GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DRTGG - DRTGG domain
Pfam: PF07085 (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: CL0365
Length: 105
Sequences: 2295
Seq/Len: 21.86
HH_delta: 0.084 (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
9_E90_S0.887233.465
43_L64_C0.880843.440
75_E79_E0.82893.237
8_G89_I0.688472.689
12_N82_K0.617542.412
81_A88_V0.580632.268
79_E82_K0.506981.980
67_L73_P0.490061.914
43_L66_I0.455741.780
12_N81_A0.447491.748
51_E76_E0.442381.728
13_G16_E0.43561.701
79_E83_E0.417711.631
12_N16_E0.415621.623
10_V17_L0.415581.623
15_E85_G0.407781.593
27_G44_V0.404261.579
55_L80_L0.371221.450
9_E92_P0.359281.403
11_L90_S0.351981.375
80_L83_E0.351921.374
16_E19_R0.342991.340
55_L83_E0.334571.307
45_I66_I0.311361.216
10_V89_I0.306491.197
78_L82_K0.306481.197
10_V13_G0.300491.174
33_D36_E0.287341.122
16_E82_K0.284791.112
75_E78_L0.282961.105
14_G82_K0.27991.093
50_R76_E0.277231.083
78_L88_V0.275271.075
13_G87_P0.268321.048
73_P90_S0.268231.048
52_D56_A0.268151.047
19_R87_P0.26611.039
28_A48_G0.266011.039
34_F44_V0.264361.032
13_G17_L0.254840.995
66_I91_T0.251420.982
50_R95_T0.247820.968
44_V57_A0.24720.965
62_I86_I0.246360.962
23_K42_D0.244250.954
64_C87_P0.241720.944
80_L84_L0.238890.933
10_V14_G0.237220.926
70_G92_P0.236780.925
52_D55_L0.235150.918
70_G90_S0.235010.918
12_N88_V0.234720.917
29_M69_G0.233690.913
46_T53_I0.229070.895
72_E90_S0.227380.888
55_L59_E0.227270.888
65_I86_I0.226090.883
23_K48_G0.224320.876
19_R63_A0.222620.869
56_A59_E0.219020.855
73_P78_L0.218510.853
24_V45_I0.215720.842
21_V87_P0.213080.832
56_A60_A0.211660.827
31_L34_F0.211530.826
52_D65_I0.208890.816
45_I68_T0.207890.812
68_T95_T0.207550.811
35_L56_A0.206310.806
49_D77_V0.206070.805
51_E74_S0.203490.795
31_L56_A0.203250.794
58_I65_I0.20190.789
59_E80_L0.200310.782
51_E79_E0.199940.781
51_E55_L0.199880.781
27_G57_A0.19960.780
54_Q77_V0.199090.778
58_I84_L0.196680.768
45_I53_I0.196220.766
11_L73_P0.196140.766
15_E19_R0.1950.762
26_V48_G0.194330.759
46_T65_I0.192860.753
91_T95_T0.192450.752
22_G41_G0.192240.751
10_V16_E0.192150.750
25_V48_G0.190330.743
65_I71_L0.189850.741
68_T91_T0.187470.732
5_T8_G0.186910.730
12_N87_P0.185420.724
87_P90_S0.18520.723
22_G66_I0.184130.719
23_K39_K0.184070.719
21_V64_C0.184060.719
46_T54_Q0.181380.708
54_Q81_A0.181130.707
38_L62_I0.18030.704
6_L68_T0.179430.701
18_D79_E0.178250.696
6_L91_T0.177310.692
21_V41_G0.17490.683
7_D93_Y0.174590.682
32_S53_I0.174060.680
26_V95_T0.17360.678
8_G57_A0.169970.664
16_E72_E0.169740.663
25_V42_D0.168680.659
72_E75_E0.168260.657
29_M37_Y0.167890.656
20_R56_A0.167350.654
14_G17_L0.166680.651
73_P88_V0.165760.647
26_V44_V0.165510.646
31_L52_D0.165410.646
41_G63_A0.165040.645
28_A95_T0.164250.641
50_R54_Q0.163870.640
8_G91_T0.163720.639
34_F53_I0.163670.639
25_V86_I0.163480.638
34_F41_G0.161840.632
59_E84_L0.161630.631
26_V29_M0.161480.631
32_S41_G0.161380.630
54_Q58_I0.161210.630
31_L65_I0.160940.629
42_D64_C0.160870.628
5_T62_I0.159880.624
28_A50_R0.159640.623
76_E79_E0.158880.620
51_E77_V0.158750.620
30_S46_T0.158740.620
26_V45_I0.15850.619
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
2iojA0.990599.70.084
1knxA0.990599.50.245
1ko7A199.40.272
3l2bA0.990599.10.384
3cwcA0.866771.40.821
3t7yA0.657171.20.822
4jb3A0.742968.80.825
2jliA0.933364.90.829
2jljA0.933364.70.829
2qwvA0.990564.60.83

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