GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CTP_transf_1 - Cytidylyltransferase family
Pfam: PF01148 (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: CL0234
Length: 259
Sequences: 2277
Seq/Len: 8.79
HH_delta: 0.956 (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
6_T232_I0.721725.902
145_F176_S0.483133.951
156_H168_E0.447733.661
216_E228_S0.418483.422
170_S210_A0.393283.216
149_V172_A0.355572.908
155_K168_E0.343852.812
141_I180_I0.296132.422
40_L109_G0.294592.409
151_R166_T0.294082.405
149_V176_S0.293252.398
136_I140_G0.292792.394
235_H241_R0.288592.360
7_A12_P0.282252.308
4_I148_L0.272882.231
149_V153_F0.272592.229
36_G238_I0.2572.102
148_L152_R0.252762.067
8_I12_P0.251142.054
142_G210_A0.2431.987
142_G209_E0.241871.978
135_G249_A0.240281.965
171_I175_I0.235391.925
43_L228_S0.233721.911
156_H167_W0.217781.781
5_I9_I0.215791.765
167_W171_I0.206551.689
135_G252_F0.205531.681
7_A11_I0.200851.642
43_L225_I0.198861.626
181_S202_S0.198371.622
137_L180_I0.193961.586
35_L238_I0.191291.564
174_F203_L0.190471.558
215_F219_I0.190041.554
157_L214_L0.189031.546
146_A173_G0.184971.513
142_G206_S0.176141.440
154_G168_E0.175521.435
20_L24_Y0.174591.428
139_L248_A0.174051.423
10_L232_I0.17331.417
145_F172_A0.171671.404
139_L245_L0.169571.387
149_V152_R0.169171.383
38_W229_G0.168431.377
23_W27_L0.167991.374
157_L167_W0.167361.369
242_F245_L0.16241.328
2_Q5_I0.160211.310
149_V175_I0.160041.309
157_L170_S0.157591.289
104_I108_F0.157521.288
17_L28_L0.157451.288
43_L223_A0.156691.281
170_S207_I0.154951.267
208_V251_V0.152961.251
38_W42_R0.14951.222
198_A202_S0.149091.219
36_G242_F0.148681.216
182_F195_W0.147911.209
209_E244_S0.146841.201
134_I202_S0.146681.199
12_P16_L0.144661.183
4_I8_I0.144421.181
177_S184_L0.144181.179
163_P217_S0.143631.174
194_S197_Q0.141941.161
248_A252_F0.140721.151
205_A252_F0.14071.151
11_I15_I0.140571.149
162_S226_K0.139651.142
39_E217_S0.139361.140
37_F41_F0.138331.131
15_I19_F0.137471.124
158_A161_I0.136711.118
178_F199_I0.13611.113
183_L187_Y0.134861.103
150_G226_K0.134671.101
40_L44_F0.134541.100
36_G239_L0.133391.091
167_W229_G0.132911.087
151_R164_K0.13291.087
201_I255_L0.132581.084
32_I242_F0.132051.080
6_T9_I0.132041.080
176_S180_I0.131961.079
100_I104_I0.131671.077
179_I183_L0.131561.076
144_S176_S0.131271.073
236_G243_D0.131271.073
24_Y28_L0.130951.071
229_G238_I0.130921.071
32_I238_I0.130721.069
197_Q255_L0.130361.066
145_F148_L0.130191.065
206_S210_A0.130081.064
33_I117_L0.128741.053
172_A244_S0.128341.049
27_L31_V0.127531.043
138_I181_S0.127471.042
150_G165_K0.127051.039
139_L228_S0.126771.037
7_A148_L0.125641.027
10_L242_F0.125441.026
182_F199_I0.125361.025
140_G241_R0.124331.017
140_G235_H0.123941.013
112_Y116_F0.122271.000
4_I152_R0.121790.996
134_I252_F0.121160.991
226_K236_G0.121060.990
37_F109_G0.120870.988
12_P140_G0.120470.985
219_I223_A0.120060.982
69_L251_V0.119520.977
178_F203_L0.119420.977
162_S165_K0.119070.974
104_I209_E0.118290.967
40_L219_I0.118210.967
225_I228_S0.117920.964
