GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UBN2_2 - gag-polypeptide of LTR copia-type
Pfam: PF14227 (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: 119
Sequences: 1324
Seq/Len: 11.13
HH_delta: 0.822 (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
5_K9_D0.748085.183
44_H74_S0.565523.918
27_L66_D0.363752.520
39_G47_E0.31782.202
40_S43_D0.309342.143
9_D13_K0.274761.904
52_V67_K0.268551.861
33_L48_F0.245451.701
82_F100_V0.232131.608
71_L97_L0.227841.579
29_K47_E0.222381.541
13_K98_E0.21751.507
80_D110_R0.212521.473
33_L44_H0.208241.443
9_D12_K0.207531.438
96_T99_E0.203431.410
3_T6_E0.202951.406
42_R105_L0.20221.401
68_V100_V0.201131.394
71_L100_V0.193181.339
35_M76_P0.192941.337
48_F52_V0.192381.333
86_L103_K0.19111.324
41_V108_E0.186371.291
39_G44_H0.185821.288
48_F71_L0.174611.210
86_L97_L0.174461.209
15_Y46_N0.174091.206
84_T107_E0.171921.191
79_Y82_F0.168821.170
81_S84_T0.168311.166
22_N26_L0.1671.157
86_L100_V0.164421.139
67_K97_L0.162781.128
8_W12_K0.162731.128
21_A24_I0.161951.122
67_K71_L0.159021.102
11_L15_Y0.157961.094
84_T110_R0.153571.064
72_L86_L0.153411.063
53_N57_S0.153181.061
56_K61_P0.150741.044
61_P78_S0.149661.037
75_L79_Y0.149021.033
97_L101_K0.146711.017
45_I101_K0.146111.012
101_K105_L0.146031.012
17_K20_F0.145381.007
50_S54_Q0.144441.001
60_V66_D0.143940.997
55_L58_L0.143180.992
10_K80_D0.141720.982
23_K65_E0.141130.978
11_L76_P0.139810.969
20_F99_E0.13860.960
31_Y73_S0.138520.960
55_L72_L0.138320.958
106_Q110_R0.137270.951
82_F86_L0.136790.948
39_G43_D0.136770.948
72_L75_L0.135350.938
46_N61_P0.134850.934
8_W104_L0.133050.922
82_F88_Y0.131380.910
5_K12_K0.131040.908
64_D71_L0.130230.902
64_D67_K0.130210.902
35_M41_V0.129340.896
24_I73_S0.128340.889
49_R53_N0.127310.882
88_Y103_K0.12530.868
11_L84_T0.124930.866
72_L83_V0.124860.865
9_D33_L0.124290.861
45_I71_L0.123480.856
31_Y70_I0.122660.850
40_S108_E0.122360.848
52_V56_K0.122310.847
6_E43_D0.122130.846
35_M78_S0.121990.845
7_M10_K0.12110.839
12_K108_E0.120520.835
27_L30_L0.120430.834
23_K74_S0.120120.832
30_L70_I0.118630.822
28_R89_S0.11820.819
84_T88_Y0.11720.812
24_I69_I0.117060.811
103_K106_Q0.1170.811
19_S38_G0.116880.810
68_V72_L0.116190.805
66_D83_V0.116150.805
59_G62_I0.116120.805
18_K22_N0.115720.802
53_N56_K0.115620.801
29_K32_S0.11530.799
10_K13_K0.115120.798
73_S89_S0.115060.797
68_V99_E0.114910.796
3_T50_S0.114860.796
6_E34_K0.113730.788
26_L29_K0.113550.787
43_D61_P0.11220.777
15_Y83_V0.112110.777
76_P101_K0.110960.769
82_F104_L0.110130.763
6_E59_G0.109770.761
93_D98_E0.109330.758
56_K96_T0.108270.750
83_V87_L0.108270.750
96_T100_V0.107470.745
53_N61_P0.107280.743
22_N31_Y0.107040.742
32_S66_D0.107030.742
49_R67_K0.106850.740
101_K106_Q0.106820.740
38_G98_E0.106570.738
84_T98_E0.106460.738
18_K58_L0.106390.737
44_H102_S0.106190.736
37_E78_S0.105760.733
28_R80_D0.105440.731
22_N81_S0.10540.730
37_E76_P0.104720.726
17_K22_N0.104660.725
6_E13_K0.104050.721
71_L103_K0.104030.721
31_Y58_L0.1040.721
28_R87_L0.103720.719
85_A88_Y0.103420.717
55_L81_S0.103390.716
7_M87_L0.103320.716
25_Y37_E0.103220.715
36_D44_H0.103190.715
90_K103_K0.102980.714
14_K18_K0.102590.711
11_L82_F0.102470.710
72_L87_L0.102270.709
24_I100_V0.102240.708
96_T101_K0.102040.707
21_A26_L0.10160.704
60_V65_E0.101490.703
56_K67_K0.100980.700
6_E9_D0.100950.699
39_G70_I0.100820.699
44_H79_Y0.100740.698
70_I74_S0.100620.697
34_K109_E0.100120.694
87_L100_V0.099950.693
33_L97_L0.099820.692
41_V77_P0.099620.690
85_A98_E0.09910.687
6_E47_E0.099050.686
40_S98_E0.098690.684
25_Y73_S0.098620.683
68_V78_S0.098420.682
15_Y68_V0.098380.682
49_R97_L0.098280.681
67_K96_T0.098210.680
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
3tirA0.773176.30.822
3g21A0.6387400.858
3g1gA0.697528.50.868
1y7qA0.789927.10.869
4bhxA0.756320.70.876
3lhrA0.747919.60.877
4e6sA0.747919.50.877
2fi2A0.756316.70.881
3iacA0.95812.70.886
4f61I0.554610.90.889
If you are interested in a protein containing this domain,
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