967779.30.746
3cueD0.967776.40.752
2bjnA0.935562.60.774
2j3wB0.9032540.785
3cueB0.967750.70.789

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