GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CTP_transf_3 - Cytidylyltransferase
Pfam: PF02348 (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: CL0110
Length: 217
Sequences: 3910
Seq/Len: 18.02
HH_delta: 0.308 (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_E62_K1.154314.807
24_K32_E1.142434.758
2_A40_I0.78723.278
28_E32_E0.701772.923
56_A61_A0.617122.570
50_E54_D0.609682.539
8_G15_G0.595312.479
15_G51_E0.582522.426
28_E59_Y0.582.416
53_D57_E0.540272.250
13_L19_K0.530682.210
34_A95_L0.514282.142
112_E116_E0.511162.129
31_I61_A0.510252.125
47_T53_D0.491632.048
199_L203_E0.486082.024
37_S108_D0.474251.975
106_S109_R0.470511.960
25_P28_E0.45681.902
119_E178_G0.437211.821
54_D58_E0.431191.796
114_I122_I0.423621.764
21_L26_L0.413431.722
109_R112_E0.412861.719
12_R147_D0.41091.711
146_D150_L0.398421.659
38_K108_D0.395131.646
25_P55_I0.394191.642
18_L51_E0.392071.633
72_D75_D0.389311.621
20_P23_G0.383771.598
146_D149_G0.380231.584
19_K199_L0.378571.577
33_R36_Q0.377761.573
25_P29_Y0.37621.567
106_S189_E0.371411.547
29_Y33_R0.370391.543
35_K43_I0.361611.506
6_A45_V0.361511.506
91_I163_R0.359261.496
28_E55_I0.358811.494
67_R83_H0.35631.484
113_D117_A0.353561.472
93_V111_I0.34861.452
53_D65_F0.341991.424
24_K29_Y0.336621.402
53_D63_V0.328691.369
67_R70_L0.322061.341
91_I114_I0.321441.339
121_Y162_I0.319381.330
40_I93_V0.317231.321
191_F201_L0.315721.315
15_G49_D0.313631.306
193_I202_A0.307991.283
12_R16_K0.307851.282
26_L193_I0.30561.273
20_P25_P0.298271.242
117_A178_G0.296551.235
27_I56_A0.294941.228
3_I80_A0.294791.228
50_E65_F0.29371.223
24_K28_E0.292471.218
45_V56_A0.290311.209
155_S159_I0.29031.209
55_I58_E0.289661.206
91_I115_R0.288891.203
4_I31_I0.288861.203
46_A80_A0.287081.196
22_G101_L0.284571.185
108_D112_E0.277781.157
77_F94_R0.274711.144
8_G52_I0.272651.136
200_E204_K0.269871.124
103_D106_S0.267631.115
125_L179_I0.266661.111
95_L107_I0.266231.109
70_L79_E0.265351.105
40_I108_D0.264311.101
44_V80_A0.261541.089
51_E54_D0.259461.081
5_P77_F0.258371.076
196_P200_E0.257641.073
11_K73_D0.257631.073
44_V62_K0.25731.072
194_D198_D0.254611.060
2_A95_L0.254151.058
31_I59_Y0.253511.056
201_L204_K0.24951.039
77_F80_A0.249441.039
112_E115_R0.249391.039
191_F202_A0.24671.027
7_R10_S0.245911.024
31_I43_I0.245281.022
23_G29_Y0.24491.020
145_F148_D0.244121.017
137_N140_P0.24251.010
113_D116_E0.242291.009
27_I52_I0.241291.005
18_L55_I0.237750.990
8_G49_D0.235550.981
44_V64_I0.23510.979
33_R104_P0.234340.976
95_L102_L0.234010.975
31_I35_K0.233810.974
37_S40_I0.230020.958
105_T109_R0.228920.953
8_G51_E0.228670.952
127_D152_L0.227050.946
10_S16_K0.226840.945
75_D79_E0.226210.942
120_D176_Q0.224910.937
4_I95_L0.22350.931
57_E62_K0.222760.928
7_R46_A0.218270.909
79_E82_K0.218130.908
127_D154_F0.217580.906
169_F172_F0.217190.905
126_V174_I0.216490.902
2_A43_I0.215770.899
3_I46_A0.215660.898
2_A93_V0.215630.898
8_G17_N0.214910.895
200_E203_E0.213220.888
56_A63_V0.212930.887
22_G29_Y0.212240.884
93_V161_Y0.21060.877
17_N52_I0.209420.872
110_A124_N0.209070.871
61_A73_D0.20890.870
155_S158_V0.208720.869
132_S135_I0.208640.869
19_K196_P0.208610.869
120_D165_N0.206490.860
54_D57_E0.205890.857
2_A34_A0.204170.850
183_R189_E0.203840.849
47_T63_V0.203580.848
76_R79_E0.203490.847
40_I111_I0.202360.843
13_L199_L0.20110.838
77_F96_Q0.200290.834
64_I83_H0.200180.834
47_T65_F0.198950.829
2_A41_D0.198230.826
16_K98_D0.197980.825
77_F81_I0.197110.821
35_K41_D0.196590.819
67_R79_E0.196380.818
49_D52_I0.195810.815
