GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NTP_transf_2 - Nucleotidyltransferase domain
Pfam: PF01909 (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: 93
Sequences: 2844
Seq/Len: 30.58
HH_delta: 0.159 (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
16_E39_I0.854762.983
23_Y28_A0.775692.707
37_L74_R0.676272.360
23_Y34_I0.604812.110
23_Y67_I0.568081.982
82_F86_I0.549831.919
55_V59_E0.548761.915
84_R88_E0.532691.859
14_V17_V0.515021.797
15_A41_D0.473581.652
54_L58_E0.448411.565
78_E81_Y0.430861.503
58_E62_E0.427211.491
20_F72_V0.424281.480
83_R87_L0.420631.468
59_E63_E0.406441.418
15_A39_I0.399491.394
73_V76_Y0.391931.368
84_R87_L0.389951.361
80_P83_R0.389431.359
11_L60_K0.382741.336
85_N88_E0.374181.306
7_I11_L0.362781.266
7_I10_E0.35431.236
51_L55_V0.348671.217
37_L73_V0.346261.208
19_L24_A0.343491.199
34_I67_I0.334131.166
24_A28_A0.316471.104
19_L34_I0.314891.099
56_E59_E0.313111.093
26_G32_S0.301691.053
42_E45_D0.30061.049
39_I74_R0.299191.044
61_L65_L0.298651.042
18_Y39_I0.296111.033
8_L14_V0.294871.029
37_L72_V0.291831.018
14_V38_I0.289791.011
22_S35_D0.289541.010
16_E74_R0.287081.002
53_E56_E0.280020.977
65_L69_V0.277890.970
22_S28_A0.275370.961
17_V36_L0.273630.955
20_F70_D0.272920.952
9_K12_F0.27210.949
81_Y85_N0.272030.949
52_E55_V0.270670.944
13_G42_E0.269690.941
38_I71_V0.268220.936
56_E60_K0.267710.934
18_Y37_L0.250490.874
19_L36_L0.247910.865
74_R78_E0.24450.853
52_E56_E0.243560.850
58_E68_E0.242820.847
28_A67_I0.241470.843
63_E66_G0.240160.838
81_Y84_R0.239560.836
8_L12_F0.239540.836
29_T83_R0.236170.824
55_V58_E0.235360.821
62_E68_E0.233390.814
54_L73_V0.232810.812
80_P84_R0.232370.811
22_S33_D0.229450.801
72_V82_F0.225370.786
62_E65_L0.223850.781
57_I61_L0.219260.765
9_K13_G0.218790.763
64_I67_I0.218690.763
74_R87_L0.217760.760
9_K17_V0.21660.756
25_R28_A0.216540.756
43_P52_E0.214690.749
24_A32_S0.21140.738
7_I64_I0.205470.717
20_F37_L0.205390.717
21_G35_D0.202990.708
21_G33_D0.202270.706
52_E60_K0.201160.702
75_E78_E0.201050.702
44_E52_E0.199550.696
40_L54_L0.199340.696
16_E76_Y0.195920.684
20_F27_D0.195690.683
28_A32_S0.195440.682
44_E78_E0.191910.670
12_F17_V0.190640.665
41_D44_E0.190120.663
77_I83_R0.189430.661
14_V40_L0.188070.656
18_Y74_R0.187910.656
25_R32_S0.18740.654
54_L71_V0.186160.650
19_L22_S0.185280.647
18_Y64_I0.18460.644
77_I87_L0.184390.643
9_K14_V0.183520.640
11_L14_V0.182950.638
36_L69_V0.182250.636
16_E84_R0.180.628
78_E84_R0.179510.626
56_E63_E0.178460.623
38_I85_N0.177360.619
11_L75_E0.176270.615
24_A75_E0.17590.614
9_K81_Y0.175890.614
40_L44_E0.175690.613
51_L54_L0.17460.609
11_L15_A0.172680.603
40_L73_V0.172360.601
53_E58_E0.172150.601
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
1no5A0.935599.50.159
1wotA0.935599.40.162
1ylqA0.946299.40.178
2rffA0.892599.10.294
4ebjA198.70.412
1knyA0.903298.60.424
4fh3A0.924798.50.46
3nybA0.95798.40.465
4e8fA0.924798.30.482
3pq1A198.20.501

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