GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TRCF - TRCF domain
Pfam: PF03461 (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: 1596
Seq/Len: 15.8
HH_delta: 0.008 (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
8_I53_V0.748723.461
25_R41_E0.639542.956
66_A74_I0.570152.635
31_S34_E0.568522.628
39_R54_E0.50112.316
32_E61_R0.499582.309
9_P50_P0.491972.274
26_L57_L0.406591.879
93_P97_K0.405921.876
22_L46_F0.39161.810
29_A38_L0.384291.776
39_R57_L0.380411.758
42_L57_L0.379271.753
1_D75_K0.352271.628
26_L38_L0.338931.566
35_L61_R0.328611.519
22_L42_L0.322651.491
58_E61_R0.312961.446
60_A63_K0.309061.428
39_R49_L0.308931.428
13_I22_L0.306091.415
7_Y19_R0.292111.350
51_E54_E0.289831.340
35_L64_I0.287091.327
10_E16_D0.285921.321
39_R61_R0.27781.284
41_E45_R0.270161.249
30_E34_E0.270041.248
37_D40_E0.262571.214
65_L68_K0.261481.209
76_Q79_N0.259821.201
40_E48_P0.252141.165
11_D52_E0.250131.156
27_A63_K0.245581.135
29_A35_L0.244751.131
86_S89_K0.241081.114
62_L74_I0.240991.114
71_I83_I0.23391.081
92_D95_K0.233531.079
3_P76_Q0.230991.068
18_E21_E0.226581.047
13_I42_L0.223981.035
16_D20_L0.221491.024
73_S84_T0.221291.023
26_L60_A0.220781.020
22_L29_A0.216210.999
6_A45_R0.215410.996
26_L35_L0.211480.977
90_K94_D0.211270.976
33_E36_E0.210640.974
6_A59_L0.20930.967
21_E25_R0.206810.956
25_R38_L0.205590.950
91_V95_K0.205340.949
19_R27_A0.204570.946
10_E19_R0.204050.943
19_R75_K0.203630.941
32_E36_E0.201280.930
61_R64_I0.199590.922
4_V59_L0.198610.918
29_A64_I0.197310.912
63_K67_R0.193320.894
41_E44_D0.190380.880
36_E39_R0.188210.870
22_L38_L0.185880.859
91_V97_K0.18520.856
44_D56_L0.183960.850
66_A71_I0.179730.831
12_Y42_L0.179480.830
39_R43_I0.178570.825
17_D21_E0.176650.816
55_N79_N0.176310.815
49_L53_V0.176290.815
89_K92_D0.175330.810
50_P56_L0.173620.802
20_L76_Q0.172150.796
43_I48_P0.17170.794
7_Y16_D0.171570.793
31_S64_I0.170580.788
51_E55_N0.168170.777
40_E43_I0.167870.776
8_I82_Y0.167510.774
1_D97_K0.166360.769
71_I74_I0.165130.763
2_L6_A0.163320.755
8_I42_L0.162960.753
20_L27_A0.162860.753
59_L67_R0.162030.749
48_P54_E0.161970.749
86_S91_V0.161920.748
91_V94_D0.160510.742
88_N95_K0.159350.736
39_R81_I0.159190.736
33_E51_E0.158940.735
87_K92_D0.158660.733
16_D24_R0.15830.732
58_E82_Y0.157920.730
12_Y56_L0.157380.727
24_R44_D0.157370.727
35_L57_L0.157120.726
57_L61_R0.156420.723
8_I26_L0.15580.720
7_Y15_D0.155070.717
63_K73_S0.154660.715
54_E58_E0.154170.713
90_K96_L0.152090.703
13_I66_A0.151820.702
37_D55_N0.151470.700
8_I13_I0.151050.698
26_L44_D0.150730.697
53_V56_L0.15040.695
36_E68_K0.150190.694
31_S68_K0.150080.694
18_E59_L0.149840.693
37_D41_E0.148960.688
86_S92_D0.14830.685
1_D17_D0.14820.685
5_D16_D0.148190.685
22_L25_R0.147570.682
41_E46_F0.146980.679
34_E37_D0.146750.678
5_D19_R0.145690.673
2_L83_I0.144770.669
88_N93_P0.144560.668
3_P78_G0.143980.665
70_G89_K0.143680.664
77_K80_S0.143240.662
72_E75_K0.141950.656
20_L24_R0.141530.654
70_G96_L0.140580.650
63_K78_G0.140490.649
46_F57_L0.140140.648
57_L94_D0.140120.648
94_D97_K0.140120.648
71_I80_S0.139640.645
18_E26_L0.139530.645
30_E65_L0.139490.645
2_L81_I0.13890.642
2_L58_E0.138360.639
11_D31_S0.138030.638
63_K70_G0.137550.636
72_E86_S0.13690.633
43_I49_L0.136760.632
26_L29_A0.136350.630
55_N63_K0.136220.630
59_L63_K0.135430.626
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
2qsrA199.90.008
2eyqA199.90.08
3bbzA0.455437.70.89
1rrzA0.366319.60.904
1scfA0.881219.20.904
1w79A0.544617.40.906
3or1C0.851513.20.91
2j0jA0.990113.10.91
3fhgA0.732712.50.911
4a69A0.534710.80.914

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