GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FtsJ - FtsJ-like methyltransferase
Pfam: PF01728 (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: 181
Sequences: 8674
Seq/Len: 47.92
HH_delta: 0.12 (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
93_D130_K1.512333.921
129_L133_G1.336923.466
38_S53_A1.323163.431
52_V92_F1.274213.304
28_L92_F1.257963.261
32_A53_A1.200833.113
26_T50_R1.110512.879
27_V41_L1.035882.686
125_A135_F0.971022.518
41_L96_L0.848312.199
32_A38_S0.826112.142
45_G48_A0.784752.035
27_V51_V0.739411.917
26_T52_V0.726511.884
26_T92_F0.695711.804
45_G49_G0.684691.775
95_V129_L0.678641.759
58_P69_Q0.66161.715
27_V94_L0.648171.680
124_L127_E0.645331.673
91_K130_K0.623131.616
124_L128_L0.616081.597
42_L51_V0.610181.582
38_S51_V0.598411.551
50_R66_S0.596371.546
163_K173_E0.571071.481
150_Y154_R0.532471.381
94_L134_T0.531981.379
25_F134_T0.520791.350
40_V43_Q0.483061.252
25_F94_L0.481331.248
94_L136_V0.480041.245
25_F93_D0.476341.235
97_S137_I0.47121.222
50_R75_P0.463731.202
36_G98_D0.463161.201
52_V68_I0.458781.189
26_T93_D0.451891.172
32_A55_D0.445961.156
119_L123_L0.435911.130
29_D38_S0.422241.095
30_L99_M0.420251.090
42_L64_N0.417031.081
29_D32_A0.416111.079
79_K83_K0.416011.079
26_T90_E0.407481.056
28_L54_V0.401831.042
31_G97_S0.401741.042
25_F49_G0.39661.028
119_L151_L0.390271.012
150_Y153_K0.389461.010
149_I153_K0.387741.005
39_Q43_Q0.386931.003
111_E114_S0.377620.979
149_I161_I0.374120.970
95_V135_F0.372150.965
81_I85_L0.367280.952
58_P78_I0.364710.946
42_L65_V0.364320.945
129_L135_F0.36320.942
92_F95_V0.362250.939
28_L95_V0.36080.935
26_T130_K0.359820.933
34_P37_W0.359210.931
97_S135_F0.358340.929
29_D35_G0.356720.925
77_N84_L0.352020.913
27_V49_G0.342530.888
158_K161_I0.342270.887
31_G99_M0.338630.878
30_L97_S0.336030.871
116_R151_L0.332590.862
92_F128_L0.330350.856
54_V70_G0.329340.854
79_K82_R0.32920.854
147_E151_L0.326470.846
92_F133_G0.3260.845
118_I139_V0.325730.845
26_T49_G0.325590.844
37_W98_D0.325270.843
36_G40_V0.32450.841
130_K133_G0.322550.836
76_E79_K0.322350.836
99_M118_I0.321860.834
28_L128_L0.32130.833
34_P138_K0.321290.833
27_V45_G0.320680.831
29_D97_S0.319040.827
166_S171_S0.317120.822
151_L155_C0.317080.822
120_S123_L0.316450.820
78_I83_K0.315760.819
28_L52_V0.313230.812
39_Q42_L0.311660.808
117_L121_Q0.311440.807
40_V44_R0.310770.806
165_P172_S0.309060.801
99_M114_S0.30860.800
66_S70_G0.307580.797
146_E150_Y0.306960.796
70_G75_P0.303370.787
140_F148_L0.302730.785
78_I81_I0.301140.781
111_E115_I0.30080.780
129_L156_F0.298040.773
122_L152_L0.297120.770
66_S84_L0.295710.767
29_D98_D0.292530.758
166_S173_E0.291520.756
29_D53_A0.291350.755
71_D74_N0.289330.750
79_K84_L0.287860.746
53_A67_F0.286230.742
81_I84_L0.285530.740
117_L120_S0.283870.736
139_V161_I0.282580.733
74_N116_R0.278910.723
118_I122_L0.278250.721
91_K131_P0.273190.708
84_L90_E0.272690.707
70_G74_N0.272170.706
126_L155_C0.270730.702
30_L125_A0.270610.702
33_A37_W0.26850.696
118_I121_Q0.266360.691
148_L152_L0.265490.688
26_T91_K0.264950.687
50_R90_E0.263580.683
98_D138_K0.263080.682
27_V48_A0.262380.680
63_Q67_F0.262280.680
36_G138_K0.259510.673
44_R136_V0.257430.667
144_E147_E0.257350.667
29_D96_L0.256730.666
148_L151_L0.254930.661
123_L126_L0.254710.660
52_V77_N0.254370.659
149_I152_L0.253790.658
74_N120_S0.253540.657
120_S124_L0.253510.657
113_I120_S0.253120.656
38_S42_L0.252770.655
56_L71_D0.252510.655
63_Q66_S0.252310.654
125_A133_G0.251810.653
45_G51_V0.251060.651
86_P91_K0.251060.651
142_G146_E0.248180.643
29_D51_V0.246240.638
151_L154_R0.246190.638
161_I165_P0.246050.638
37_W125_A0.245940.638
143_P146_E0.245580.637
147_E150_Y0.243390.631
55_D67_F0.243060.630
53_A65_V0.242220.628
159_V163_K0.241310.626
29_D37_W0.239220.620
144_E172_S0.23830.618
156_F159_V0.235240.610
70_G77_N0.234490.608
95_V125_A0.234190.607
41_L51_V0.231050.599
77_N85_L0.230750.598
41_L49_G0.230740.598
35_G53_A0.229320.595
158_K162_V0.229230.594
164_P171_S0.229160.594
81_I97_S0.228430.592
30_L81_I0.228140.591
38_S41_L0.227090.589
145_I148_L0.227040.589
157_S160_K0.226430.587
95_V128_L0.225160.584
165_P173_E0.223450.579
36_G136_V0.222190.576
41_L94_L0.221670.575
157_S161_I0.221140.573
99_M138_K0.220490.572
56_L117_L0.218960.568
41_L45_G0.21860.567
134_T162_V0.217820.565
163_K166_S0.217570.564
27_V96_L0.217210.563
93_D132_G0.216230.561
31_G37_W0.216060.560
68_I74_N0.215970.560
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
3douA0.972499.90.12
2plwA0.977999.90.208
2nyuA0.977999.80.238
3gczA0.928299.80.278
3evfA0.889599.80.298
1ej0A0.977999.80.3
3eldA0.928299.80.308
2px2A0.88499.70.319
2oxtA0.856499.70.322
2wa2A0.856499.70.34

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