GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Methyltransf_4 - Putative methyltransferase
Pfam: PF02390 (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: CL0063
Length: 195
Sequences: 3988
Seq/Len: 20.45
HH_delta: 0.207 (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
90_D124_K0.86683.895
123_L127_G0.747353.358
37_K64_R0.689993.100
26_C46_G0.619012.781
43_N70_R0.573862.578
20_L43_N0.549432.469
32_L46_G0.548482.464
22_L89_V0.520382.338
86_P121_R0.497442.235
86_P122_V0.486452.186
92_I119_L0.478622.150
118_L121_R0.47762.146
136_E140_E0.468662.106
61_A69_V0.455572.047
39_N44_F0.438061.968
177_E181_L0.413971.860
94_I129_L0.402471.808
51_K73_R0.396991.784
178_R182_A0.389571.750
57_A71_F0.385671.733
94_I97_P0.369821.662
21_I42_I0.366911.649
81_R118_L0.366851.648
180_W185_K0.350681.576
21_I93_Y0.349781.572
24_I76_A0.347041.559
21_I91_R0.334111.501
33_I60_K0.321771.446
46_G57_A0.317871.428
48_E54_V0.315581.418
34_E38_R0.315311.417
113_P148_E0.31361.409
91_R128_E0.312551.404
34_E37_K0.311931.402
54_V71_F0.296711.333
51_K55_A0.296211.331
78_E82_R0.293761.320
85_P88_S0.293181.317
141_W145_Q0.288521.296
89_V92_I0.285491.283
60_K64_R0.274581.234
45_I72_L0.273821.230
81_R121_R0.26821.205
39_N42_I0.266681.198
114_E117_E0.261311.174
45_I84_F0.260941.172
91_R130_Y0.257811.158
20_L89_V0.252421.134
138_Y176_Y0.252331.134
96_F99_P0.248981.119
162_L165_S0.247931.114
31_F93_Y0.247391.112
20_L90_D0.240171.079
58_L62_E0.239511.076
31_F95_N0.239181.075
131_F142_M0.23881.073
146_F153_F0.238241.070
120_A153_F0.237291.066
32_L44_F0.2361.060
118_L122_V0.235211.057
101_P104_R0.234041.052
36_A68_N0.233891.051
23_E26_C0.233891.051
129_L146_F0.233441.049
115_F119_L0.231351.039
136_E186_P0.231311.039
50_R53_R0.231011.038
47_I72_L0.228731.028
45_I89_V0.227431.022
176_Y179_K0.226981.020
120_A152_G0.226011.015
173_P178_R0.223261.003
26_C57_A0.221790.997
31_F35_L0.221210.994
128_E156_I0.220520.991
53_R176_Y0.219670.987
46_G69_V0.217210.976
61_A71_F0.216770.974
26_C48_E0.212250.954
33_I36_A0.210370.945
33_I37_K0.209920.943
20_L45_I0.209320.940
35_L93_Y0.20920.940
89_V122_V0.208630.937
179_K183_E0.208060.935
59_R62_E0.206390.927
20_L124_K0.205910.925
94_I98_D0.204640.919
26_C32_L0.202790.911
59_R63_K0.202320.909
23_E46_G0.201730.906
47_I79_L0.201230.904
49_I75_D0.200020.899
138_Y142_M0.199980.899
113_P117_E0.19860.892
35_L39_N0.198590.892
58_L71_F0.196890.885
120_A185_K0.19630.882
46_G71_F0.196160.881
100_W104_R0.193710.870
96_F132_A0.192890.867
51_K129_L0.192140.863
74_G79_L0.192010.863
76_A80_L0.191820.862
87_G122_V0.191290.859
28_K56_K0.191040.858
80_L118_L0.190140.854
26_C54_V0.188080.845
99_P102_K0.187450.842
113_P145_Q0.187260.841
180_W183_E0.187020.840
176_Y180_W0.186220.837
54_V73_R0.186010.836
20_L88_S0.185230.832
