GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GCV_T_C - Glycine cleavage T-protein C-terminal barrel domain
Pfam: PF08669 (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: 95
Sequences: 3784
Seq/Len: 39.83
HH_delta: 0.018 (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
38_P46_P1.413023.296
26_T61_K1.357883.167
11_R15_R1.080072.519
36_G49_R1.061722.476
80_E87_R1.034972.414
25_L64_A0.945582.206
78_E89_P0.942392.198
6_Q10_A0.934442.180
2_D6_Q0.919072.144
39_V66_A0.901312.102
82_E85_G0.889112.074
56_S59_L0.882172.058
82_E87_R0.851121.985
40_Y87_R0.822731.919
28_D91_T0.805531.879
80_E89_P0.77191.800
50_V64_A0.760791.775
25_L66_A0.743791.735
78_E91_T0.726241.694
26_T91_T0.714991.668
79_L90_A0.711671.660
8_A12_Q0.692831.616
40_Y82_E0.643021.500
7_E10_A0.635521.482
2_D7_E0.606061.414
38_P82_E0.606031.414
40_Y46_P0.601511.403
74_E77_T0.539651.259
7_E11_R0.53431.246
22_L65_L0.53331.244
39_V81_V0.532451.242
45_K69_D0.513441.198
23_V68_V0.512171.195
41_D45_K0.511381.193
55_Y60_G0.507711.184
28_D89_P0.504221.176
27_L90_A0.481571.123
47_V72_Y0.480871.122
69_D72_Y0.455921.063
13_K16_G0.439881.026
25_L90_A0.429841.003
28_D78_E0.422760.986
10_A14_A0.419830.979
81_V90_A0.417150.973
22_L67_Y0.406720.949
40_Y80_E0.405880.947
33_P62_N0.402480.939
34_R84_R0.399880.933
72_Y77_T0.39930.931
34_R53_G0.395840.923
53_G62_N0.388540.906
41_D72_Y0.388470.906
33_P81_V0.387750.904
11_R14_A0.386230.901
68_V79_L0.384830.898
31_A88_V0.383440.894
26_T93_V0.367280.857
56_S63_I0.366390.855
34_R57_P0.357360.834
21_R70_R0.355370.829
77_T92_V0.354830.828
41_D47_V0.353790.825
12_Q17_V0.353160.824
31_A62_N0.345540.806
33_P37_E0.340450.794
46_P49_R0.339880.793
83_I88_V0.339450.792
12_Q15_R0.33680.786
44_G87_R0.336680.785
3_F6_Q0.335630.783
55_Y62_N0.335340.782
30_D34_R0.332850.776
34_R37_E0.329260.768
76_G91_T0.311480.727
5_G8_A0.309860.723
8_A11_R0.309010.721
3_F9_L0.305570.713
24_G63_I0.305120.712
18_K70_R0.301950.704
18_K69_D0.300380.701
56_S61_K0.297530.694
68_V92_V0.295280.689
4_I12_Q0.294220.686
4_I8_A0.292340.682
27_L33_P0.291710.680
50_V53_G0.289320.675
20_R49_R0.287940.672
25_L79_L0.286080.667
41_D79_L0.28130.656
54_A62_N0.280160.653
32_P62_N0.27990.653
47_V69_D0.279530.652
11_R16_G0.278140.649
32_P55_Y0.277730.648
15_R18_K0.272460.636
37_E81_V0.27140.633
40_Y44_G0.269080.628
52_S65_L0.26740.624
17_V21_R0.265740.620
25_L50_V0.265520.619
2_D10_A0.265170.618
35_G53_G0.263230.614
24_G57_P0.262580.612
25_L81_V0.262370.612
51_T65_L0.25740.600
29_G33_P0.254540.594
41_D80_E0.253390.591
6_Q9_L0.250380.584
2_D89_P0.248160.579
49_R67_Y0.246020.574
9_L16_G0.245920.574
44_G80_E0.243940.569
8_A14_A0.240890.562
29_G62_N0.238560.556
11_R18_K0.237740.555
24_G65_L0.237310.554
79_L92_V0.233220.544
30_D62_N0.230.536
76_G92_V0.227670.531
27_L62_N0.22540.526
47_V79_L0.224170.523
45_K70_R0.223490.521
83_I86_K0.22310.520
70_R73_A0.221910.518
32_P53_G0.221610.517
80_E88_V0.219960.513
68_V73_A0.219350.512
85_G88_V0.218360.509
30_D55_Y0.218210.509
31_A55_Y0.218070.509
29_G88_V0.216920.506
22_L51_T0.216570.505
21_R73_A0.21540.502
28_D65_L0.215350.502
3_F13_K0.215070.502
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
3girA0.989599.80.018
3tfiA0.978999.80.038
1yx2A0.978999.80.056
1pj5A0.968499.80.057
3ttgA0.968499.80.094
1wsrA0.978999.80.1
1v5vA0.968499.80.107
2gagA0.989599.70.127
1vloA0.936899.70.129
1wosA0.947499.70.143

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