GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CTP_transf_2 - Cytidylyltransferase
Pfam: PF01467 (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: CL0039
Length: 157
Sequences: 5412
Seq/Len: 34.47
HH_delta: 0.184 (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
21_R64_N1.198113.593
47_S50_E1.11863.355
9_P55_L1.11563.346
52_L56_R0.938982.816
53_E56_R0.779122.337
7_D46_F0.708882.126
101_D104_E0.698042.093
53_E57_A0.676412.029
17_L31_V0.650761.952
9_P58_A0.645211.935
153_E156_E0.627591.882
18_R62_D0.593771.781
15_N18_R0.586651.759
19_E22_E0.577051.731
104_E107_K0.565831.697
15_N19_E0.565111.695
46_F50_E0.546031.638
46_F54_M0.543641.630
48_F52_L0.538921.616
50_E54_M0.532851.598
24_F112_I0.529531.588
50_E53_E0.524161.572
105_I111_I0.520991.563
9_P14_L0.517191.551
14_L59_F0.50091.502
40_K91_D0.475641.426
11_N14_L0.469241.407
7_D44_P0.451871.355
54_M57_A0.443011.329
9_P54_M0.442391.327
9_P17_L0.428891.286
7_D45_I0.426471.279
5_S38_P0.41971.259
26_E63_P0.416641.250
18_R61_D0.416041.248
49_E53_E0.40551.216
86_F90_A0.398471.195
21_R62_D0.396961.191
5_S37_S0.391031.173
36_N39_H0.388471.165
86_F111_I0.386661.160
121_P124_T0.379581.138
57_A60_K0.378931.136
11_N149_I0.375191.125
19_E23_L0.366971.101
2_F16_L0.364361.093
55_L59_F0.360441.081
104_E108_E0.353221.059
151_S155_R0.352841.058
1_L87_V0.344841.034
8_P46_F0.344251.032
11_N54_M0.339411.018
14_L18_R0.336481.009
6_F16_L0.334171.002
11_N50_E0.332760.998
2_F17_L0.331270.994
86_F89_G0.331010.993
24_F140_F0.329850.989
14_L58_A0.329740.989
15_N147_N0.328740.986
103_Q107_K0.319410.958
37_S40_K0.319160.957
18_R22_E0.3140.942
50_E149_I0.311410.934
106_L111_I0.308890.926
2_F6_F0.301670.905
18_R60_K0.300920.902
35_D55_L0.296620.890
117_G146_R0.295090.885
36_N48_F0.2930.879
59_F62_D0.286730.860
10_H154_I0.286520.859
20_A87_V0.285030.855
113_V147_N0.281230.843
87_V91_D0.276090.828
102_W106_L0.275060.825
33_P37_S0.273890.821
15_N53_E0.272110.816
17_L55_L0.271920.816
122_I126_S0.270970.813
4_G10_H0.269050.807
86_F91_D0.265840.797
99_W105_I0.264770.794
120_D142_L0.264390.793
102_W114_V0.261220.783
32_V55_L0.260610.782
117_G144_P0.259430.778
91_D116_R0.256090.768
1_L86_F0.255350.766
35_D48_F0.255240.765
3_G99_W0.253460.760
152_T155_R0.253420.760
88_I91_D0.25340.760
146_R149_I0.252880.758
145_P148_E0.250370.751
113_V141_I0.249840.749
31_V59_F0.248510.745
14_L54_M0.247420.742
30_I35_D0.245320.736
15_N143_D0.245220.735
91_D155_R0.244550.733
125_I140_F0.243930.732
15_N145_P0.24290.728
113_V116_R0.242580.728
22_E26_E0.24080.722
140_F143_D0.240650.722
31_V55_L0.240020.720
4_G13_H0.238820.716
49_E56_R0.238620.716
23_L140_F0.237890.713
114_V153_E0.237590.713
32_V86_F0.235880.707
35_D115_S0.235840.707
123_E126_S0.235810.707
113_V144_P0.231320.694
40_K43_K0.231040.693
5_S44_P0.229460.688
31_V34_S0.229280.688
26_E87_V0.228740.686
149_I154_I0.228590.686
101_D110_N0.226010.678
20_A115_S0.223810.671
16_L114_V0.223280.670
24_F29_V0.221810.665
16_L19_E0.221560.664
40_K151_S0.220460.661
3_G7_D0.220010.660
87_V90_A0.219930.660
115_S143_D0.219630.659
110_N140_F0.219440.658
9_P31_V0.217890.653
58_A61_D0.217780.653
17_L29_V0.217070.651
10_H34_S0.216880.650
14_L155_R0.216610.650
38_P113_V0.214210.642
122_I125_I0.213780.641
56_R60_K0.213050.639
106_L114_V0.213050.639
48_F87_V0.212550.637
15_N22_E0.212310.637
5_S35_D0.212280.637
34_S89_G0.212220.636
148_E153_E0.209540.628
23_L143_D0.209350.628
19_E144_P0.209250.628
15_N146_R0.207740.623
114_V144_P0.20690.621
38_P152_T0.206050.618
39_H44_P0.205510.616
102_W109_V0.204780.614
103_Q109_V0.204660.614
5_S33_P0.204610.614
6_F13_H0.203140.609
52_L55_L0.202850.608
144_P147_N0.201270.604
57_A61_D0.200620.602
141_I146_R0.19810.594
13_H150_S0.197550.592
3_G33_P0.195960.588
34_S48_F0.195520.586
103_Q126_S0.194780.584
23_L115_S0.194310.583
105_I154_I0.193270.580
39_H102_W0.191920.576
51_R54_M0.191920.576
26_E29_V0.191320.574
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
1kqnA0.987399.90.184
1yumA0.987399.90.19
1nupA0.987399.90.192
3h05A0.783499.90.209
2h29A0.923699.90.212
1k4mA0.993699.90.225
1kamA0.923699.90.244
2qtrA0.923699.90.253
2qjoA0.834499.80.393
2qjtB0.847199.80.403

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