147_Y235_H0.11780.963
113_F116_F0.117250.959
163_P226_K0.116530.953
147_Y163_P0.11590.948
7_A10_L0.115870.947
153_F164_K0.11550.944
103_I107_L0.11490.940
162_S243_D0.114420.936
162_S213_D0.113990.932
167_W170_S0.113330.927
149_V167_W0.112910.923
19_F171_I0.1120.916
7_A140_G0.111590.912
215_F247_F0.11090.907
16_L20_L0.110630.905
162_S236_G0.11050.904
146_A149_V0.11040.903
35_L229_G0.110390.903
157_L160_K0.110360.902
165_K226_K0.109940.899
36_G113_F0.109530.896
174_F206_S0.109120.892
143_D169_G0.109040.892
217_S235_H0.108540.888
23_W26_L0.108150.884
138_I142_G0.10810.884
119_L123_F0.107690.881
162_S234_G0.107360.878
150_G162_S0.107050.875
133_L137_L0.106770.873
143_D165_K0.106630.872
139_L209_E0.106150.868
157_L210_A0.106050.867
165_K169_G0.105980.867
141_I176_S0.105780.865
140_G146_A0.105580.863
162_S217_S0.105180.860
164_K170_S0.105110.860
128_G138_I0.1050.859
168_E235_H0.104540.855
138_I202_S0.104540.855
60_S64_F0.104490.854
174_F178_F0.103980.850
16_L19_F0.103840.849
105_S113_F0.103460.846
6_T10_L0.10340.846
121_L232_I0.10330.845
235_H243_D0.103230.844
213_D216_E0.103210.844
71_F75_W0.103180.844
25_F121_L0.103140.843
31_V137_L0.102740.840
3_R6_T0.102670.840
29_V121_L0.102630.839
234_G237_G0.102230.836
113_F246_L0.10210.835
81_F84_I0.10190.833
145_F173_G0.101650.831
164_K167_W0.101520.830
227_D236_G0.101370.829
112_Y246_L0.100880.825
2_Q6_T0.100760.824
245_L249_A0.10070.823
162_S237_G0.100590.823
163_P243_D0.100560.822
237_G243_D0.100460.821
217_S243_D0.100250.820
46_I111_I0.100230.820
39_E163_P0.10010.819
86_I96_G0.099790.816
234_G243_D0.099630.815
171_I174_F0.099540.814
202_S206_S0.099390.813
135_G209_E0.099280.812
40_L239_L0.098950.809
9_I13_I0.097970.801
160_K167_W0.097530.798
41_F109_G0.097510.797
183_L186_Y0.097460.797
11_I148_L0.09720.795
11_I160_K0.09710.794
213_D226_K0.096580.790
217_S226_K0.09650.789
73_L199_I0.096480.789
31_V73_L0.09640.788
25_F208_V0.096250.787
4_I7_A0.09580.783
236_G240_D0.095670.782
215_F218_A0.095660.782
196_W200_L0.095440.780
161_I249_A0.095350.780
25_F117_L0.095140.778
158_A170_S0.094950.776
165_K217_S0.094860.776
149_V174_F0.094730.775
157_L171_I0.094350.772
162_S212_G0.094240.771
227_D243_D0.094210.770
216_E245_L0.094190.770
142_G148_L0.09390.768
139_L216_E0.093610.765
162_S227_D0.093390.764
142_G177_S0.093330.763
216_E239_L0.093290.763
217_S220_K0.093170.762
226_K234_G0.092880.760
213_D217_S0.092850.759
17_L21_G0.092850.759
195_W199_I0.092750.758
221_R243_D0.092660.758
224_G230_N0.092620.757
163_P213_D0.092580.757
86_I91_L0.092540.757
136_I245_L0.092530.757
177_S206_S0.092530.757
217_S221_R0.092520.757
159_P164_K0.092510.756
29_V182_F0.092470.756
181_S185_L0.092420.756
213_D233_P0.092360.755
213_D228_S0.092170.754
36_G155_K0.091950.752
135_G245_L0.091910.752
37_F40_L0.091760.750
217_S227_D0.091750.750
142_G173_G0.091660.750
158_A166_T0.091460.748
138_I177_S0.091430.748
163_P235_H0.091410.747
27_L125_W0.091290.746
205_A248_A0.091250.746
84_I87_I0.091210.746
115_I246_L0.091190.746
