GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GFA - Glutathione-dependent formaldehyde-activating enzyme
Pfam: PF04828 (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: 92
Sequences: 2697
Seq/Len: 29.32
HH_delta: 0.055 (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
37_K52_P0.889513.284
2_V18_A0.663072.448
37_K53_T0.620092.289
23_P26_D0.58152.147
6_S9_R0.569972.104
5_C8_C0.560352.069
10_K77_D0.553512.044
50_F55_G0.543342.006
29_W59_F0.534981.975
3_C8_C0.526761.945
20_A73_A0.512721.893
38_E47_E0.501571.852
35_N53_T0.473131.747
11_W57_P0.445931.646
34_E52_P0.433561.601
22_V27_F0.423811.565
24_K61_E0.413811.528
12_S74_G0.405081.496
49_Y61_E0.396231.463
47_E61_E0.395481.460
4_H87_H0.391241.444
24_K67_D0.380311.404
40_Q47_E0.375611.387
38_E49_Y0.372311.375
46_V60_S0.36921.363
19_W70_G0.3641.344
11_W48_R0.363031.340
35_N52_P0.359771.328
49_Y59_F0.356691.317
21_I70_G0.354581.309
72_N75_T0.350341.293
17_S72_N0.338951.251
34_E39_Y0.320541.183
36_L39_Y0.311491.150
43_G46_V0.304171.123
19_W72_N0.303521.121
57_P60_S0.298281.101
78_D81_E0.292411.080
2_V74_G0.27441.013
83_K86_A0.274051.012
24_K27_F0.271581.003
2_V16_F0.27111.001
7_D60_S0.266550.984
36_L49_Y0.265990.982
40_Q44_K0.263910.974
6_S10_K0.262380.969
65_D68_L0.259470.958
31_S34_E0.255010.942
24_K69_V0.250590.925
51_C55_G0.250030.923
48_R60_S0.247030.912
13_G74_G0.245830.908
29_W58_L0.242140.894
4_H16_F0.238020.879
15_P73_A0.233930.864
9_R74_G0.233670.863
28_R33_S0.230420.851
40_Q43_G0.230110.850
2_V87_H0.227930.842
48_R57_P0.227850.841
60_S72_N0.222950.823
58_L75_T0.221570.818
21_I68_L0.221120.816
13_G72_N0.220260.813
22_V26_D0.220010.812
20_A76_L0.219780.811
34_E37_K0.218820.808
45_G63_E0.213170.787
34_E53_T0.21170.782
10_K56_S0.210550.777
57_P72_N0.205630.759
72_N76_L0.205130.757
25_D67_D0.204470.755
2_V19_W0.204250.754
21_I46_V0.20130.743
19_W60_S0.20110.742
73_A76_L0.199920.738
51_C54_C0.198410.733
11_W56_S0.197820.730
55_G71_V0.192430.710
10_K50_F0.191910.709
4_H13_G0.190930.705
33_S52_P0.190810.704
25_D83_K0.190560.704
2_V15_P0.190510.703
46_V62_D0.189410.699
64_R68_L0.189050.698
7_D11_W0.18870.697
80_D83_K0.187760.693
11_W70_G0.187290.691
36_L52_P0.1870.690
9_R13_G0.185470.685
13_G57_P0.183770.678
60_S70_G0.18310.676
18_A73_A0.180350.666
27_F69_V0.179770.664
11_W46_V0.17850.659
12_S72_N0.178440.659
44_K63_E0.17840.659
71_V84_P0.177480.655
42_S45_G0.176930.653
59_F71_V0.175560.648
25_D79_P0.175150.647
12_S73_A0.174760.645
40_Q53_T0.173390.640
26_D35_N0.172580.637
22_V28_R0.172570.637
16_F72_N0.172360.636
82_F87_H0.172280.636
38_E61_E0.169550.626
6_S78_D0.169460.626
32_G36_L0.167270.618
13_G19_W0.165580.611
48_R77_D0.164590.608
18_A74_G0.164480.607
21_I86_A0.160960.594
17_S23_P0.159120.587
62_D65_D0.158870.587
50_F57_P0.158360.585
12_S17_S0.158280.584
16_F70_G0.156570.578
32_G37_K0.155960.576
24_K58_L0.15570.575
33_S49_Y0.15410.569
19_W62_D0.153390.566
13_G56_S0.153310.566
57_P70_G0.15290.565
21_I24_K0.152440.563
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
1x6mA0.989199.80.055
3facA0.956599.60.218
3cngA0.541.70.861
2a6hD0.554337.90.864
3j20Y0.521728.70.872
3lu0D0.554323.30.877
4kn7D0.554323.30.877
2k4xA0.543522.70.877
2lcqA0.380419.90.88
1hqmD0.554317.70.883

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