GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ThiF - ThiF family
Pfam: PF00899 (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: CL0063
Length: 135
Sequences: 52666
Seq/Len: 390.12
HH_delta: 0.123 (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
4_R28_K2.897083.076
4_R30_T2.352132.497
20_N24_S2.213842.351
32_V51_E2.193612.329
100_V104_A2.112612.243
96_V100_V2.063952.191
10_A33_D1.861351.976
36_I40_S1.766771.876
15_S19_K1.762981.872
7_I18_A1.713551.819
5_V26_V1.695611.800
20_N23_R1.682761.787
96_V104_A1.652441.754
107_L111_E1.63471.736
5_V21_L1.61071.710
62_K66_Q1.53611.631
60_A63_E1.535091.630
79_E122_D1.532481.627
35_D38_E1.48151.573
104_A108_L1.445961.535
18_A31_L1.42721.515
16_E19_K1.426931.515
51_E60_A1.401271.488
30_T49_T1.395881.482
112_I116_Y1.392091.478
40_S43_N1.309721.391
58_A62_K1.29771.378
19_K23_R1.28521.365
60_A64_R1.243851.321
3_K26_V1.241911.319
59_E63_E1.229791.306
112_I115_E1.228161.304
63_E67_E1.223681.299
62_K112_I1.220361.296
6_L32_V1.199841.274
63_E66_Q1.180821.254
111_E115_E1.172491.245
94_D97_I1.171791.244
30_T68_I1.167621.240
15_S42_L1.162841.235
62_K115_E1.161311.233
104_A107_L1.160031.232
113_C118_I1.149261.220
5_V76_A1.111031.180
58_A111_E1.077791.144
108_L112_I1.074771.141
33_D39_P1.064971.131
99_C103_L1.060541.126
64_R68_I1.042981.107
108_L111_E1.041051.105
30_T47_L1.040261.104
16_E20_N1.030551.094
111_E114_R1.028881.092
91_K94_D1.022281.085
6_L64_R1.017871.081
58_A108_L1.015041.078
37_V40_S1.005671.068
40_S44_R0.992171.053
54_G100_V0.977881.038
15_S41_N0.977251.038
21_L26_V0.971211.031
110_N120_F0.965031.025
38_E41_N0.962711.022
17_V78_P0.952351.011
92_D96_V0.941861.000
75_E78_P0.938340.996
11_G15_S0.932930.991
39_P48_Y0.93010.988
37_V41_N0.92020.977
101_D105_A0.919130.976
12_G16_E0.915970.973
28_K47_L0.909340.965
6_L68_I0.905830.962
36_I50_E0.894430.950
31_L46_F0.89260.948
113_C120_F0.879650.934
41_N45_Q0.855740.909
106_R110_N0.85530.908
110_N114_R0.848560.901
59_E62_K0.8480.900
80_K123_A0.847030.899
17_V21_L0.846340.899
11_G38_E0.845290.897
78_P81_I0.842550.895
36_I39_P0.841470.893
102_S105_A0.838580.890
8_I79_E0.829240.880
109_L120_F0.818320.869
53_V105_A0.81760.868
105_A108_L0.810680.861
10_A31_L0.805560.855
49_T67_E0.805280.855
19_K22_A0.799990.849
73_E78_P0.79910.848
18_A29_I0.787260.836
14_G18_A0.784830.833
106_R122_D0.781150.829
86_I89_L0.778140.826
19_K45_Q0.769560.817
8_I32_V0.747460.794
32_V64_R0.742510.788
17_V20_N0.735450.781
18_A22_A0.733920.779
62_K116_Y0.732860.778
93_Y96_V0.727440.772
22_A29_I0.727350.772
41_N44_R0.72530.770
83_E98_D0.72120.766
83_E101_D0.715230.759
97_I101_D0.712390.756
106_R109_L0.710460.754
13_V17_V0.710280.754
121_I125_V0.707950.752
39_P50_E0.707280.751
123_A126_N0.706110.750
17_V80_K0.703960.747
15_S45_Q0.700850.744
113_C116_Y0.698560.742
49_T64_R0.697570.741
66_Q116_Y0.692940.736
73_E76_A0.691380.734
103_L107_L0.691180.734
6_L30_T0.689950.733
4_R73_E0.682950.725
34_D80_K0.682330.724
39_P43_N0.680470.722
43_N48_Y0.679660.722
122_D125_V0.678850.721
79_E82_D0.676990.719
49_T52_D0.676190.718
83_E97_I0.67540.717
47_L68_I0.67240.714
26_V29_I0.664820.706
64_R67_E0.660950.702
58_A61_A0.647960.688
11_G35_D0.642160.682
43_N46_F0.639240.679
61_A64_R0.621920.660
28_K73_E0.621140.659
34_D37_V0.613290.651
65_L68_I0.611120.649
95_I99_C0.608660.646
30_T67_E0.608240.646
84_E127_G0.607860.645
7_I17_V0.606210.644
93_Y97_I0.605840.643
22_A46_F0.599160.636
87_E90_L0.597410.634
78_P82_D0.596070.633
113_C117_G0.594270.631
26_V76_A0.594020.631
95_I98_D0.590680.627
98_D102_S0.58950.626
33_D38_E0.589350.626
11_G33_D0.585440.622
6_L74_V0.58270.619
95_I107_L0.578680.614
48_Y60_A0.57530.611
10_A34_D0.575170.611
54_G101_D0.574460.610
3_K75_E0.572030.607
77_I109_L0.564580.599
51_E64_R0.56340.598
33_D36_I0.561620.596
8_I109_L0.559120.594
47_L50_E0.54870.583
75_E80_K0.544060.578
105_A109_L0.538590.572
22_A45_Q0.538420.572
86_I90_L0.537880.571
61_A65_L0.536930.570
101_D124_G0.529560.562
35_D39_P0.527530.560
65_L77_I0.523930.556
87_E91_K0.52330.556
33_D48_Y0.516490.548
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
1tt5A199.50.123
1y8qB199.50.132
3cmmA199.50.134
4gslA0.992699.50.147
1y8qA0.992699.50.148
3ruiA0.992699.50.154
2nvuB0.992699.50.157
3cmmA0.970499.50.159
3vh1A0.992699.40.17
1zud1199.40.17

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