GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GTP_EFTU_D3 - Elongation factor Tu C-terminal domain
Pfam: PF03143 (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. )
Length: 99
Sequences: 3507
Seq/Len: 35.42
HH_delta: 0.123 (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
7_R68_E1.279853.746
9_E64_V1.180943.457
57_L63_A1.124993.293
7_R66_E0.995522.914
9_E66_E0.98812.892
12_V65_V0.801152.345
41_V68_E0.790922.315
42_K66_E0.758792.221
11_Q64_V0.72962.136
29_L38_C0.656921.923
34_A71_K0.646331.892
81_F93_G0.613471.796
31_I75_V0.605031.771
20_P56_F0.58661.717
8_F69_F0.576861.689
23_P43_I0.572621.676
22_S56_F0.541841.586
7_R41_V0.521641.527
10_A81_F0.502161.470
31_I73_I0.497081.455
23_P42_K0.489191.432
11_Q96_T0.47811.400
75_V95_V0.462281.353
29_L67_L0.458821.343
38_C67_L0.455861.334
58_K61_D0.451121.321
39_R68_E0.449481.316
6_N72_P0.443891.299
41_V66_E0.436291.277
6_N68_E0.435211.274
11_Q62_R0.431681.264
31_I34_A0.428531.254
24_G39_R0.413651.211
83_L91_A0.402921.179
38_C69_F0.396171.160
28_V35_D0.392431.149
8_F67_L0.387961.136
84_R89_T0.372621.091
34_A73_I0.36041.055
14_V91_A0.354071.036
29_L69_F0.346771.015
37_P70_Q0.33460.979
15_L59_P0.3340.978
69_F73_I0.326210.955
27_P90_I0.320130.937
9_E96_T0.313610.918
27_P38_C0.312650.915
19_K25_Y0.310050.908
29_L83_L0.309260.905
11_Q94_V0.308580.903
26_Q39_R0.305980.896
36_V73_I0.302760.886
10_A65_V0.302170.885
36_V71_K0.290840.851
23_P40_I0.287410.841
89_T92_V0.278440.815
64_V96_T0.277730.813
26_Q70_Q0.277050.811
43_I49_T0.276260.809
40_I67_L0.276030.808
82_I92_V0.272990.799
49_T52_K0.272780.799
22_S55_K0.271210.794
13_I62_R0.263880.772
10_A67_L0.263320.771
24_G40_I0.262040.767
90_I93_G0.261120.764
12_V91_A0.2590.758
28_V37_P0.257260.753
40_I83_L0.252250.738
5_V69_F0.244060.714
14_V60_G0.243230.712
42_K65_V0.239840.702
79_S82_I0.238650.699
87_G92_V0.238250.697
80_R84_R0.236910.694
4_A72_P0.23570.690
80_R94_V0.235390.689
43_I50_G0.233850.685
29_L81_F0.233370.683
30_H35_D0.232770.681
42_K52_K0.229840.673
32_H74_C0.229180.671
9_E77_P0.229090.671
32_H82_I0.228870.670
33_T81_F0.227450.666
14_V57_L0.223880.655
78_F94_V0.219780.643
88_K91_A0.219450.642
29_L73_I0.218220.639
14_V21_I0.217270.636
20_P58_K0.216640.634
75_V79_S0.21220.621
82_I87_G0.211770.620
27_P60_G0.208330.610
25_Y28_V0.208250.610
13_I16_D0.206540.605
34_A74_C0.205470.601
5_V75_V0.205450.601
6_N37_P0.204080.597
3_K7_R0.202430.593
28_V90_I0.200720.588
4_A75_V0.200610.587
3_K77_P0.199930.585
8_F75_V0.199710.585
2_I5_V0.199340.584
37_P86_G0.199110.583
51_K55_K0.199110.583
16_D88_K0.198960.582
14_V59_P0.198760.582
83_L86_G0.198060.580
2_I74_C0.197870.579
77_P94_V0.197050.577
13_I33_T0.196280.575
40_I65_V0.195310.572
42_K68_E0.19530.572
30_H84_R0.193570.567
16_D59_P0.192980.565
42_K63_A0.192210.563
89_T94_V0.191690.561
6_N41_V0.191090.559
60_G78_F0.189380.554
66_E77_P0.187720.550
15_L92_V0.187590.549
22_S26_Q0.185560.543
84_R91_A0.18380.538
34_A61_D0.182280.534
8_F25_Y0.181850.532
19_K85_D0.181570.532
89_T93_G0.18150.531
3_K56_F0.180190.527
13_I94_V0.180050.527
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
1f60A199.80.123
3e1yE199.80.125
3j2k7199.80.133
1r5bA199.80.142
3izq1199.80.15
1jnyA199.80.157
3p26A199.80.163
3mcaA0.959699.70.191
1zunB0.969799.70.226
2c78A0.919299.70.237

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