GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Spt5-NGN - Early transcription elongation factor of RNA pol II NGN section
Pfam: PF03439 (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: CL0439
Length: 84
Sequences: 1827
Seq/Len: 21.75
HH_delta: 0.107 (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_A20_M1.039674.239
77_I81_E0.883913.604
36_S50_E0.740783.020
33_N54_E0.729912.976
35_Y50_E0.639882.609
24_E30_N0.581292.370
15_V67_I0.45571.858
22_K64_I0.412121.680
19_L67_I0.399731.630
78_E81_E0.391091.595
43_L83_L0.386111.574
11_Q66_H0.382021.558
51_A57_V0.379521.547
27_A30_N0.368271.501
50_E77_I0.360641.470
6_K69_G0.352781.438
7_C12_E0.348061.419
48_Y80_M0.341691.393
76_P79_E0.341081.391
8_K11_Q0.32861.340
43_L48_Y0.322061.313
17_I21_N0.310441.266
48_Y75_V0.297271.212
18_S64_I0.293221.195
6_K68_R0.291251.187
12_E45_G0.286441.168
18_S22_K0.285891.166
58_K62_R0.280971.146
4_A71_R0.275241.122
75_V80_M0.266921.088
51_A61_I0.261841.068
15_V64_I0.26121.065
11_Q14_E0.260511.062
14_E17_I0.259511.058
13_R41_D0.25461.038
43_L75_V0.25381.035
8_K66_H0.252851.031
23_A34_I0.250631.022
19_L26_L0.249661.018
38_F41_D0.247921.011
59_E63_G0.247081.007
78_E82_D0.245681.002
54_E57_V0.244450.997
58_K71_R0.23970.977
23_A27_A0.238280.971
18_S63_G0.237440.968
46_Y71_R0.2360.962
48_Y83_L0.22570.920
20_M24_E0.22360.912
22_K63_G0.222620.908
13_R16_A0.222170.906
7_C11_Q0.219630.895
14_E18_S0.218920.893
37_I40_P0.216940.884
5_V67_I0.209510.854
6_K11_Q0.206340.841
26_L30_N0.19910.812
9_P39_A0.197050.803
1_K77_I0.195140.796
22_K60_A0.194610.793
19_L61_I0.193950.791
76_P81_E0.19250.785
15_V47_I0.191130.779
14_E66_H0.189740.774
25_D50_E0.189230.772
25_D60_A0.188350.768
6_K45_G0.184760.753
15_V19_L0.184520.752
59_E62_R0.184150.751
19_L49_V0.183540.748
43_L46_Y0.182220.743
51_A58_K0.17920.731
21_N56_D0.177520.724
7_C75_V0.176440.719
17_I20_M0.17560.716
58_K72_P0.175560.716
38_F52_E0.175060.714
19_L22_K0.172910.705
33_N56_D0.172380.703
18_S21_N0.171780.700
21_N25_D0.171290.698
33_N52_E0.1690.689
26_L29_K0.168180.686
23_A49_V0.166650.679
11_Q65_R0.165670.675
5_V49_V0.165550.675
67_I72_P0.163720.668
9_P65_R0.163460.666
29_K32_L0.162460.662
53_R56_D0.160440.654
24_E48_Y0.159240.649
20_M36_S0.15910.649
21_N66_H0.15820.645
40_P45_G0.157840.644
35_Y57_V0.156010.636
7_C59_E0.155120.632
2_I83_L0.155040.632
7_C13_R0.154960.632
27_A38_F0.154830.631
22_K33_N0.154010.628
17_I75_V0.153740.627
55_S79_E0.153660.626
19_L23_A0.153590.626
15_V71_R0.153180.625
5_V59_E0.152050.620
12_E37_I0.151710.619
64_I68_R0.151320.617
77_I80_M0.151280.617
4_A75_V0.150970.616
45_G73_G0.150140.612
52_E59_E0.149710.610
9_P15_V0.149420.609
7_C71_R0.148920.607
46_Y61_I0.148350.605
2_I44_K0.148320.605
32_L63_G0.148290.605
33_N57_V0.148080.604
25_D38_F0.147620.602
73_G76_P0.14730.601
51_A72_P0.147210.600
27_A42_S0.14620.596
35_Y39_A0.145940.595
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
3p8bB0.952499.70.107
3lpeA0.952499.70.114
2ougA0.976299.50.199
1nz8A199.50.213
2jvvA199.50.213
2lq8A199.40.262
1m1hA199.30.286
2exuA199.30.286
3h7hB199.30.294
2xhcA198.60.487

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