GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DHFR_1 - Dihydrofolate reductase
Pfam: PF00186 (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: CL0387
Length: 161
Sequences: 5593
Seq/Len: 34.74
HH_delta: 0.021 (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_R48_E1.318563.247
10_K119_D1.158142.852
59_I75_E1.121122.761
138_L141_E1.094782.696
4_L110_A1.04222.567
13_G124_G1.007752.482
96_V106_F0.914722.253
4_L103_Y0.878952.165
3_S114_Y0.821372.023
6_V115_L0.80671.987
86_L90_K0.78281.928
8_V12_G0.770681.898
101_E105_Q0.761351.875
63_L102_I0.755111.860
86_L89_D0.750061.847
3_S37_G0.747541.841
14_I100_A0.743061.830
8_V117_R0.736761.814
36_T57_G0.730111.798
9_D13_G0.719691.772
79_S82_E0.717051.766
75_E90_K0.713021.756
80_L106_F0.704811.736
30_F34_L0.6761.665
39_P61_I0.665861.640
45_K49_S0.635731.566
41_I94_I0.627331.545
107_L113_L0.626821.544
31_F116_T0.624861.539
38_N92_E0.611071.505
8_V115_L0.605221.490
3_S93_E0.58961.452
38_N95_F0.587821.448
3_S112_R0.581111.431
39_P59_I0.542051.335
9_D122_F0.538511.326
42_M47_F0.535841.320
40_V60_N0.531451.309
9_D120_G0.530381.306
45_K48_E0.516461.272
82_E85_E0.511481.260
39_P94_I0.50981.255
6_V103_Y0.505811.246
78_S82_E0.500721.233
10_K121_D0.499171.229
42_M98_G0.492391.213
64_S68_D0.491281.210
65_R101_E0.488111.202
77_V86_L0.481331.185
16_K123_E0.480291.183
29_K33_K0.463811.142
106_F109_Y0.462591.139
64_S67_P0.459111.131
39_P91_D0.458881.130
101_E104_E0.457221.126
60_N97_I0.444731.095
40_V97_I0.438821.081
104_E108_P0.433331.067
82_E86_L0.42931.057
38_N93_E0.422191.040
81_E109_Y0.422091.039
41_I106_F0.418521.031
66_N69_Y0.41561.023
31_F35_T0.415281.023
32_K36_T0.415151.022
2_I96_V0.412481.016
100_A104_E0.411771.014
11_N121_D0.402010.990
110_A113_L0.401810.990
63_L83_A0.398910.982
85_E89_D0.395350.974
42_M50_L0.394510.972
13_G126_T0.392430.966
102_I106_F0.388140.956
20_L28_L0.386820.953
96_V102_I0.384150.946
45_K101_E0.382180.941
83_A87_A0.382050.941
83_A86_L0.381170.939
28_L32_K0.380230.936
84_L106_F0.380140.936
43_G98_G0.379140.934
54_P60_N0.378780.933
61_I87_A0.377020.928
30_F114_Y0.376290.927
10_K117_R0.37580.925
50_L60_N0.375750.925
64_S69_Y0.374080.921
2_I84_L0.373820.921
13_G127_F0.370760.913
11_N123_E0.36460.898
81_E85_E0.361220.890
5_I95_F0.359220.885
67_P78_S0.357570.881
34_L114_Y0.354990.874
24_L28_L0.35360.871
25_P28_L0.350430.863
59_I90_K0.349440.861
59_I91_D0.347080.855
113_L131_I0.347060.855
41_I102_I0.346370.853
2_I110_A0.346330.853
60_N64_S0.34180.842
47_F74_V0.340920.840
46_T98_G0.337010.830
93_E112_R0.336610.829
126_T129_P0.336180.828
80_L109_Y0.336110.828
48_E69_Y0.334290.823
61_I77_V0.327350.806
6_V14_I0.326850.805
44_R69_Y0.325990.803
102_I105_Q0.325490.802
44_R64_S0.322460.794
95_F114_Y0.321810.792
44_R65_R0.321570.792
13_G122_F0.321120.791
6_V128_F0.320260.789
27_D30_F0.319370.786
32_K35_T0.312850.770
96_V110_A0.312290.769
35_T95_F0.31180.768
4_L96_V0.310960.766
42_M97_I0.309390.762
105_Q108_P0.306510.755
8_V113_L0.304520.750
30_F33_K0.303620.748
23_H28_L0.30320.747
87_A90_K0.297610.733
84_L87_A0.296980.731
12_G117_R0.296720.731
48_E68_D0.295130.727
63_L106_F0.293850.724
25_P29_K0.291960.719
3_S95_F0.290050.714
135_E138_L0.289330.713
121_D136_F0.288410.710
64_S76_V0.286440.705
47_F51_P0.282530.696
28_L31_F0.282030.695
2_I94_I0.281990.694
18_G49_S0.281980.694
88_K92_E0.280950.692
51_P60_N0.280830.692
120_G135_E0.28030.690
5_I116_T0.279880.689
84_L94_I0.279120.687
50_L97_I0.277060.682
5_I34_L0.276990.682
53_R60_N0.27660.681
8_V127_F0.271390.668
2_I111_D0.270.665
12_G130_E0.269840.665
9_D124_G0.26970.664
29_K32_K0.268370.661
56_P78_S0.268330.661
16_K19_K0.265810.655
113_L136_F0.264730.652
4_L107_L0.264240.651
67_P76_V0.263850.650
2_I106_F0.263050.648
20_L23_H0.261640.644
28_L35_T0.261560.644
32_K56_P0.26050.642
80_L105_Q0.259440.639
61_I83_A0.259330.639
27_D116_T0.257960.635
7_A99_G0.257750.635
67_P70_E0.256560.632
64_S78_S0.256430.631
26_E29_K0.256350.631
48_E70_E0.255820.630
31_F34_L0.254580.627
33_K36_T0.254390.626
41_I63_L0.254130.626
20_L24_L0.253530.624
10_K120_G0.253370.624
84_L88_K0.252060.621
117_R138_L0.251510.619
7_A118_I0.249480.614
35_T58_R0.248280.611
37_G93_E0.248140.611
33_K142_E0.247220.609
15_G22_W0.244630.602
8_V128_F0.244160.601
5_I50_L0.243350.599
80_L83_A0.240820.593
15_G125_D0.240790.593
2_I109_Y0.239330.589
91_D94_I0.239270.589
31_F97_I0.239150.589
22_W116_T0.238290.587
46_T106_F0.2370.584
14_I99_G0.23520.579
103_Y110_A0.235140.579
30_F116_T0.233830.576
7_A22_W0.233090.574
87_A91_D0.232920.574
14_I103_Y0.230930.569
62_V69_Y0.230.566
100_A122_F0.227610.561
100_A126_T0.226860.559
47_F50_L0.226350.557
107_L110_A0.225150.554
126_T130_E0.225060.554
73_G76_V0.224940.554
59_I87_A0.223770.551
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
3ix9A11000.021
3tq8A0.98761000.021
3s9uA0.98761000.025
3dauA0.98141000.029
3ia4A0.98761000.032
1zdrA0.99381000.051
3dfrA0.98761000.059
3rg9A11000.064
3nzbX11000.08
2w9hA0.96891000.085

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