134_I229_G0.091150.745
40_L105_S0.090720.742
213_D236_G0.090690.742
95_L160_K0.090390.739
14_F44_F0.090050.736
21_G210_A0.089870.735
242_F247_F0.089840.735
248_A254_I0.089790.734
143_D150_G0.08970.733
18_L131_L0.089670.733
117_L120_L0.089540.732
212_G243_D0.089440.731
112_Y216_E0.089140.729
75_W89_L0.089120.729
111_I254_I0.088890.727
112_Y219_I0.088880.727
60_S73_L0.088770.726
213_D244_S0.088750.726
15_I18_L0.088740.726
89_L254_I0.08860.725
15_I188_L0.088520.724
134_I181_S0.08850.724
31_V35_L0.088370.723
105_S242_F0.088350.722
134_I218_A0.088320.722
162_S220_K0.088130.721
216_E233_P0.088050.720
99_R102_R0.088050.720
237_G241_R0.087910.719
146_A176_S0.087750.718
76_L79_Y0.087540.716
89_L125_W0.08750.716
73_L174_F0.08750.716
204_L207_I0.087460.715
4_I144_S0.087370.714
150_G236_G0.087310.714
140_G250_P0.086990.711
247_F253_Y0.086880.710
154_G169_G0.086650.709
42_R45_R0.086640.708
153_F168_E0.086630.708
168_E238_I0.086580.708
45_R48_S0.086510.707
80_F84_I0.08640.707
128_G131_L0.086370.706
86_I247_F0.086360.706
186_Y199_I0.086080.704
11_I17_L0.08580.702
172_A217_S0.085730.701
61_W66_I0.085720.701
177_S180_I0.085650.700
150_G240_D0.085530.699
46_I225_I0.085530.699
48_S225_I0.08540.698
64_F110_L0.085260.697
79_Y82_A0.085220.697
237_G240_D0.08520.697
162_S221_R0.085010.695
152_R166_T0.084980.695
150_G169_G0.084930.694
232_I238_I0.084880.694
163_P236_G0.084790.693
13_I17_L0.084730.693
234_G240_D0.084580.692
70_F183_L0.084510.691
238_I242_F0.084320.690
14_F247_F0.08410.688
203_L207_I0.083950.686
44_F100_I0.08390.686
213_D239_L0.083890.686
165_K236_G0.083620.684
165_K172_A0.08340.682
163_P221_R0.08320.680
87_I90_L0.083180.680
161_I173_G0.083160.680
140_G157_L0.083140.680
21_G218_A0.083110.680
131_L135_G0.083090.679
5_I12_P0.083090.679
27_L34_F0.083020.679
178_F200_L0.083010.679
21_G24_Y0.082970.678
11_I249_A0.082930.678
24_Y200_L0.082720.676
145_F214_L0.082710.676
103_I218_A0.082710.676
48_S51_K0.082580.675
152_R203_L0.082450.674
28_L229_G0.082390.674
11_I136_I0.082320.673
166_T169_G0.082270.673
147_Y162_S0.082260.673
67_L86_I0.082180.672
28_L238_I0.082070.671
84_I88_A0.082060.671
105_S223_A0.081980.670
6_T209_E0.081890.670
101_R106_T0.081880.670
168_E210_A0.081830.669
26_L30_A0.081780.669
140_G216_E0.081670.668
35_L45_R0.081650.668
213_D243_D0.081590.667
236_G241_R0.081410.666
6_T233_P0.081380.665
120_L132_A0.08130.665
48_S175_I0.081280.665
40_L215_F0.08120.664
141_I144_S0.081180.664
7_A241_R0.081110.663
158_A218_A0.081020.663
10_L13_I0.080840.661
143_D154_G0.080830.661
142_G170_S0.080820.661
166_T207_I0.080640.659
65_L78_P0.080560.659
134_I138_I0.080420.658
32_I215_F0.080410.658
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
3hd6A0.8301260.956
2b2hA0.814713.20.961
1u7gA0.830110.80.963
1fqjC0.1395.10.967
4gbaF0.10044.10.969
3b9wA0.83013.20.97
3qrxB0.10043.10.971
3mk7C0.2512.20.972
2ls2A0.10041.80.974
2wscJ0.08111.70.974
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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