GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2204 - Nucleotidyl transferase of unknown function (DUF2204)
Pfam: PF09970 (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: CL0260
Length: 181
Sequences: 1334
Seq/Len: 7.37
HH_delta: 0.504 (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
106_R124_D0.352743.317
137_D140_D0.245192.305
23_G129_K0.240152.258
22_V128_L0.234892.209
23_G132_A0.220132.070
121_S124_D0.216032.031
25_A37_T0.197871.861
129_K140_D0.189541.782
26_A125_L0.188731.775
136_E140_D0.188661.774
109_R118_K0.176221.657
53_A57_R0.172311.620
23_G91_L0.170221.601
156_D159_Y0.169551.594
126_I141_I0.167521.575
158_D161_R0.160611.510
26_A119_V0.155011.458
120_I128_L0.153851.447
158_D162_E0.152661.435
111_K114_G0.150071.411
159_Y162_E0.150031.411
22_V120_I0.149781.408
8_I56_L0.148271.394
129_K132_A0.147291.385
8_I88_I0.146981.382
111_K116_R0.145521.368
22_V91_L0.145281.366
16_G105_E0.143771.352
129_K134_R0.143421.349
23_G128_L0.142891.344
45_E48_S0.141611.332
52_E90_L0.140571.322
23_G37_T0.138941.306
43_F91_L0.138721.304
37_T129_K0.137271.291
129_K137_D0.137071.289
156_D162_E0.136211.281
134_R137_D0.134931.269
24_G27_V0.131351.235
71_D84_E0.131311.235
24_G39_D0.131151.233
61_E64_G0.130331.225
6_K113_G0.130141.224
48_S51_L0.127321.197
94_I97_F0.125691.182
25_A40_I0.124061.167
24_G137_D0.122471.152
16_G58_E0.122091.148
91_L128_L0.120751.135
23_G120_I0.119431.123
51_L54_D0.118911.118
23_G125_L0.116371.094
23_G38_K0.116331.094
35_R140_D0.116291.093
43_F136_E0.115861.089
37_T132_A0.115741.088
64_G82_G0.114681.078
48_S75_P0.113671.069
18_E118_K0.112791.061
7_E34_R0.11221.055
126_I160_L0.110761.041
18_E45_E0.110281.037
83_G89_D0.109441.029
39_D89_D0.10941.029
11_E63_N0.109241.027
137_D144_L0.108141.017
22_V132_A0.107981.015
27_V125_L0.107931.015
12_L17_V0.107481.011
57_R82_G0.107281.009
132_A140_D0.107251.008
8_I11_E0.107091.007
13_N115_V0.106941.006
37_T128_L0.106060.997
54_D58_E0.105870.995
139_E142_D0.105580.993
134_R140_D0.105560.993
37_T40_I0.105370.991
22_V43_F0.103940.977
65_W130_A0.102940.968
91_L129_K0.102410.963
30_A40_I0.10160.955
73_G76_R0.101450.954
51_L58_E0.101060.950
23_G134_R0.100170.942
8_I85_D0.100110.941
19_Y118_K0.099650.937
20_V119_V0.099080.932
30_A128_L0.098410.925
83_G90_L0.098260.924
125_L129_K0.097820.920
16_G69_W0.097770.919
14_K51_L0.09760.918
48_S111_K0.097530.917
49_P92_E0.097220.914
25_A32_G0.0970.912
31_Y122_P0.096940.912
86_V144_L0.096890.911
96_D128_L0.096680.909
74_T78_V0.096470.907
8_I40_I0.096180.904
24_G81_V0.096110.904
68_G71_D0.095820.901
56_L79_V0.095720.900
22_V37_T0.094810.891
25_A36_T0.09460.890
13_N19_Y0.093980.884
6_K10_E0.093890.883
136_E139_E0.093870.883
15_R58_E0.093780.882
25_A28_N0.093760.882
