GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FLgD_tudor - FlgD Tudor-like domain
Pfam: PF13861 (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: 61
Sequences: 289
Seq/Len: 4.74
HH_delta: 0.648 (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
10_L15_V0.305672.166
17_V52_V0.286392.030
14_E28_S0.242191.716
14_E30_R0.234391.661
34_V57_V0.227441.612
43_L57_V0.223391.583
32_E46_G0.215791.529
6_Q11_I0.209711.486
4_M36_F0.19391.374
17_V27_V0.192321.363
45_L48_G0.186711.323
8_A60_V0.184861.310
36_F41_P0.181251.284
46_G52_V0.178441.265
48_G58_T0.176441.250
24_T34_V0.169941.204
4_M31_V0.167341.186
40_G54_L0.161171.142
35_T53_P0.160991.141
53_P56_D0.15941.130
10_L54_L0.155361.101
4_M9_S0.150811.069
16_L28_S0.150381.066
10_L45_L0.150191.064
36_F43_L0.142841.012
31_V43_L0.141061.000
16_L59_E0.138820.984
30_R34_V0.137690.976
54_L57_V0.136550.968
32_E42_M0.133510.946
6_Q52_V0.132550.939
23_A26_L0.13240.938
9_S36_F0.131270.930
6_Q36_F0.131130.929
35_T55_S0.12950.918
49_G54_L0.129020.914
23_A35_T0.12890.913
4_M8_A0.12870.912
7_A45_L0.128220.909
7_A17_V0.125440.889
41_P44_N0.124480.882
10_L49_G0.123840.878
17_V23_A0.123710.877
6_Q9_S0.123090.872
34_V44_N0.121820.863
28_S42_M0.121020.858
8_A13_K0.120590.855
48_G59_E0.12020.852
25_T31_V0.11870.841
37_S41_P0.117020.829
13_K60_V0.11540.818
26_L58_T0.113340.803
15_V40_G0.113080.801
16_L27_V0.11230.796
28_S56_D0.111820.792
4_M43_L0.111420.790
6_Q47_G0.110460.783
14_E26_L0.109750.778
45_L49_G0.10950.776
18_P24_T0.10920.774
49_G53_P0.107780.764
11_I16_L0.107490.762
8_A11_I0.107040.759
7_A14_E0.106110.752
33_S48_G0.105190.745
9_S44_N0.104710.742
55_S60_V0.104410.740
47_G52_V0.103790.736
16_L35_T0.102830.729
9_S53_P0.101660.720
40_G43_L0.099910.708
48_G57_V0.099730.707
36_F53_P0.099270.703
6_Q56_D0.098410.697
14_E56_D0.098210.696
4_M41_P0.098050.695
15_V52_V0.097980.694
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
3c12A0.868992.90.648
3osvA0.852590.20.672
3ruxA0.9508700.736
2g3rA0.901644.30.773
1biaA0.91842.20.776
2eayA0.901636.40.783
3rkxA0.901635.30.784
2ej9A0.91832.10.789
1ib8A0.9672280.795
3pv9D0.672126.10.798
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