GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Prenyltrans_2 - Prenyltransferase-like
Pfam: PF13249 (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: 113
Sequences: 5113
Seq/Len: 45.25
HH_delta: 0.16 (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
42_R45_A1.133093.678
99_D103_S0.767862.492
52_L93_A0.725492.355
49_E53_S0.660772.145
3_W7_R0.64522.094
30_L81_A0.583071.893
8_Q12_G0.571571.855
55_Q59_G0.566161.838
8_Q14_W0.550341.786
11_D21_S0.548051.779
23_V51_L0.526451.709
2_D6_S0.492541.599
9_N21_S0.485961.577
100_W104_C0.478771.554
58_D70_P0.475491.543
73_Y77_V0.459971.493
9_N15_G0.457471.485
4_L32_A0.446671.450
55_Q61_W0.445521.446
9_N13_G0.439741.427
56_N62_G0.439271.426
48_V52_L0.437381.420
99_D102_L0.435151.412
105_Q109_G0.433551.407
55_Q97_A0.412831.340
60_G70_P0.411561.336
48_V82_L0.406551.320
55_Q96_K0.403961.311
4_L29_A0.398351.293
13_G21_S0.396141.286
50_W54_Q0.394831.282
105_Q111_W0.390391.267
72_V101_L0.384971.250
52_L87_R0.382311.241
27_A81_A0.382091.240
98_V102_L0.381191.237
93_A97_A0.381011.237
51_L78_A0.38011.234
96_K99_D0.375291.218
56_N70_P0.371951.207
76_Y80_A0.368811.197
28_F31_L0.365121.185
95_R99_D0.362761.177
22_D28_F0.361661.174
77_V80_A0.357711.161
25_D29_A0.352111.143
87_R90_D0.350161.137
49_E52_L0.348651.132
31_L80_A0.345241.121
4_L33_L0.344411.118
54_Q62_G0.335151.088
48_V85_L0.33231.079
94_V97_A0.331611.076
14_W29_A0.330971.074
94_V98_V0.328541.066
5_L38_E0.324081.052
95_R98_V0.323031.048
38_E41_D0.312671.015
2_D5_L0.309221.004
27_A31_L0.306070.993
106_N110_G0.302670.982
93_A96_K0.298920.970
71_D74_T0.297730.966
48_V87_R0.29770.966
7_R15_G0.292950.951
80_A84_L0.292390.949
61_W97_A0.284770.924
31_L35_A0.282580.917
75_T79_L0.281930.915
37_G41_D0.27370.888
13_G50_W0.272820.886
60_G100_W0.272630.885
87_R93_A0.272380.884
23_V78_A0.271740.882
24_W28_F0.271470.881
81_A84_L0.271280.881
32_A35_A0.271130.880
102_L111_W0.270480.878
24_W27_A0.270250.877
76_Y101_L0.268610.872
43_D87_R0.264240.858
27_A35_A0.262460.852
35_A84_L0.260750.846
89_D92_E0.260380.845
51_L81_A0.25740.835
30_L48_V0.256230.832
23_V54_Q0.254990.828
68_G73_Y0.254540.826
69_P77_V0.252670.820
44_R49_E0.250910.814
28_F36_L0.249280.809
73_Y76_Y0.246640.801
8_Q44_R0.244320.793
79_L94_V0.243570.791
25_D50_W0.243290.790
28_F63_S0.241320.783
103_S107_P0.238520.774
30_L34_A0.237970.772
7_R17_F0.236690.768
54_Q65_P0.235470.764
74_T77_V0.232210.754
23_V63_S0.231950.753
79_L83_E0.228430.741
92_E95_R0.228270.741
26_T30_L0.226670.736
63_S76_Y0.225710.733
15_G19_G0.223510.725
13_G22_D0.22130.718
55_Q63_S0.221210.718
5_L8_Q0.21950.712
51_L82_L0.217680.707
80_A83_E0.216550.703
49_E90_D0.214940.698
5_L102_L0.214880.697
37_G40_P0.214650.697
72_V104_C0.214450.696
90_D98_V0.213020.691
63_S74_T0.211260.686
50_W93_A0.210830.684
26_T31_L0.209810.681
92_E102_L0.208550.677
20_P28_F0.20850.677
16_G22_D0.208470.677
25_D28_F0.208470.677
24_W71_D0.207950.675
75_T82_L0.206510.670
22_D25_D0.206450.670
21_S29_A0.203220.660
48_V55_Q0.20270.658
70_P74_T0.201280.653
79_L101_L0.199380.647
54_Q57_P0.199270.647
92_E98_V0.199040.646
79_L97_A0.198940.646
16_G19_G0.198710.645
104_C111_W0.198510.644
100_W103_S0.198160.643
16_G68_G0.196420.638
11_D54_Q0.196230.637
56_N60_G0.195720.635
22_D63_S0.195390.634
52_L92_E0.194760.632
71_D77_V0.191110.620
14_W111_W0.190510.618
56_N71_D0.190410.618
50_W105_Q0.189780.616
29_A32_A0.189490.615
19_G22_D0.18940.615
4_L36_L0.188870.613
74_T78_A0.188070.610
83_E87_R0.186890.607
27_A51_L0.185940.604
13_G26_T0.185240.601
55_Q93_A0.184930.600
22_D71_D0.183410.595
83_E89_D0.18280.593
21_S25_D0.181920.590
34_A85_L0.181680.590
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
2h6fB0.982399.70.16
3dssB0.982399.70.201
2sqcA0.973599.60.213
1n4qB0.991299.60.214
3dssB0.982399.60.215
3q7aB0.982399.60.216
1w6kA0.991299.60.228
2h6fB0.982399.60.23
1w6kA0.982399.60.251
2sqcA0.982399.60.252

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