GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Prenyltrans_1 - Prenyltransferase-like
Pfam: PF13243 (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: CL0059
Length: 109
Sequences: 4299
Seq/Len: 39.44
HH_delta: 0.246 (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
100_E104_S0.722762.492
60_N66_G0.616582.126
7_W11_Q0.578061.993
6_E10_S0.567241.956
56_L94_A0.565261.949
12_Q16_G0.544091.876
53_D57_S0.540461.863
15_D24_S0.518611.788
12_Q18_W0.496591.712
12_Q50_K0.494791.706
33_I82_A0.482631.664
101_W105_H0.478451.650
59_Q98_G0.478151.648
50_K53_D0.443491.529
29_T32_L0.4421.524
96_E100_E0.439011.514
9_L47_A0.425851.468
5_A9_L0.419891.448
59_Q97_R0.408791.409
100_E103_L0.408561.409
59_Q65_W0.407021.403
13_N19_G0.404061.393
18_W51_A0.403661.392
59_Q94_A0.394471.360
13_N24_S0.378621.305
76_T79_A0.374171.290
95_V98_G0.36911.273
46_E49_K0.363061.252
31_A34_L0.359861.241
5_A36_L0.355911.227
26_V55_L0.355871.227
29_T51_A0.352891.217
88_V92_D0.349111.204
52_I56_L0.348841.203
33_I51_A0.343431.184
13_N17_S0.339921.172
26_V79_A0.336911.162
99_L103_L0.336031.158
34_L38_A0.334021.152
62_D71_E0.331721.144
97_R100_E0.330881.141
8_L32_L0.327791.130
94_A97_R0.323261.114
73_V102_I0.319841.103
8_L35_A0.318791.099
93_E96_E0.318181.097
75_M79_A0.316291.090
41_D45_D0.316081.090
48_I51_A0.314781.085
30_A34_L0.311281.073
27_F31_A0.308471.063
28_V31_A0.305921.055
42_A45_D0.303411.046
78_A81_A0.302131.042
5_A41_D0.293481.012
67_Y75_M0.29261.009
17_S54_W0.291551.005
33_I37_A0.283890.979
56_L92_D0.282960.976
29_T33_I0.282860.975
65_W98_G0.281470.970
6_E9_L0.279270.963
81_A85_L0.279240.963
28_V32_L0.275410.950
25_D32_L0.274980.948
64_G71_E0.27330.942
27_F30_A0.269620.930
17_S24_S0.267670.923
11_Q19_G0.265910.917
53_D56_L0.265620.916
25_D67_Y0.263850.910
64_G101_W0.260160.897
55_L82_A0.255560.881
55_L79_A0.255490.881
25_D31_A0.254030.876
20_Y31_A0.25330.873
78_A82_A0.252370.870
91_D94_A0.251770.868
101_W104_S0.248710.857
49_K53_D0.247110.852
43_A47_A0.246690.850
73_V105_H0.245730.847
28_V55_L0.244880.844
48_I52_I0.244670.844
94_A98_G0.243340.839
9_L41_D0.242990.838
41_D44_V0.242740.837
76_T82_A0.242630.836
9_L44_V0.240750.830
3_R6_E0.23990.827
24_S69_G0.23950.826
12_Q51_A0.238450.822
6_E43_A0.236860.817
14_P50_K0.23680.816
95_V99_L0.235830.813
74_S78_A0.234870.810
80_I95_V0.234220.807
39_A44_V0.230990.796
47_A50_K0.230960.796
44_V47_A0.230310.794
18_W65_W0.229060.790
80_I99_L0.227120.783
55_L83_L0.225970.779
26_V58_H0.224660.775
87_G90_P0.224570.774
54_W58_H0.223230.770
52_I88_V0.222930.769
18_W32_L0.22140.763
59_Q67_Y0.220120.759
77_A81_A0.219570.757
92_D96_E0.219570.757
88_V100_E0.219420.756
56_L88_V0.219380.756
87_G91_D0.218280.753
77_A80_I0.218230.752
17_S20_Y0.218080.752
82_A86_A0.214910.741
32_L36_L0.214840.741
20_Y23_G0.214510.740
9_L45_D0.213430.736
30_A78_A0.213280.735
60_N64_G0.212990.734
42_A47_A0.212830.734
75_M78_A0.212790.734
11_Q30_A0.211980.731
49_K52_I0.211860.730
88_V93_E0.21130.728
81_A84_A0.209910.724
70_G74_S0.209080.721
56_L91_D0.209050.721
27_F75_M0.207830.717
54_W79_A0.20650.712
5_A44_V0.206310.711
7_W10_S0.205370.708
6_E49_K0.202810.699
72_Y101_W0.200570.691
26_V65_W0.200380.691
16_G50_K0.199210.687
56_L65_W0.198850.686
77_A82_A0.198820.685
96_E99_L0.198780.685
59_Q63_G0.196860.679
5_A12_Q0.194860.672
26_V68_S0.194140.669
78_A84_A0.193610.667
11_Q21_N0.192930.665
92_D95_V0.192230.663
77_A102_I0.192210.663
29_T54_W0.19220.663
35_A38_A0.192060.662
56_L93_E0.191920.662
49_K96_E0.191530.660
74_S77_A0.191320.660
73_V77_A0.190520.657
64_G76_T0.19030.656
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
2h6fB0.990899.60.246
2h6fB0.981799.50.256
2sqcA0.990899.50.259
1w6kA0.990899.50.26
2sqcA0.990899.50.271
1w6kA199.50.271
3q7aB0.990899.50.291
3dssB0.981799.50.293
3dssB0.981799.40.301
3q7aB0.990899.40.312

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