GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MurB_C - UDP-N-acetylenolpyruvoylglucosamine reductase C-terminal domain
Pfam: PF02873 (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: 105
Sequences: 1852
Seq/Len: 17.64
HH_delta: 0.003 (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
90_K96_E1.394243.776
57_A73_A1.065062.884
49_L88_R1.028792.786
31_K98_E0.941382.549
42_W46_Q0.931552.523
56_G72_G0.838392.270
53_R58_Q0.801562.171
84_E88_R0.775462.100
52_F84_E0.761752.063
53_R70_H0.757112.050
41_G64_A0.710361.924
36_D42_W0.707261.915
76_A80_A0.693911.879
5_R9_Q0.659781.787
58_Q70_H0.649771.760
58_Q61_E0.640061.733
2_E6_E0.63881.730
86_R99_P0.62761.700
49_L52_F0.611511.656
87_E91_E0.609951.652
49_L84_E0.600551.626
59_V85_V0.598241.620
13_R17_L0.585171.585
32_N65_N0.576571.561
7_A10_E0.575471.558
54_I84_E0.570281.544
23_L68_V0.566561.534
47_A89_V0.559411.515
50_K64_A0.553861.500
45_E50_K0.54381.473
88_R91_E0.543611.472
60_S63_H0.540891.465
56_G70_H0.525821.424
83_E86_R0.523711.418
88_R92_K0.52351.418
79_L103_I0.520831.410
67_I78_V0.51421.392
29_V67_I0.501561.358
86_R96_E0.499341.352
47_A92_K0.493351.336
29_V82_I0.484991.313
40_A43_L0.476081.289
44_I85_V0.465411.260
56_G77_D0.460491.247
52_F88_R0.434011.175
55_G77_D0.433631.174
82_I99_P0.428231.160
57_A81_L0.412861.118
3_E7_A0.412841.118
47_A93_F0.409721.110
26_A29_V0.407291.103
53_R56_G0.393971.067
19_Q66_F0.385441.044
3_E6_E0.380871.031
90_K94_G0.379721.028
26_A101_V0.377811.023
4_I8_M0.376411.019
77_D80_A0.369991.002
99_P103_I0.367950.996
41_G50_K0.366660.993
73_A78_V0.359980.975
10_E14_K0.352250.954
56_G71_G0.347970.942
89_V93_F0.341980.926
6_E10_E0.318930.864
80_A84_E0.317750.860
9_Q13_R0.312210.845
60_S66_F0.310330.840
39_S42_W0.302810.820
80_A87_E0.300060.813
57_A78_V0.292890.793
33_P40_A0.292230.791
84_E87_E0.28960.784
54_I80_A0.286750.777
14_K18_K0.286470.776
46_Q93_F0.280530.760
79_L99_P0.278220.753
11_I14_K0.276140.748
36_D95_I0.273320.740
8_M12_R0.270170.732
26_A67_I0.264760.717
59_V78_V0.26450.716
47_A88_R0.261620.708
83_E103_I0.261390.708
22_E62_K0.260140.704
40_A89_V0.257720.698
49_L85_V0.251310.681
1_K5_R0.249620.676
33_P95_I0.247470.670
69_N73_A0.245640.665
79_L86_R0.245120.664
75_A103_I0.241960.655
61_E70_H0.24080.652
57_A67_I0.239550.649
22_E68_V0.238710.646
59_V81_L0.237280.643
83_E87_E0.236220.640
23_L70_H0.228250.618
12_R45_E0.226890.614
86_R104_I0.225950.612
67_I81_L0.22390.606
67_I73_A0.222620.603
18_K62_K0.222110.601
35_G39_S0.218660.592
43_L47_A0.218450.592
26_A78_V0.217120.588
75_A79_L0.217010.588
28_S100_E0.216460.586
18_K25_S0.215620.584
28_S45_E0.214030.580
43_L97_L0.213780.579
32_N39_S0.210590.570
57_A75_A0.209250.567
87_E96_E0.206870.560
50_K78_V0.206660.560
18_K32_N0.205640.557
81_L85_V0.204890.555
53_R80_A0.204390.553
20_P33_P0.198980.539
87_E90_K0.196530.532
73_A77_D0.194060.526
18_K65_N0.193560.524
59_V67_I0.193260.523
44_I59_V0.192440.521
8_M11_I0.190820.517
18_K66_F0.19080.517
30_F82_I0.190010.515
53_R71_G0.189090.512
3_E53_R0.188090.509
6_E9_Q0.187010.506
65_N101_V0.186820.506
82_I103_I0.184150.499
24_P28_S0.183980.498
15_R28_S0.183970.498
67_I82_I0.18360.497
12_R65_N0.182910.495
4_I31_K0.182650.495
2_E80_A0.182610.494
15_R24_P0.181620.492
15_R63_H0.181560.492
74_T77_D0.180690.489
28_S41_G0.180530.489
72_G87_E0.180520.489
1_K4_I0.180320.488
46_Q92_K0.180250.488
4_I11_I0.179090.485
80_A96_E0.178590.484
7_A14_K0.178330.483
15_R26_A0.176830.479
6_E13_R0.176670.478
28_S39_S0.176190.477
25_S32_N0.175570.475
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
3tx1A0.9811000.003
3i99A0.99051000.008
1uxyA11000.037
2gqtA0.90481000.111
1hskA0.98199.90.347
3ih1A0.866748.80.914
3m8uA0.895247.50.914
3eooA0.857144.20.916
2hjpA0.838142.80.917
3tpaA0.8952420.917

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