28_E31_I0.195530.814
68_G72_D0.194990.812
198_D201_L0.194970.812
68_G71_A0.193390.805
6_A27_I0.193230.805
12_R98_D0.192110.800
171_Y174_I0.191820.799
156_E160_P0.190990.795
78_I81_I0.189570.790
38_K112_E0.188010.783
60_G63_V0.187550.781
87_D90_D0.187170.780
3_I44_V0.18710.779
137_N142_K0.184190.767
138_F142_K0.183010.762
152_L199_L0.182740.761
76_R80_A0.181350.755
50_E57_E0.181050.754
197_E201_L0.18060.752
9_G71_A0.180590.752
4_I34_A0.180360.751
91_I111_I0.179180.746
145_F174_I0.179030.746
191_F198_D0.178340.743
34_A93_V0.177380.739
32_E36_Q0.177250.738
44_V84_F0.177180.738
78_I82_K0.176490.735
17_N98_D0.176380.735
154_F158_V0.17610.733
102_L107_I0.175590.731
36_Q104_P0.174850.728
196_P201_L0.174740.728
104_P108_D0.174620.727
32_E35_K0.174290.726
110_A122_I0.17420.725
47_T52_I0.174010.725
33_R107_I0.173580.723
33_R102_L0.173330.722
81_I92_V0.172010.716
121_Y177_V0.171080.713
50_E53_D0.170960.712
135_I158_V0.170360.710
110_A180_Y0.169880.708
132_S136_F0.169280.705
138_F161_Y0.169140.704
5_P96_Q0.168960.704
156_E159_I0.168890.703
126_V143_V0.168830.703
190_R193_I0.168280.701
5_P94_R0.168090.700
193_I198_D0.166870.695
93_V110_A0.166060.692
2_A37_S0.165650.690
10_S15_G0.16490.687
122_I180_Y0.164450.685
110_A114_I0.16420.684
7_R48_D0.163850.682
165_N168_E0.16380.682
21_L199_L0.163520.681
160_P163_R0.163470.681
57_E68_G0.163060.679
72_D76_R0.161610.673
164_R204_K0.161420.672
145_F149_G0.16080.670
83_H87_D0.160650.669
96_Q99_S0.160480.668
3_I92_V0.15990.666
109_R113_D0.159710.665
120_D163_R0.15950.664
3_I94_R0.158960.662
82_K85_L0.158790.661
33_R37_S0.15870.661
201_L205_I0.157670.657
154_F181_A0.157490.656
123_S181_A0.157480.656
7_R15_G0.156210.651
56_A60_G0.156160.650
136_F179_I0.155910.649
109_R180_Y0.155560.648
184_K189_E0.155340.647
139_N178_G0.155180.646
95_L159_I0.154960.645
57_E63_V0.154310.643
42_E54_D0.153740.640
52_I56_A0.15320.638
162_I166_P0.153050.637
34_A43_I0.153030.637
119_E176_Q0.152850.637
56_A59_Y0.152710.636
133_V160_P0.152590.635
157_H194_D0.151870.633
30_V97_G0.151250.630
51_E55_I0.151190.630
64_I84_F0.150810.628
5_P157_H0.149970.625
57_E60_G0.149960.625
162_I173_Y0.148770.620
70_L73_D0.148570.619
124_N205_I0.148090.617
161_Y166_P0.148080.617
153_Y160_P0.147970.616
68_G76_R0.146780.611
10_S17_N0.146650.611
158_V161_Y0.146620.611
128_P132_S0.146530.610
113_D122_I0.146140.609
75_D191_F0.145740.607
110_A113_D0.145630.607
164_R168_E0.145620.606
101_L202_A0.145550.606
91_I164_R0.145430.606
4_I45_V0.145150.605
57_E61_A0.144070.600
36_Q108_D0.144060.600
19_K203_E0.143460.597
22_G25_P0.143390.597
126_V130_G0.142810.595
35_K60_G0.142780.595
76_R96_Q0.142320.593
45_V61_A0.14140.589
18_L25_P0.141220.588
176_Q205_I0.140980.587
113_D178_G0.140870.587
134_E137_N0.140810.586
32_E59_Y0.140660.586
169_F174_I0.139680.582
136_F158_V0.139240.580
73_D96_Q0.139120.579
23_G203_E0.139070.579
110_A161_Y0.13870.578
60_G68_G0.138550.577
155_S160_P0.138460.577
144_L156_E0.138410.576
53_D67_R0.138070.575
36_Q105_T0.13770.573
178_G181_A0.137560.573
108_D111_I0.136670.569
192_T202_A0.136570.569
33_R103_D0.136540.569
90_D105_T0.136460.568
77_F84_F0.136360.568
64_I87_D0.136140.567
144_L147_D0.136030.567
154_F183_R0.135780.565
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
3oamA0.94931000.308
3k8dA0.940199.90.33
4fcuA0.958599.90.33
1qwjA0.958599.90.339
3tqdA0.935599.90.352
1h7eA0.953999.90.37
1eziA0.958599.90.379
2y6pA0.907899.90.392
1vicA0.963199.90.395
1fxoA0.963199.90.398

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