128_L132_A0.093010.875
10_E20_V0.0930.874
62_E68_G0.092930.874
18_E105_E0.092380.869
133_G136_E0.092280.868
88_I146_R0.091680.862
13_N111_K0.091450.860
23_G26_A0.091390.859
47_P98_Y0.090910.855
28_N34_R0.090710.853
27_V36_T0.090580.852
56_L76_R0.090290.849
72_F75_P0.090230.848
110_V119_V0.090030.847
27_V87_R0.089790.844
139_E143_I0.089740.844
135_E139_E0.089190.839
24_G35_R0.089170.838
156_D160_L0.088780.835
155_I160_L0.088640.833
76_R89_D0.088560.833
28_N37_T0.088440.832
105_E130_A0.088330.831
9_L40_I0.088110.828
51_L112_I0.087820.826
7_E10_E0.087220.820
19_Y119_V0.087130.819
6_K40_I0.087010.818
122_P156_D0.086750.816
16_G114_G0.086730.816
126_I144_L0.086660.815
40_I134_R0.086620.814
70_T78_V0.086460.813
110_V114_G0.086050.809
25_A139_E0.086040.809
84_E103_I0.086010.809
11_E15_R0.085880.808
17_V50_N0.085850.807
57_R65_W0.085720.806
43_F128_L0.085420.803
63_N97_F0.085330.802
42_L88_I0.085320.802
49_P141_I0.085310.802
24_G136_E0.085070.800
59_V101_E0.084940.799
64_G73_G0.084890.798
109_R116_R0.084630.796
12_L52_E0.084330.793
55_A62_E0.084290.793
21_I36_T0.084270.792
51_L159_Y0.084130.791
35_R39_D0.084070.790
6_K11_E0.0840.790
10_E14_K0.0840.790
37_T119_V0.083840.788
23_G92_E0.083740.787
27_V129_K0.083290.783
45_E102_E0.083230.783
103_I114_G0.083120.782
64_G77_Y0.082910.780
24_G122_P0.08280.779
19_Y22_V0.082730.778
37_T126_I0.082580.776
21_I126_I0.08230.774
37_T137_D0.082290.774
28_N42_L0.082270.774
18_E102_E0.082090.772
42_L138_I0.081720.768
132_A136_E0.081680.768
44_I132_A0.081570.767
50_N145_A0.081560.767
9_L15_R0.081270.764
156_D161_R0.080920.761
89_D136_E0.080680.759
25_A29_L0.080360.756
6_K112_I0.080320.755
13_N117_V0.080080.753
74_T94_I0.079820.751
83_G115_V0.079740.750
20_V45_E0.079410.747
51_L123_E0.079260.745
26_A97_F0.079220.745
26_A124_D0.07910.744
117_V122_P0.079050.743
52_E55_A0.078970.743
94_I120_I0.078830.741
19_Y129_K0.078680.740
66_D109_R0.078630.739
72_F78_V0.078580.739
36_T113_G0.078570.739
155_I161_R0.078290.736
31_Y100_P0.078170.735
37_T87_R0.078140.735
11_E14_K0.07810.734
48_S52_E0.0780.733
88_I143_I0.077710.731
93_N97_F0.07770.731
73_G89_D0.077660.730
25_A31_Y0.07760.730
29_L108_K0.077530.729
87_R91_L0.077520.729
98_Y113_G0.077470.728
93_N127_V0.077350.727
38_K129_K0.077310.727
13_N16_G0.077240.726
22_V139_E0.077090.725
37_T140_D0.076910.723
140_D143_I0.076870.723
29_L54_D0.076850.723
135_E141_I0.076740.722
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
2fclA0.806699.60.504
4e8jA0.762499.40.584
1vfgA0.878593.60.856
1ou5A0.889593.60.857
3h38A0.917193.20.859
1miwA0.872991.30.866
3aqlA0.872985.80.879
1ylqA0.508346.30.909
1no5A0.563545.90.909
2rffA0.519334.10.915
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0838 seconds.