GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LEA_2 - Late embryogenesis abundant protein
Pfam: PF03168 (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: 101
Sequences: 1207
Seq/Len: 11.95
HH_delta: 0.242 (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
11_G38_T0.453.221
3_S44_S0.309532.215
22_Y27_R0.295982.119
5_R42_R0.241121.726
14_Y39_I0.235561.686
61_L64_D0.232971.668
15_D81_T0.225161.612
62_L65_L0.217211.555
40_P43_S0.201421.442
5_R44_S0.199691.429
20_D27_R0.193891.388
37_F80_G0.193121.382
21_V28_V0.190981.367
53_V56_S0.190261.362
59_P62_L0.188331.348
17_I79_R0.183551.314
8_N82_F0.179941.288
3_S46_T0.179431.284
9_S42_R0.17911.282
23_Y72_F0.177051.267
53_V57_D0.17441.248
25_G61_L0.173751.244
23_Y34_L0.171431.227
37_F53_V0.166671.193
82_F95_V0.165591.185
64_D75_T0.165521.185
60_R63_K0.165281.183
91_G95_V0.162481.163
16_S33_S0.157981.131
59_P63_K0.157781.129
57_D74_V0.155711.115
54_D81_T0.155631.114
4_V37_F0.155421.112
58_L64_D0.154691.107
61_L65_L0.154631.107
91_G94_R0.154131.103
32_G53_V0.151781.086
79_R83_K0.151051.081
13_R38_T0.150181.075
33_S46_T0.145191.039
31_G75_T0.141951.016
64_D76_Y0.141391.012
73_D77_R0.140151.003
54_D73_D0.13991.001
22_Y25_G0.139070.995
2_L14_Y0.138430.991
16_S82_F0.13810.988
12_I38_T0.137520.984
37_F43_S0.136770.979
37_F45_T0.136480.977
38_T79_R0.134230.961
2_L72_F0.13270.950
44_S48_P0.132540.949
82_F93_V0.131870.944
71_P74_V0.130660.935
10_F14_Y0.127710.914
20_D57_D0.126750.907
2_L25_G0.126420.905
3_S60_R0.126370.905
8_N14_Y0.125590.899
40_P45_T0.125180.896
4_V47_V0.125080.895
43_S93_V0.124830.893
10_F39_I0.124160.889
11_G37_F0.12350.884
31_G76_Y0.123480.884
55_Y64_D0.123160.882
28_V70_V0.122770.879
20_D93_V0.12260.878
18_E94_R0.121580.870
18_E60_R0.120660.864
40_P78_I0.120060.859
21_V29_G0.118850.851
9_S59_P0.118360.847
39_I80_G0.118270.847
22_Y77_R0.118150.846
37_F47_V0.117520.841
17_I52_S0.117150.839
50_P55_Y0.116290.832
50_P75_T0.11620.832
11_G39_I0.115980.830
35_P41_A0.115430.826
23_Y70_V0.115350.826
17_I36_P0.115230.825
19_Y62_L0.115160.824
4_V14_Y0.114240.818
7_P12_I0.113270.811
13_R83_K0.112780.807
16_S36_P0.112580.806
59_P64_D0.112050.802
7_P55_Y0.1120.802
17_I34_L0.111690.799
31_G70_V0.111570.799
10_F40_P0.110730.793
7_P41_A0.110250.789
18_E81_T0.110020.787
60_R77_R0.10990.787
31_G50_P0.109610.785
29_G64_D0.108560.777
13_R58_L0.108090.774
19_Y23_Y0.107320.768
19_Y77_R0.107080.766
15_D83_K0.1070.766
39_I43_S0.106750.764
19_Y76_Y0.106640.763
2_L42_R0.106630.763
29_G78_I0.106310.761
10_F38_T0.10560.756
19_Y32_G0.105120.752
26_Q74_V0.103640.742
51_V62_L0.103270.739
72_F78_I0.102920.737
24_N65_L0.102770.736
62_L70_V0.102640.735
45_T71_P0.102350.733
18_E47_V0.102330.732
4_V66_L0.101860.729
70_V81_T0.101820.729
12_I39_I0.101540.727
5_R47_V0.100980.723
14_Y34_L0.100250.718
23_Y66_L0.100110.717
76_Y92_S0.099890.715
29_G93_V0.099630.713
21_V49_V0.099560.713
20_D48_P0.099550.713
23_Y64_D0.099510.712
31_G48_P0.099480.712
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
1yycA0.960499.30.242
1xo8A0.960499.30.25
3butA0.9505990.345
4djmA0.683265.20.808
2co7B0.673354.50.819
1l4iA0.673349.30.824
4ay0A0.673341.60.832
1klfA0.663438.10.835
2z4tA0.970324.80.85
3e38A0.722821.50.853

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