GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GCV_H - Glycine cleavage H-protein
Pfam: PF01597 (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: CL0105
Length: 122
Sequences: 1970
Seq/Len: 16.15
HH_delta: -0.031 (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
111_S114_E1.470564.382
70_T99_K1.285043.829
88_D91_G1.273953.796
51_F96_I1.078683.215
73_E97_K0.87482.607
19_R97_K0.848472.528
68_S105_E0.776382.314
24_D27_Q0.741782.211
104_E107_D0.704782.100
110_L118_F0.654061.949
45_L65_S0.640091.907
102_D105_E0.620921.850
81_N84_L0.620571.849
44_K101_S0.603961.800
1_L90_Y0.59961.787
18_V100_P0.582111.735
88_D92_D0.55731.661
44_K70_T0.553721.650
85_L95_L0.544111.621
51_F63_L0.539641.608
53_S60_V0.537261.601
12_P18_V0.536081.598
112_A116_E0.534591.593
77_E81_N0.526421.569
17_V97_K0.524411.563
46_K49_D0.523391.560
24_D28_D0.518631.546
5_E118_F0.511191.523
116_E120_K0.50561.507
78_L95_L0.481251.434
10_V18_V0.480451.432
47_K108_E0.475721.418
67_V100_P0.466621.391
52_A63_L0.463191.380
84_L93_G0.456831.361
1_L11_K0.453631.352
15_D99_K0.445621.328
46_K68_S0.44021.312
40_K43_T0.432351.288
117_K120_K0.42861.277
42_G70_T0.413791.233
81_N87_S0.40481.206
8_L57_S0.402311.199
53_S57_S0.401191.196
43_T49_D0.400011.192
76_E80_D0.392751.170
77_E92_D0.386161.151
27_Q86_N0.383291.142
11_K19_R0.382511.140
17_V99_K0.38121.136
77_E84_L0.362481.080
90_Y112_A0.360521.074
45_L51_F0.358141.067
34_V57_S0.357361.065
73_E76_E0.355861.060
103_P107_D0.348591.039
77_E80_D0.346161.032
50_P62_D0.345951.031
38_L74_V0.345711.030
25_F29_E0.342651.021
12_P106_F0.341081.016
67_V98_I0.333060.993
12_P103_P0.330210.984
41_V74_V0.327470.976
38_L95_L0.326610.973
2_Y111_S0.326290.972
55_E58_K0.326240.972
25_F119_L0.319090.951
39_P71_V0.315940.942
12_P100_P0.315190.939
9_W21_G0.31250.931
114_E117_K0.30720.915
69_G98_I0.305720.911
20_V96_I0.298480.889
47_K105_E0.296250.883
3_Y90_Y0.293950.876
37_E53_S0.291060.867
30_L61_S0.287570.857
84_L87_S0.284220.847
14_G17_V0.27740.827
63_L96_I0.277340.826
36_V78_L0.27720.826
84_L92_D0.277130.826
6_D64_Y0.275190.820
17_V72_V0.275050.820
76_E79_L0.274180.817
100_P103_P0.272020.811
72_V99_K0.271610.809
1_L112_A0.270530.806
68_S101_S0.268760.801
22_I54_I0.267780.798
33_I52_A0.26220.781
4_T8_L0.261710.780
113_E117_K0.259820.774
103_P106_F0.259650.774
3_Y112_A0.258310.770
39_P74_V0.257290.767
4_T23_T0.256590.765
13_E97_K0.256370.764
29_E33_I0.25510.760
10_V67_V0.254050.757
101_S105_E0.25080.747
3_Y23_T0.249970.745
78_L84_L0.249050.742
56_S59_A0.246750.735
102_D106_F0.239780.715
54_I95_L0.238420.710
72_V98_I0.236670.705
20_V98_I0.232340.692
65_S98_I0.230980.688
7_H31_G0.229730.685
24_D90_Y0.229450.684
13_E17_V0.226870.676
33_I54_I0.226610.675
14_G100_P0.225810.673
41_V76_E0.225560.672
36_V84_L0.225440.672
43_T80_D0.225150.671
27_Q90_Y0.225110.671
45_L71_V0.225070.671
15_D70_T0.223240.665
41_V73_E0.222620.663
63_L95_L0.221010.659
71_V98_I0.21790.649
4_T109_L0.216620.646
8_L34_V0.212710.634
13_E19_R0.211690.631
113_E116_E0.210340.627
35_Y58_K0.20910.623
6_D65_S0.208830.622
11_K90_Y0.201210.600
35_Y59_A0.20120.600
2_Y12_P0.200690.598
39_P56_S0.198740.592
43_T46_K0.198630.592
34_V60_V0.198510.592
6_D59_A0.196540.586
114_E118_F0.194370.579
53_S62_D0.191620.571
108_E113_E0.191110.570
58_K86_N0.189820.566
2_Y106_F0.189520.565
27_Q59_A0.188640.562
26_A61_S0.188520.562
40_K46_K0.187890.560
74_V79_L0.187440.559
65_S68_S0.184030.548
23_T89_P0.18270.544
17_V73_E0.182210.543
110_L115_Y0.181610.541
6_D63_L0.181590.541
56_S60_V0.181440.541
37_E54_I0.1810.539
36_V82_P0.18060.538
8_L26_A0.179820.536
47_K67_V0.179650.535
35_Y55_E0.178090.531
32_D83_E0.177770.530
5_E108_E0.177710.530
4_T118_F0.177280.528
50_P54_I0.17710.528
10_V72_V0.177010.527
31_G35_Y0.176150.525
50_P79_L0.175770.524
25_F59_A0.175640.523
4_T10_V0.174720.521
26_A34_V0.174160.519
34_V55_E0.174120.519
2_Y107_D0.171720.512
50_P96_I0.17130.510
32_D57_S0.170510.508
83_E87_S0.170030.507
30_L59_A0.169590.505
5_E87_S0.168320.502
25_F32_D0.168170.501
79_L85_L0.167750.500
94_W97_K0.16460.491
112_A115_Y0.164440.490
101_S104_E0.164360.490
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
3hgbA0.9918100-0.031
3mxuA0.9754100-0.014
3klrA0.9918100-0.003
3tzuA0.97541000.033
3a7lA11000.046
1onlA0.99181000.063
1hpcA0.99181000.07
1zkoA0.99181000.104
1gjxA0.663998.10.769
3u9tA0.770597.40.806

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