GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GTP_EFTU - Elongation factor Tu GTP binding domain
Pfam: PF00009 (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: CL0023
Length: 188
Sequences: 40115
Seq/Len: 213.38
HH_delta: 0.113 (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
128_V167_I2.124232.685
22_A172_G2.116782.675
165_I181_A2.072722.620
103_A129_L1.823752.305
181_A184_E1.686442.131
143_I147_K1.562741.975
100_V130_N1.533011.938
7_A94_A1.489411.882
132_M166_P1.455861.840
98_I128_V1.451671.835
19_L100_V1.449751.832
104_N134_L1.394811.763
163_P181_A1.387651.754
128_V178_L1.345321.700
129_L166_P1.30021.643
138_E141_E1.289241.629
8_I20_L1.281591.620
167_I178_L1.278711.616
110_Q114_H1.266911.601
174_G177_E1.25181.582
132_M173_D1.216141.537
5_N73_T1.142641.444
126_I181_A1.107711.400
102_D105_D1.105641.397
62_S71_K1.104051.395
110_Q113_E1.091781.380
143_I166_P1.082861.369
142_I147_K1.082611.368
8_I98_I1.078531.363
126_I165_I1.075551.359
103_A132_M1.05691.336
72_I183_V1.054341.333
107_I110_Q1.050871.328
143_I146_I1.049621.327
18_T169_A1.046331.322
140_E144_E1.036911.311
130_N169_A1.014591.282
107_I111_T1.010521.277
108_Q111_T1.00681.272
145_E149_K0.999881.264
96_I126_I0.991121.253
19_L175_I0.988531.249
180_E184_E0.988331.249
141_E145_E0.977941.236
70_R183_V0.975261.233
19_L178_L0.968181.224
138_E142_I0.961741.216
176_D180_E0.945181.195
142_I145_E0.941391.190
140_E143_I0.941291.190
142_I146_I0.940251.188
102_D131_K0.924111.168
22_A175_I0.923141.167
57_D61_I0.921991.165
112_E116_K0.921021.164
84_I87_M0.918131.160
101_V127_V0.916161.158
110_Q115_L0.911461.152
101_V164_V0.902611.141
53_G56_I0.901171.139
177_E180_E0.899411.137
133_D168_S0.898361.135
139_L143_I0.885181.119
58_L61_I0.883641.117
52_R56_I0.879871.112
101_V129_L0.869651.099
54_I57_D0.85941.086
115_L119_R0.849911.074
56_I61_I0.845981.069
19_L169_A0.843791.066
111_T115_L0.827151.045
6_I96_I0.824351.042
61_I64_E0.819311.036
64_E71_K0.814561.030
21_G25_G0.812391.027
114_H118_L0.811561.026
109_P113_E0.811141.025
109_P112_E0.806311.019
144_E147_K0.803691.016
96_I182_L0.801011.012
98_I182_L0.798241.009
87_M90_G0.779730.985
98_I126_I0.778160.984
60_F73_T0.777260.982
179_L182_L0.776550.981
68_N183_V0.775530.980
50_R53_G0.774740.979
114_H117_I0.768790.972
83_F86_E0.763420.965
146_I150_L0.759460.960
113_E117_I0.759190.960
168_S171_T0.758590.959
98_I178_L0.75760.958
131_K134_L0.752090.951
86_E90_G0.747780.945
52_R55_T0.739840.935
111_T114_H0.731270.924
136_E139_L0.724390.916
50_R55_T0.720030.910
180_E183_V0.7160.905
178_L182_L0.714990.904
177_E181_A0.714510.903
51_E54_I0.713190.901
136_E140_E0.705520.892
88_I117_I0.705050.891
23_L179_L0.700190.885
175_I179_L0.696810.881
139_L142_I0.696360.880
21_G27_A0.695320.879
20_L74_L0.693670.877
83_F87_M0.691340.874
7_A77_T0.682970.863
86_E89_R0.680470.860
54_I59_S0.678430.857
106_G146_I0.676010.854
54_I61_I0.675850.854
129_L164_V0.674560.853
51_E55_T0.673980.852
112_E149_K0.673490.851
116_K120_E0.672470.850
116_K119_R0.671040.848
141_E144_E0.669120.846
11_H111_T0.665150.841
56_I59_S0.664330.840
19_L167_I0.663860.839
91_L94_A0.657480.831
97_A123_I0.65540.828
19_L128_V0.654520.827
22_A26_K0.652280.824
140_E166_P0.650110.822
128_V169_A0.645610.816
112_E115_L0.642630.812
127_V164_V0.641850.811
67_E179_L0.640010.809
113_E116_K0.639170.808
99_L127_V0.639070.808
140_E147_K0.632910.800
99_L115_L0.631330.798
55_T61_I0.626980.792
137_K141_E0.626920.792
117_I120_E0.623680.788
117_I121_L0.620780.785
26_K176_D0.619720.783
114_H119_R0.61880.782
76_D79_G0.612470.774
55_T58_L0.611580.773
67_E70_R0.611160.772
6_I72_I0.611080.772
5_N75_I0.6090.770
10_G15_G0.608280.769
62_S73_T0.602180.761
171_T174_G0.602030.761
64_E69_N0.597480.755
21_G24_L0.596720.754
6_I182_L0.591770.748
51_E56_I0.587410.742
107_I112_E0.584340.739
53_G57_D0.577560.730
83_F90_G0.576740.729
10_G16_K0.570910.722
11_H14_S0.568650.719
20_L61_I0.566730.716
54_I58_L0.566270.716
53_G58_L0.562760.711
143_I164_V0.560930.709
19_L23_L0.560820.709
7_A97_A0.560590.709
50_R54_I0.555130.702
14_S102_D0.553330.699
92_R121_L0.551980.698
67_E180_E0.551050.696
137_K140_E0.550860.696
70_R73_T0.549970.695
115_L118_L0.547170.692
107_I114_H0.546450.691
126_I178_L0.542630.686
135_I139_L0.540310.683
169_A172_G0.538620.681
53_G61_I0.537260.679
179_L183_V0.5360.677
165_I174_G0.534680.676
59_S62_S0.53460.676
147_K164_V0.533770.675
163_P166_P0.531790.672
103_A135_I0.526980.666
102_D130_N0.525250.664
138_E143_I0.523330.661
172_G175_I0.52110.659
165_I177_E0.51510.651
50_R57_D0.513880.649
81_E87_M0.51210.647
136_E142_I0.511210.646
12_V80_H0.509670.644
139_L166_P0.509010.643
128_V165_I0.507840.642
50_R56_I0.499690.632
22_A169_A0.497950.629
51_E57_D0.494210.625
94_A97_A0.493380.624
80_H87_M0.491890.622
52_R59_S0.489490.619
84_I90_G0.488960.618
106_G142_I0.485080.613
57_D60_F0.483910.612
81_E85_K0.483680.611
55_T60_F0.477250.603
108_Q112_E0.47320.598
109_P114_H0.47260.597
147_K150_L0.471570.596
52_R57_D0.470580.595
173_D177_E0.464610.587
109_P115_L0.464080.587
81_E84_I0.464070.587
100_V167_I0.463010.585
107_I117_I0.461740.584
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
3j25A0.98499.90.113
3tr5A0.989499.90.114
3vqtA0.989499.90.122
3cb4D0.946899.90.15
3mcaA0.978799.90.151
3avxA0.968199.90.152
3izyP0.877799.90.152
2yweA0.946899.90.155
3j2k70.98499.90.158
1d2eA0.968199.90.165

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