GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
S-AdoMet_synt_N - S-adenosylmethionine synthetase N-terminal domain
Pfam: PF00438 (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: 100
Sequences: 1413
Seq/Len: 14.13
HH_delta: -0.048 (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
44_L53_A1.686254.779
73_K86_Y1.310813.715
30_C37_A1.205873.418
66_K70_E0.949782.692
29_A32_K0.905362.566
18_I75_I0.839852.380
19_C45_V0.839442.379
78_D82_Y0.743772.108
73_K87_D0.742382.104
41_C56_I0.712232.019
30_C58_S0.688631.952
33_Q60_A0.662311.877
25_A67_I0.646791.833
44_L51_I0.645891.831
46_S96_H0.63451.798
21_Q25_A0.614971.743
52_I64_I0.600891.703
52_I68_V0.599571.699
23_S43_T0.572141.622
21_Q71_V0.56831.611
25_A71_V0.549821.558
63_D66_K0.544391.543
70_E73_K0.528261.497
49_M90_E0.511541.450
78_D86_Y0.491611.393
27_L39_V0.479391.359
19_C44_L0.478691.357
45_V50_V0.477721.354
49_M92_L0.476191.350
59_R100_P0.469171.330
26_I41_C0.442831.255
37_A59_R0.442311.254
79_D82_Y0.440291.248
50_V72_I0.431561.223
70_E74_D0.427651.212
61_Y97_E0.427391.211
72_I89_C0.42571.207
38_R57_T0.424951.204
29_A62_V0.420121.191
71_V74_D0.408851.159
11_S19_C0.388121.100
66_K97_E0.387761.099
49_M94_A0.385371.092
29_A33_Q0.383291.086
62_V67_I0.380921.080
18_I45_V0.380231.078
72_I84_F0.369941.049
80_S88_T0.366061.038
29_A67_I0.365171.035
18_I22_I0.356571.011
51_I94_A0.353541.002
18_I72_I0.353311.001
57_T100_P0.352530.999
64_I93_V0.344560.977
36_N59_R0.329380.934
30_C56_I0.326320.925
30_C62_V0.32560.923
41_C95_I0.323670.917
48_G90_E0.319810.906
61_Y95_I0.31960.906
11_S65_E0.317790.901
26_I64_I0.313870.890
46_S49_M0.311330.882
90_E94_A0.302060.856
65_E94_A0.298040.845
19_C50_V0.294240.834
7_S10_V0.292780.830
84_F88_T0.280750.796
73_K78_D0.279910.793
51_I92_L0.275560.781
81_E87_D0.273210.774
48_G94_A0.271250.769
51_I90_E0.271160.769
31_L37_A0.268370.761
45_V84_F0.267640.759
84_F89_C0.260130.737
61_Y64_I0.257720.730
19_C53_A0.254490.721
34_D37_A0.254120.720
33_Q58_S0.248810.705
21_Q31_L0.240340.681
68_V71_V0.238890.677
9_S12_E0.238250.675
37_A60_A0.236010.669
46_S65_E0.235710.668
53_A93_V0.233920.663
72_I77_Y0.233880.663
27_L52_I0.231470.656
22_I45_V0.227750.646
78_D87_D0.226360.642
34_D39_V0.225350.639
90_E96_H0.221970.629
79_D87_D0.221440.628
52_I95_I0.22060.625
50_V68_V0.220520.625
14_H17_K0.220310.624
48_G80_S0.219770.623
43_T99_S0.219050.621
10_V14_H0.21880.620
80_S85_D0.217810.617
82_Y86_Y0.215970.612
33_Q62_V0.215520.611
12_E75_I0.214780.609
65_E68_V0.214040.607
7_S23_S0.211350.599
38_R53_A0.21090.598
8_E14_H0.207160.587
56_I64_I0.206690.586
8_E16_D0.206560.585
80_S84_F0.206510.585
30_C60_A0.204360.579
37_A58_S0.203490.577
15_P99_S0.203230.576
47_T96_H0.201930.572
54_G98_Q0.200630.569
55_E98_Q0.200430.568
36_N66_K0.199310.565
40_A54_G0.197890.561
67_I71_V0.196270.556
8_E15_P0.195830.555
46_S94_A0.195350.554
13_G16_D0.190210.539
18_I84_F0.190110.539
65_E93_V0.189840.538
40_A55_E0.187460.531
34_D58_S0.187160.530
8_E17_K0.186880.530
11_S81_E0.186490.529
40_A98_Q0.186320.528
50_V84_F0.185680.526
65_E96_H0.183070.519
46_S53_A0.182040.516
11_S53_A0.178870.507
82_Y85_D0.178230.505
5_F47_T0.178170.505
30_C64_I0.176640.501
36_N74_D0.17520.497
6_T10_V0.175130.496
25_A31_L0.174160.494
9_S77_Y0.172980.490
63_D97_E0.172010.488
34_D57_T0.171810.487
31_L34_D0.170740.484
85_D89_C0.17030.483
57_T97_E0.167090.474
70_E100_P0.165650.470
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
3so4A1100-0.048
3imlA1100-0.045
3s82A1100-0.043
2p02A1100-0.041
1p7lA1100-0.037
4l7iA0.9992.40.893
4hpvA0.9992.40.893
2wyhA0.9545.60.929
3sv0A0.7444.90.929
3uzpA0.6936.10.933

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