GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
THF_DHG_CYH - Tetrahydrofolate dehydrogenasecyclohydrolase catalytic domain
Pfam: PF00763 (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: 117
Sequences: 2487
Seq/Len: 21.26
HH_delta: -0.041 (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
80_E109_A1.356873.427
78_L81_K1.161392.933
72_E105_K1.088822.750
80_E84_E1.083652.737
4_D7_P1.060082.677
31_K62_E0.981112.478
28_I89_H0.950442.400
76_L109_A0.934732.361
70_I75_L0.920632.325
13_K56_K0.909962.298
93_V106_I0.836832.113
64_I78_L0.821152.074
24_K29_T0.760981.922
17_K21_E0.692371.748
36_L44_I0.686361.733
31_K60_E0.685211.730
13_K53_A0.672961.699
66_L70_I0.621811.570
60_E87_S0.613911.550
39_D44_I0.609881.540
47_V94_Q0.594971.503
16_L57_L0.585831.479
45_S49_S0.581271.468
72_E76_L0.575971.455
18_E21_E0.573821.449
12_I16_L0.57331.448
62_E88_V0.560161.415
95_L107_L0.559641.413
51_Q63_L0.548751.386
7_P11_E0.54561.378
66_L78_L0.541861.368
20_I59_I0.538751.361
14_E18_E0.526191.329
60_E88_V0.509771.287
69_D74_E0.502771.270
33_A82_L0.500651.264
48_R52_K0.493641.247
39_D68_E0.492261.243
32_L116_V0.490591.239
51_Q65_E0.45961.161
44_I65_E0.45771.156
22_K26_K0.453391.145
71_S74_E0.450261.137
72_E102_D0.447031.129
54_A59_I0.445161.124
102_D105_K0.444991.124
6_K10_K0.443791.121
51_Q55_E0.44221.117
21_E25_E0.43551.100
8_V11_E0.429141.084
64_I81_K0.422371.067
83_N111_D0.420881.063
33_A88_V0.419391.059
3_L8_V0.415541.049
33_A64_I0.414511.047
77_E81_K0.41161.039
18_E22_K0.410291.036
36_L65_E0.408821.032
82_L91_I0.406751.027
29_T60_E0.402661.017
35_I82_L0.400961.013
49_S52_K0.398121.005
50_K94_Q0.397691.004
39_D65_E0.395150.998
10_K14_E0.39310.993
45_S48_R0.390060.985
22_K25_E0.389830.984
52_K56_K0.388490.981
44_I48_R0.383650.969
34_I51_Q0.383650.969
76_L80_E0.381250.963
62_E85_D0.379770.959
93_V110_I0.379460.958
74_E77_E0.371660.939
13_K57_L0.368560.931
82_L88_V0.368560.931
72_E101_I0.366810.926
34_I61_F0.366640.926
76_L105_K0.35970.908
14_E17_K0.358180.905
73_E77_E0.357080.902
23_L27_G0.355740.898
76_L106_I0.352210.889
91_I110_I0.336620.850
104_R108_E0.33410.844
41_P45_S0.333320.842
23_L28_I0.33040.834
16_L19_E0.327370.827
47_V50_K0.327240.826
55_E60_E0.32550.822
95_L103_E0.324390.819
53_A57_L0.323880.818
19_E23_L0.32130.811
10_K56_K0.318840.805
5_G9_A0.317630.802
104_R107_L0.313490.792
70_I78_L0.307040.775
43_S50_K0.306230.773
11_E15_E0.303620.767
84_E109_A0.301710.762
31_K88_V0.300060.758
64_I82_L0.292690.739
81_K85_D0.292530.739
15_E18_E0.291610.736
21_E24_K0.287730.727
43_S94_Q0.287590.726
75_L106_I0.285920.722
54_A61_F0.284860.719
76_L101_I0.283580.716
34_I92_L0.282510.713
16_L20_I0.281210.710
9_A13_K0.280350.708
84_E111_D0.279170.705
50_K95_L0.277770.701
52_K55_E0.274070.692
34_I50_K0.271480.686
37_V75_L0.270330.683
50_K93_V0.265880.671
12_I15_E0.264990.669
47_V63_L0.263370.665
37_V98_P0.263110.664
75_L101_I0.262760.664
15_E19_E0.261390.660
17_K56_K0.256810.649
34_I63_L0.256750.648
20_I30_P0.255210.644
43_S47_V0.254340.642
53_A56_K0.254120.642
49_S53_A0.251250.634
83_N114_K0.248890.629
97_L106_I0.248210.627
11_E14_E0.247150.624
47_V92_L0.244630.618
20_I23_L0.243870.616
103_E107_L0.242320.612
20_I57_L0.242310.612
19_E22_K0.241880.611
24_K28_I0.240340.607
67_P70_I0.239860.606
77_E80_E0.239210.604
80_E111_D0.236920.598
14_E56_K0.236570.597
36_L47_V0.236560.597
105_K109_A0.235950.596
50_K117_D0.23590.596
20_I27_G0.228330.577
13_K16_L0.228320.577
45_S103_E0.224760.568
33_A62_E0.223530.564
43_S95_L0.222370.562
14_E73_E0.222090.561
79_I111_D0.221150.558
76_L83_N0.220840.558
70_I101_I0.220440.557
92_L103_E0.218520.552
37_V97_L0.21840.552
86_P89_H0.217590.549
75_L97_L0.217250.549
55_E59_I0.214880.543
101_I106_I0.213760.540
8_V16_L0.212880.538
62_E87_S0.211060.533
54_A57_L0.210690.532
10_K13_K0.210080.531
7_P10_K0.208730.527
33_A63_L0.207970.525
79_I93_V0.206430.521
34_I49_S0.204580.517
35_I79_I0.204410.516
61_F92_L0.200520.506
79_I106_I0.200030.505
35_I106_I0.197470.499
13_K17_K0.197450.499
34_I117_D0.196750.497
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
2c2xA1100-0.041
1b0aA1100-0.034
1a4iA1100-0.027
4a26A1100-0.021
3p2oA1100-0.018
3ngxA0.9658100-0.016
3l07A1100-0.013
4a5oA1100-0.011
4b4uA1100-0.007
1edzA0.97441000.01

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