GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATE_C - Arginine-tRNA-protein transferase C terminus
Pfam: PF04377 (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: CL0257
Length: 128
Sequences: 651
Seq/Len: 5.09
HH_delta: 0.845 (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
81_T117_F0.580454.757
2_E45_R0.33012.706
9_R71_D0.31742.601
89_E92_R0.249912.048
53_V69_F0.246912.024
81_T116_R0.240911.975
91_A99_Y0.239891.966
44_Y86_R0.235141.927
70_Y75_S0.219711.801
105_I111_M0.212381.741
1_E25_Q0.212181.739
3_H43_E0.199131.632
56_V65_A0.197591.619
65_A87_E0.195581.603
9_R73_D0.1941.590
15_H110_K0.186681.530
45_R48_G0.184431.512
49_K71_D0.182211.493
68_T83_S0.181841.490
8_E12_M0.18111.484
91_A96_L0.166611.366
10_Y15_H0.166461.364
31_F55_V0.161531.324
19_D62_G0.16071.317
89_E93_E0.159161.304
46_L51_I0.158011.295
39_T45_R0.154041.263
124_D127_R0.151181.239
4_Y8_E0.150071.230
7_Y87_E0.14751.209
74_Y77_R0.147391.208
74_Y79_L0.1471.205
8_E22_P0.145591.193
108_C112_N0.144571.185
104_W120_H0.144441.184
51_I74_Y0.143771.178
62_G96_L0.14271.170
51_I79_L0.142281.166
6_L121_E0.141261.158
3_H28_Y0.139471.143
48_G92_R0.137951.131
15_H111_M0.137181.124
4_Y15_H0.134431.102
88_I94_L0.134371.101
56_V87_E0.133231.092
115_A122_L0.132441.085
13_A73_D0.131571.078
118_R127_R0.131361.077
11_Q22_P0.130931.073
49_K74_Y0.127681.046
32_L55_V0.12721.043
13_A88_I0.127041.041
98_Y121_E0.1271.041
4_Y110_K0.126741.039
5_E8_E0.126031.033
1_E5_E0.125491.029
49_K70_Y0.125441.028
9_R72_P0.124551.021
11_Q15_H0.124331.019
7_Y31_F0.123141.009
6_L9_R0.12291.007
61_D97_P0.121930.999
106_H122_L0.121560.996
7_Y10_Y0.120760.990
41_H55_V0.120470.987
64_S67_Y0.119610.980
29_R39_T0.118320.970
18_G21_D0.114610.939
19_D22_P0.114570.939
44_Y83_S0.114560.939
71_D127_R0.114520.939
90_L94_L0.113630.931
30_R38_G0.112940.926
46_L74_Y0.112710.924
90_L93_E0.112340.921
5_E13_A0.112160.919
71_D74_Y0.112080.919
71_D76_K0.111580.915
75_S115_A0.109840.900
28_Y42_L0.109830.900
86_R89_E0.109560.898
44_Y52_A0.109120.894
63_L88_I0.109090.894
44_Y68_T0.10890.893
22_P27_Q0.108510.889
106_H112_N0.108430.889
40_Y58_I0.108220.887
57_D64_S0.105340.863
17_D21_D0.105340.863
32_L68_T0.104920.860
31_F68_T0.104860.859
76_K93_E0.104650.858
25_Q70_Y0.103950.852
35_S39_T0.103940.852
47_D73_D0.103880.851
41_H87_E0.103490.848
6_L73_D0.10340.847
84_I108_C0.103310.847
44_Y65_A0.103290.847
72_P115_A0.103110.845
14_R20_M0.102930.844
15_H20_M0.1020.836
10_Y64_S0.101650.833
10_Y110_K0.101450.831
1_E92_R0.100890.827
78_S92_R0.100510.824
66_V111_M0.100350.822
17_D32_L0.099970.819
84_I99_Y0.099920.819
37_L62_G0.099820.818
115_A120_H0.099590.816
72_P85_L0.099140.813
11_Q21_D0.098810.810
112_N116_R0.098680.809
47_D51_I0.098290.806
15_H64_S0.098220.805
23_P31_F0.09810.804
116_R127_R0.0980.803
5_E12_M0.097950.803
62_G101_L0.097880.802
104_W115_A0.09780.802
101_L116_R0.097090.796
38_G122_L0.096970.795
38_G90_L0.096690.792
15_H18_G0.096320.789
29_R81_T0.095670.784
42_L107_G0.095630.784
10_Y59_L0.095580.783
75_S125_P0.095520.783
55_V60_P0.095040.779
65_A83_S0.094750.777
4_Y27_Q0.094350.773
2_E93_E0.094110.771
11_Q110_K0.093810.769
67_Y111_M0.09380.769
4_Y59_L0.093770.769
11_Q23_P0.093710.768
1_E26_E0.093530.767
58_I96_L0.093410.766
16_P21_D0.092980.762
83_S115_A0.092720.760
8_E19_D0.092550.759
52_A83_S0.092510.758
5_E98_Y0.092070.755
107_G112_N0.091970.754
77_R83_S0.091890.753
118_R122_L0.091570.751
14_R68_T0.091490.750
3_H69_F0.091270.748
36_P39_T0.091210.748
53_V59_L0.091060.746
25_Q118_R0.090590.742
90_L121_E0.090470.741
46_L49_K0.090330.740
16_P35_S0.090020.738
51_I77_R0.089890.737
20_M69_F0.089790.736
13_A76_K0.089760.736
119_P123_L0.089280.732
82_Y96_L0.089260.732
2_E95_G0.088980.729
26_E34_S0.088750.727
103_Y111_M0.088730.727
115_A126_G0.088620.726
34_S60_P0.088510.725
33_C41_H0.088510.725
66_V126_G0.08850.725
98_Y116_R0.088260.723
5_E49_K0.08810.722
61_D69_F0.087740.719
34_S59_L0.087720.719
41_H112_N0.087680.719
48_G126_G0.087530.717
51_I54_A0.087460.717
30_R60_P0.087110.714
109_P124_D0.087110.714
4_Y111_M0.086870.712
56_V95_G0.086770.711
49_K107_G0.086570.710
62_G97_P0.086550.709
43_E53_V0.086480.709
49_K126_G0.08640.708
11_Q41_H0.086390.708
82_Y88_I0.086330.708
95_G106_H0.086310.707
62_G104_W0.085570.701
75_S103_Y0.08550.701
32_L110_K0.085480.701
85_L111_M0.085360.700
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
3gkrA0.960997.60.845
1lrzA0.960996.20.878
4h89A1960.881
4jxqA195.70.883
3dr6A195.50.885
3f5bA0.968895.30.887
2aj6A1950.889
2r1iA0.968894.90.89
2o28A0.937594.70.891
3owcA194.70.891
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