GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UBN2_3 - gag-polypeptide of LTR copia-type
Pfam: PF14244 (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: CL0523
Length: 152
Sequences: 1341
Seq/Len: 8.82
HH_delta: 0.896 (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
85_K89_D0.693584.665
59_D84_A0.469673.159
63_L87_I0.431872.905
70_I78_I0.336052.260
59_D83_T0.324242.181
22_S92_K0.312082.099
33_G57_R0.305412.054
18_Y21_W0.281621.894
78_I87_I0.268911.809
120_S123_E0.263581.773
119_K127_K0.251941.695
128_L132_W0.250631.686
26_E35_W0.243681.639
110_E127_K0.240751.619
18_Y92_K0.237271.596
36_G39_D0.232871.566
74_I95_F0.228481.537
114_L128_L0.225281.515
22_S26_E0.224251.508
29_L38_I0.223641.504
81_C87_I0.217751.465
36_G58_K0.217441.463
25_M88_W0.211731.424
103_R107_L0.206341.388
38_I62_V0.203911.372
13_L17_N0.200081.346
43_P46_P0.198891.338
119_K123_E0.196821.324
35_W38_I0.196531.322
28_A32_K0.194921.311
18_Y22_S0.192561.295
66_L87_I0.192221.293
89_D92_K0.191611.289
62_V65_W0.187431.261
18_Y88_W0.186571.255
35_W39_D0.18631.253
26_E39_D0.184911.244
89_D93_E0.182661.229
30_R56_E0.179541.208
45_P55_W0.175621.181
17_N21_W0.174021.171
107_L131_L0.172591.161
116_Q124_Y0.172591.161
23_Q27_M0.169581.141
30_R60_Q0.168511.133
14_N71_S0.167991.130
26_E82_E0.163571.100
26_E30_R0.163331.099
62_V69_S0.161631.087
23_Q75_L0.161531.087
77_T94_R0.16141.086
24_Q72_P0.160211.078
27_M67_L0.156481.053
101_A105_F0.154811.041
39_D47_E0.154131.037
22_S88_W0.151881.022
15_G95_F0.149291.004
53_E56_E0.148911.002
81_C90_A0.148831.001
24_Q34_L0.147360.991
63_L67_L0.143590.966
25_M66_L0.142910.961
66_L126_N0.142910.961
86_E89_D0.142620.959
36_G40_G0.142310.957
29_L34_L0.141150.949
67_L87_I0.140330.944
70_I87_I0.139190.936
29_L33_G0.138950.935
20_S72_P0.138560.932
54_K86_E0.138460.931
15_G18_Y0.137710.926
53_E57_R0.134760.906
103_R110_E0.134650.906
50_P54_K0.134510.905
119_K124_Y0.134370.904
102_S107_L0.134340.904
52_Y55_W0.133120.895
112_H115_K0.133040.895
106_Q110_E0.132660.892
51_A54_K0.131440.884
43_P66_L0.131430.884
37_F62_V0.131190.882
38_I85_K0.130.874
44_K56_E0.128760.866
118_D124_Y0.128730.866
91_L120_S0.127820.860
55_W59_D0.126990.854
47_E84_A0.125940.847
40_G44_K0.124460.837
86_E93_E0.124430.837
125_F129_K0.124240.836
37_F58_K0.124150.835
74_I124_Y0.12380.833
114_L124_Y0.120220.809
64_S75_L0.120130.808
20_S24_Q0.12010.808
13_L18_Y0.119980.807
34_L57_R0.119560.804
111_L119_K0.119210.802
29_L62_V0.118390.796
24_Q75_L0.117960.793
20_S76_S0.117680.792
30_R33_G0.117310.789
43_P55_W0.117280.789
121_V124_Y0.116850.786
30_R63_L0.116580.784
47_E53_E0.114420.770
76_S82_E0.114380.769
121_V125_F0.114220.768
59_D81_C0.113290.762
13_L21_W0.112990.760
74_I96_S0.112820.759
64_S80_F0.112680.758
13_L105_F0.11250.757
78_I91_L0.112360.756
104_V108_R0.112210.755
108_R114_L0.112130.754
54_K58_K0.111530.750
77_T127_K0.111410.749
32_K65_W0.111390.749
22_S96_S0.110060.740
22_S99_S0.109930.739
116_Q132_W0.10990.739
61_L121_V0.109670.738
37_F59_D0.109660.738
116_Q119_K0.109220.735
19_L78_I0.109010.733
111_L128_L0.108590.730
63_L79_I0.107970.726
55_W84_A0.107730.725
42_I45_P0.107340.722
95_F126_N0.10720.721
12_K71_S0.107050.720
101_A111_L0.106740.718
41_T89_D0.106720.718
12_K15_G0.106350.715
90_A94_R0.105540.710
73_D109_N0.10510.707
15_G74_I0.105070.707
59_D126_N0.104550.703
40_G43_P0.104490.703
12_K16_S0.104460.703
39_D86_E0.104290.701
125_F132_W0.104280.701
50_P120_S0.104160.701
97_Q101_A0.104040.700
25_M42_I0.102990.693
86_E120_S0.102940.692
111_L132_W0.102550.690
29_L64_S0.102490.689
13_L124_Y0.102060.686
76_S80_F0.101960.686
58_K61_L0.101650.684
38_I88_W0.101360.682
70_I103_R0.101260.681
128_L131_L0.101070.680
14_N105_F0.101040.680
33_G36_G0.100780.678
65_W68_N0.100310.675
42_I46_P0.100140.674
11_I24_Q0.099840.672
22_S25_M0.099030.666
48_T51_A0.098940.666
13_L16_S0.098320.661
33_G53_E0.098270.661
41_T47_E0.098230.661
64_S67_L0.097680.657
41_T45_P0.097460.656
43_P49_D0.096940.652
81_C86_E0.096580.650
30_R35_W0.096330.648
102_S105_F0.096290.648
101_A128_L0.096270.648
45_P48_T0.096260.647
111_L131_L0.096190.647
68_N106_Q0.095730.644
43_P113_S0.09570.644
26_E63_L0.095560.643
34_L60_Q0.095390.642
101_A104_V0.095050.639
44_K115_K0.094710.637
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
3eg5B0.960541.90.896
2paqA0.9408150.915
2bnxA0.967111.50.919
3pl5A0.960511.20.919
2a0uA0.736811.10.92
3ecsA0.46719.70.922
3fysA0.96058.80.923
4l1jA0.91458.20.924
4b4tO0.58558.10.924
3fdjA0.94747.90.925
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