21_I35_L0.184830.830
51_K58_L0.184550.829
143_L147_E0.183490.824
32_L57_A0.182480.820
116_L120_A0.181430.815
156_I162_L0.181310.815
182_A186_P0.180090.809
159_S162_L0.178450.802
23_E44_F0.178110.800
156_I160_D0.176860.795
21_I44_F0.176290.792
20_L42_I0.175590.789
36_A69_V0.175130.787
147_E155_N0.174240.783
157_E160_D0.17410.782
74_G78_E0.173760.781
117_E120_A0.172360.774
55_A58_L0.171480.770
57_A61_A0.170490.766
98_D102_K0.169920.763
117_E121_R0.169530.762
121_R124_K0.16860.758
174_T177_E0.168170.756
116_L131_F0.16690.750
147_E160_D0.163560.735
137_E140_E0.163490.735
23_E27_G0.162960.732
144_E148_E0.162620.731
179_K182_A0.162230.729
123_L129_L0.162090.728
155_N162_L0.161430.725
33_I61_A0.160990.723
92_I127_G0.160650.722
30_E178_R0.160160.720
94_I99_P0.160160.720
173_P181_L0.159530.717
74_G83_L0.158610.713
48_E135_V0.158160.711
143_L162_L0.157360.707
133_T139_A0.157330.707
74_G82_R0.157310.707
95_N99_P0.157120.706
138_Y174_T0.156910.705
126_G186_P0.156550.703
26_C50_R0.155510.699
54_V171_Y0.155510.699
88_S124_K0.155190.697
39_N170_D0.155150.697
23_E175_K0.154750.695
143_L158_E0.15390.691
141_W144_E0.153210.688
33_I57_A0.153170.688
22_L47_I0.152420.685
21_I39_N0.151730.682
24_I119_L0.151490.681
47_I76_A0.151050.679
183_E186_P0.150410.676
114_E118_L0.15040.676
78_E183_E0.149740.673
116_L173_P0.148780.668
99_P104_R0.148530.667
75_D78_E0.14810.665
87_G124_K0.147040.661
99_P134_D0.146620.659
64_R67_K0.146110.656
117_E152_G0.145990.656
50_R54_V0.145730.655
116_L129_L0.145680.655
138_Y141_W0.145640.654
42_I90_D0.144740.650
26_C61_A0.144670.650
48_E72_L0.144490.649
99_P133_T0.144160.648
69_V73_R0.144110.647
45_I70_R0.143830.646
78_E83_L0.142770.641
155_N160_D0.142360.640
87_G125_P0.141990.638
153_F175_K0.14140.635
68_N174_T0.140930.633
56_K59_R0.140610.632
95_N98_D0.140440.631
48_E145_Q0.140390.631
49_I92_I0.139950.629
38_R126_G0.13990.629
145_Q153_F0.139730.628
62_E67_K0.139540.627
36_A61_A0.139190.625
37_K147_E0.139020.625
78_E117_E0.138920.624
55_A173_P0.138570.623
135_V138_Y0.138130.621
31_F44_F0.13780.619
36_A174_T0.137290.617
135_V139_A0.137230.617
72_L83_L0.137130.616
43_N68_N0.136960.615
27_G99_P0.136570.614
84_F88_S0.136560.614
142_M145_Q0.136290.612
75_D175_K0.135720.610
48_E69_V0.135620.609
26_C53_R0.135610.609
175_K178_R0.13550.609
95_N100_W0.135460.609
94_I119_L0.134930.606
23_E29_G0.134920.606
36_A46_G0.134910.606
62_E65_G0.133730.601
64_R128_E0.132570.596
48_E71_F0.132140.594
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
3dxyA0.98461000.207
2fcaA0.979599.90.255
2vdvE0.994999.90.275
1yzhA0.974499.90.278
3ckkA0.994999.90.282
4gekA0.943699.80.392
4htfA0.917999.80.433
3dtnA0.938599.80.436
3mggA0.923199.80.442
1vl5A0.882199.80.45

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