GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GATase_7 - Glutamine amidotransferase domain
Pfam: PF13537 (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: CL0052
Length: 125
Sequences: 6922
Seq/Len: 55.38
HH_delta: 0.037 (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
45_R64_E1.999584.206
41_E75_R1.682333.538
94_L116_F1.45743.065
17_V25_V1.177722.477
47_H64_E1.167892.456
71_D74_K1.118552.353
28_F55_S1.038622.184
58_I76_L0.980982.063
62_Y72_F0.945031.988
86_D89_K0.908311.910
83_V94_L0.880411.852
94_L104_L0.873941.838
69_G93_F0.853781.796
23_E87_K0.844821.777
12_G53_S0.803091.689
109_T113_G0.800751.684
23_E88_D0.771861.623
61_L68_W0.771051.622
47_H63_E0.767581.614
82_F95_A0.764131.607
40_R43_E0.735271.546
79_P102_R0.732231.540
61_L72_F0.721421.517
47_H60_H0.718151.510
79_P101_I0.704471.482
117_A122_A0.698181.468
115_A123_L0.682331.435
84_I93_F0.667051.403
26_L59_L0.665811.400
40_R44_E0.661971.392
62_Y84_I0.646881.361
69_G84_I0.624071.313
61_L76_L0.62221.309
34_N38_L0.618761.301
41_E45_R0.617961.300
68_W75_R0.614721.293
108_R114_L0.606111.275
85_W92_L0.590151.241
43_E46_G0.576391.212
23_E63_E0.566741.192
72_F76_L0.565951.190
62_Y69_G0.559591.177
120_I124_L0.55241.162
81_A104_L0.55161.160
39_R49_F0.54731.151
10_D13_A0.54281.142
34_N37_E0.542281.141
73_L95_A0.539991.136
51_S56_E0.532571.120
80_F95_A0.530221.115
105_Y123_L0.523041.100
41_E64_E0.51541.084
109_T115_A0.508761.070
26_L55_S0.501861.056
62_Y93_F0.496011.043
3_R29_N0.491141.033
11_E52_D0.483951.018
37_E40_R0.473650.996
36_E40_R0.461530.971
60_H63_E0.456110.959
121_K124_L0.446530.939
110_D113_G0.440170.926
24_L86_D0.43960.925
39_R43_E0.436430.918
106_Y116_F0.435830.917
17_V22_G0.435050.915
41_E44_E0.434050.913
70_E74_K0.432980.911
105_Y120_I0.431580.908
97_D101_I0.429310.903
80_F98_R0.421660.887
27_V83_V0.418950.881
48_Q60_H0.416540.876
1_H28_F0.414850.873
29_N54_D0.41210.867
46_G49_F0.408520.859
23_E86_D0.406870.856
107_G112_N0.397920.837
109_T112_N0.395290.831
83_V116_F0.39370.828
94_L106_Y0.391850.824
32_I58_I0.389170.818
73_L76_L0.386020.812
7_D11_E0.385740.811
68_W72_F0.38390.807
97_D102_R0.382830.805
106_Y114_L0.381150.802
37_E77_D0.380950.801
35_R39_R0.379720.799
33_Y79_P0.378630.796
108_R113_G0.377950.795
83_V92_L0.371050.780
9_S12_G0.369580.777
24_L88_D0.366940.772
28_F32_I0.366810.771
35_R57_L0.362120.762
15_P54_D0.360040.757
109_T114_L0.359090.755
34_N78_G0.357390.752
73_L80_F0.3560.749
11_E50_S0.355840.748
4_L14_Q0.35410.745
22_G63_E0.350740.738
71_D75_R0.34760.731
58_I72_F0.346130.728
24_L63_E0.345570.727
81_A101_I0.337080.709
81_A102_R0.336780.708
96_R101_I0.333430.701
49_F57_L0.327290.688
33_Y77_D0.326580.687
25_V87_K0.324610.683
108_R112_N0.324350.682
58_I82_F0.323150.680
12_G52_D0.322730.679
29_N118_S0.320850.675
6_T31_E0.32040.674
12_G51_S0.318450.670
1_H55_S0.316960.667
34_N40_R0.315770.664
43_E48_Q0.314840.662
37_E41_E0.31440.661
73_L93_F0.312450.657
69_G95_A0.309180.650
32_I35_R0.308930.650
17_V87_K0.306360.644
1_H14_Q0.303670.639
29_N55_S0.301250.634
56_E60_H0.301160.633
22_G50_S0.301040.633
32_I80_F0.300280.632
69_G72_F0.297970.627
117_A121_K0.296660.624
42_L75_R0.293930.618
22_G87_K0.290810.612
86_D93_F0.290380.611
72_F93_F0.286990.604
73_L82_F0.286910.603
24_L62_Y0.284860.599
25_V85_W0.283060.595
42_L46_G0.278050.585
1_H13_A0.277860.584
98_R101_I0.27590.580
31_E79_P0.275190.579
42_L49_F0.272650.573
31_E119_E0.27070.569
37_E75_R0.267350.562
3_R30_G0.262530.552
89_K94_L0.261450.550
17_V63_E0.261010.549
104_L116_F0.260130.547
117_A123_L0.259640.546
16_F55_S0.257930.542
76_L80_F0.257410.541
77_D97_D0.25740.541
57_L61_L0.256830.540
43_E49_F0.255980.538
16_F51_S0.253320.533
16_F53_S0.253250.533
14_Q29_N0.251390.529
97_D123_L0.251390.529
27_V116_F0.250490.527
89_K110_D0.248790.523
107_G120_I0.248630.523
49_F56_E0.248370.522
3_R54_D0.248210.522
39_R57_L0.248050.522
64_E68_W0.245450.516
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
1ct9A0.9699.90.037
1ao0A0.97699.90.051
1ecfA0.99299.90.094
2bplA0.94499.90.106
1jgtA0.9299.90.115
1xffA0.94499.90.126
1q15A0.90499.90.132
3mdnA0.9699.90.182
1ea0A0.92899.80.255
1ofdA0.92899.80.266

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