GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AdoHcyase_NAD - S-adenosyl-L-homocysteine hydrolase NAD binding domain
Pfam: PF00670 (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: 162
Sequences: 16636
Seq/Len: 102.69
HH_delta: 0.261 (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
25_R48_R2.335723.280
26_V42_L2.061022.894
43_R68_E1.981332.782
21_L24_K1.970422.767
27_V79_A1.961132.754
59_A63_A1.880842.641
60_L64_M1.865862.620
147_I151_E1.797162.523
56_P60_L1.789182.512
27_V52_T1.737972.440
39_A67_F1.700192.387
31_Y51_V1.661742.333
105_I130_E1.608532.259
60_L63_A1.573922.210
80_D101_K1.563812.196
53_E59_A1.522832.138
105_I132_R1.520032.134
48_R68_E1.499852.106
48_R69_V1.481132.080
59_A70_M1.452442.039
100_M106_L1.331331.869
82_F100_M1.324661.860
61_Q64_M1.28971.811
50_T79_A1.259361.768
100_M104_A1.226941.723
147_I150_A1.206551.694
25_R50_T1.176591.652
100_M129_E1.157571.625
25_R80_D1.141871.603
24_K105_I1.135281.594
82_F96_H1.117261.569
29_I96_H1.09461.537
29_I52_T1.066211.497
44_G153_R1.054971.481
56_P59_A1.043961.466
39_A51_V1.033171.451
44_G148_L1.013991.424
55_D58_R0.968481.360
148_L153_R0.943741.325
103_G128_R0.929761.305
144_R147_I0.908331.275
56_P71_T0.904791.270
38_I83_V0.893021.254
84_T87_G0.890431.250
139_T142_D0.876331.230
57_I60_L0.875471.229
144_R148_L0.851531.196
27_V99_Q0.850131.194
50_T69_V0.84511.187
20_M47_A0.841231.181
29_I82_F0.827431.162
41_A148_L0.825081.158
63_A69_V0.817221.147
146_I150_A0.808791.136
24_K80_D0.807431.134
51_V62_A0.767091.077
31_Y39_A0.758391.065
28_V38_I0.754641.060
82_F106_L0.753071.057
24_K81_I0.748851.051
31_Y62_A0.746141.048
39_A49_V0.742121.042
31_Y53_E0.739391.038
96_H106_L0.727411.021
36_K61_Q0.71971.011
76_L79_A0.718611.009
20_M24_K0.716871.007
86_T91_V0.714191.003
38_I85_A0.700370.983
54_I59_A0.69870.981
12_G109_A0.69420.975
63_A70_M0.687980.966
51_V67_F0.682080.958
119_D122_E0.677950.952
42_L47_A0.677330.951
28_V42_L0.664180.933
41_A145_R0.646790.908
95_E98_R0.644880.905
37_G41_A0.638650.897
84_T106_L0.637920.896
114_V117_D0.625740.879
42_L49_V0.624760.877
79_A82_F0.619650.870
93_T98_R0.617830.867
25_R79_A0.616780.866
40_R65_D0.615550.864
143_G147_I0.61140.858
148_L152_G0.601540.845
148_L151_E0.599390.842
92_I108_N0.584840.821
86_T110_G0.582860.818
26_V47_A0.581010.816
25_R78_D0.580330.815
128_R137_R0.577080.810
38_I109_A0.57190.803
85_A109_A0.570470.801
26_V81_I0.554610.779
20_M81_I0.55320.777
54_I72_L0.552430.776
93_T115_E0.543590.763
30_G85_A0.542070.761
62_A70_M0.532170.747
81_I107_A0.53140.746
55_D71_T0.529350.743
62_A67_F0.529060.743
28_V51_V0.527050.740
107_A132_R0.524260.736
29_I91_V0.522030.733
82_F104_A0.517560.727
53_E70_M0.516930.726
41_A45_L0.513530.721
59_A71_T0.513470.721
81_I105_I0.511960.719
82_F99_Q0.511260.718
117_D121_L0.506790.712
53_E58_R0.506350.711
138_Y142_D0.501080.704
27_V82_F0.497940.699
26_V83_V0.497640.699
34_V85_A0.488750.686
39_A65_D0.48640.683
89_K93_T0.485070.681
93_T117_D0.475220.667
22_A46_G0.475020.667
137_R142_D0.471640.662
33_K58_R0.465250.653
37_G40_R0.464990.653
95_E99_Q0.464640.652
22_A45_L0.462660.650
40_R43_R0.461540.648
108_N131_V0.452750.636
102_D127_E0.451750.634
12_G38_I0.451620.634
21_L81_I0.450270.632
90_D95_E0.449980.632
39_A62_A0.442430.621
47_A81_I0.435820.612
89_K114_V0.435720.612
84_T110_G0.435130.611
28_V35_G0.433390.609
136_D139_T0.430740.605
36_K65_D0.43020.604
88_N91_V0.429250.603
108_N112_F0.428310.601
72_L75_A0.422080.593
13_I20_M0.421080.591
149_L154_L0.419680.589
34_V109_A0.418720.588
32_G85_A0.418310.587
91_V96_H0.41470.582
39_A43_R0.414560.582
56_P63_A0.41360.581
84_T108_N0.409990.576
135_V139_T0.407560.572
33_K36_K0.404330.568
81_I84_T0.403610.567
73_E95_E0.403350.566
106_L131_V0.401320.563
50_T68_E0.400060.562
53_E71_T0.39970.561
50_T76_L0.399650.561
25_R69_V0.397160.558
83_V107_A0.396340.556
84_T96_H0.396080.556
13_I45_L0.394620.554
102_D128_R0.393990.553
29_I95_E0.393680.553
35_G53_E0.392170.551
49_V68_E0.39030.548
79_A99_Q0.389340.547
59_A62_A0.387860.545
91_V95_E0.38340.538
23_G47_A0.383120.538
90_D93_T0.379220.532
50_T78_D0.378870.532
54_I71_T0.378210.531
87_G110_G0.376680.529
36_K58_R0.37490.526
135_V138_Y0.374510.526
28_V39_A0.373650.525
20_M26_V0.372660.523
140_L143_G0.37260.523
136_D140_L0.371630.522
116_I121_L0.369970.519
93_T119_D0.368480.517
92_I116_I0.36790.517
43_R49_V0.367310.516
118_V121_L0.365930.514
25_R77_R0.364820.512
57_I61_Q0.355730.499
150_A153_R0.355410.499
115_E119_D0.355350.499
100_M128_R0.353880.497
137_R140_L0.353410.496
40_R44_G0.351910.494
128_R135_V0.351860.494
117_D120_A0.351730.494
143_G146_I0.350420.492
122_E136_D0.349160.490
61_Q65_D0.349130.490
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
3gvpA0.993899.70.261
3n58A0.987799.70.269
3twoA0.975399.70.29
3h9uA199.70.302
3s2eA0.975399.70.309
1uufA0.975399.70.313
2dphA0.975399.60.319
1piwA0.969199.60.32
3jv7A0.981599.60.322
2cf5A0.969199.60.325

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