GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pterin_4a - Pterin 4 alpha carbinolamine dehydratase
Pfam: PF01329 (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: 95
Sequences: 1313
Seq/Len: 13.82
HH_delta: -0.006 (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
76_A80_T0.816862.731
69_V90_I0.69132.312
30_R91_D0.664062.220
44_V62_L0.637042.130
31_T68_T0.622962.083
6_S9_E0.613862.053
41_V48_A0.604192.020
71_L90_I0.572741.915
71_L86_L0.52981.772
13_A84_F0.528441.767
59_D63_G0.527411.764
34_F43_F0.50351.684
36_D39_E0.488381.633
81_E85_I0.47431.586
19_G30_R0.47181.578
47_V90_I0.463941.551
57_H74_H0.462821.548
41_V45_N0.461361.543
82_K85_I0.448511.500
54_E85_I0.440481.473
27_R70_T0.430181.438
41_V44_V0.416171.392
50_L89_R0.410831.374
5_L10_I0.404411.352
44_V60_I0.40191.344
54_E82_K0.395291.322
51_A58_P0.39341.315
79_L84_F0.38871.300
43_F67_V0.38711.294
29_E70_T0.365421.222
32_F90_I0.364331.218
64_Y74_H0.357531.195
8_E12_E0.356931.193
41_V62_L0.353921.183
60_I69_V0.353241.181
22_L79_L0.353031.180
50_L54_E0.339561.135
56_H74_H0.337981.130
23_D29_E0.33251.112
31_T66_R0.328481.098
84_F88_A0.327651.096
35_K39_E0.323171.081
32_F94_A0.32291.080
42_E45_N0.321751.076
5_L14_L0.318641.065
37_F40_A0.308631.032
7_E11_A0.30711.027
49_A53_E0.306151.024
50_L93_L0.302541.012
86_L90_I0.300251.004
38_A46_R0.299711.002
43_F94_A0.297240.994
27_R72_T0.29390.983
29_E68_T0.288770.966
41_V60_I0.28620.957
40_A62_L0.285340.954
10_I22_L0.280610.938
59_D74_H0.280560.938
19_G91_D0.271770.909
10_I79_L0.267850.896
42_E49_A0.267510.894
21_K29_E0.265440.888
11_A15_A0.263870.882
18_P30_R0.263290.880
14_L22_L0.253250.847
16_E88_A0.252680.845
57_H64_Y0.25260.845
38_A52_E0.250870.839
7_E22_L0.250590.838
7_E10_I0.250540.838
63_G66_R0.249760.835
13_A17_L0.249750.835
32_F69_V0.249070.833
56_H83_D0.245910.822
73_T82_K0.242750.812
10_I84_F0.242210.810
40_A67_V0.242090.809
33_K65_N0.237940.796
38_A49_A0.236060.789
54_E89_R0.235330.787
22_L28_L0.23480.785
17_L84_F0.234420.784
81_E84_F0.22960.768
43_F47_V0.227790.762
44_V48_A0.22610.756
32_F91_D0.224970.752
16_E94_A0.223320.747
82_K86_L0.222330.743
85_I89_R0.221680.741
34_F37_F0.221270.740
73_T83_D0.216850.725
7_E18_P0.21340.714
47_V69_V0.21080.705
57_H83_D0.210070.702
73_T77_G0.208570.697
4_P7_E0.208150.696
36_D45_N0.207880.695
37_F48_A0.207160.693
7_E12_E0.206870.692
8_E11_A0.206570.691
38_A42_E0.20550.687
43_F58_P0.204870.685
37_F58_P0.203370.680
13_A16_E0.203130.679
85_I88_A0.203030.679
45_N49_A0.202810.678
49_A52_E0.200010.669
61_S68_T0.195090.652
32_F43_F0.194070.649
50_L53_E0.193510.647
13_A88_A0.191330.640
14_L17_L0.190580.637
37_F86_L0.190480.637
26_G59_D0.189550.634
9_E81_E0.187570.627
21_K31_T0.186360.623
12_E15_A0.186280.623
7_E24_G0.186080.622
89_R92_D0.185880.622
22_L84_F0.184640.617
54_E86_L0.184530.617
17_L91_D0.182870.611
56_H73_T0.182430.610
10_I26_G0.180140.602
40_A52_E0.178760.598
56_H64_Y0.178280.596
37_F41_V0.17810.596
35_K66_R0.176620.591
9_E13_A0.174130.582
30_R43_F0.171520.574
8_E15_A0.170920.572
38_A55_N0.170770.571
12_E16_E0.170510.570
13_A79_L0.170490.570
4_P14_L0.169940.568
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
2v6uA0.989599.9-0.006
3hxaA199.9-0.002
3jstA199.9-0.001
2ebbA0.978999.90.002
1ru0A199.90.005
1usmA0.810599.90.119
1gweA0.968443.40.887
1si8A0.957931.40.895
2j2mA0.957929.10.896
4eacA0.978925.10.899

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