GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TOM20_plant - Plant specific mitochondrial import receptor subunit TOM20
Pfam: PF06552 (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: CL0020
Length: 186
Sequences: 11226
Seq/Len: 60.35
HH_delta: 0.287 (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
6_F9_H2.358233.909
84_F98_K1.766392.928
40_Q53_D1.62522.694
59_E75_L1.392482.308
115_L118_K1.36982.271
76_G103_F1.362492.259
72_L102_Y1.344712.229
32_G58_F1.319382.187
133_I151_S1.30492.163
137_G152_S1.289572.138
15_E31_W1.27832.119
14_A30_N1.219652.022
28_L57_K1.146181.900
58_F74_C1.139061.888
149_S153_A1.097531.819
11_R15_E1.077571.786
75_L102_Y1.053911.747
100_T104_Q1.029471.707
55_I59_E0.978981.623
140_Q147_S0.95081.576
11_R38_L0.943581.564
31_W35_L0.941821.561
136_Q140_Q0.938891.556
31_W57_K0.918161.522
124_A136_Q0.887641.472
140_Q145_G0.872531.446
136_Q151_S0.870671.443
75_L79_Y0.862351.430
120_L124_A0.856881.421
35_L53_D0.846141.403
11_R35_L0.835321.385
55_I79_Y0.833251.381
18_Y28_L0.827521.372
11_R31_W0.823841.366
134_H138_L0.822681.364
140_Q151_S0.79951.325
9_H12_K0.790071.310
83_A96_F0.786751.304
55_I75_L0.777021.288
35_L57_K0.759721.259
55_I82_L0.754981.252
79_Y102_Y0.750261.244
53_D56_S0.746871.238
98_K101_E0.74411.234
55_I78_A0.743641.233
16_A20_K0.735841.220
8_E38_L0.734191.217
61_A71_A0.732471.214
35_L40_Q0.729641.210
79_Y98_K0.728391.208
29_T74_C0.725871.203
123_A135_K0.721321.196
148_S152_S0.708511.175
72_L105_K0.707861.173
141_Q152_S0.684061.134
135_K138_L0.682591.132
105_K109_E0.681561.130
118_K121_E0.680831.129
147_S150_S0.679631.127
158_K161_S0.671311.113
17_A20_K0.667141.106
62_L72_L0.660911.096
133_I154_K0.66031.095
60_E63_K0.65971.094
161_S164_F0.65971.094
120_L140_Q0.648271.075
151_S154_K0.645191.070
137_G155_S0.64181.064
33_G74_C0.641611.064
11_R34_A0.633651.050
13_K17_A0.618891.026
25_A61_A0.617361.023
24_D27_N0.613181.017
68_K71_A0.612081.015
76_G106_A0.597870.991
74_C77_N0.592820.983
10_A34_A0.589830.978
60_E64_I0.587970.975
52_E82_L0.583970.968
18_Y31_W0.577690.958
76_G99_A0.576370.955
72_L106_A0.572160.949
36_L58_F0.571940.948
7_F34_A0.571690.948
141_Q146_A0.561240.930
65_N68_K0.55610.922
138_L142_A0.552070.915
16_A19_A0.549470.911
17_A27_N0.548460.909
69_H106_A0.547480.908
13_K16_A0.54010.895
10_A14_A0.539390.894
105_K108_D0.536720.890
130_H155_S0.536120.889
14_A34_A0.527810.875
18_Y27_N0.527270.874
122_M126_A0.525670.871
118_K122_M0.524290.869
79_Y84_F0.523110.867
30_N33_G0.52280.867
57_K60_E0.521840.865
34_A38_L0.519130.861
34_A78_A0.518570.860
15_E19_A0.517150.857
62_L71_A0.513690.852
116_Y139_G0.51040.846
129_L132_E0.508060.842
139_G143_M0.503690.835
41_F78_A0.500840.830
104_Q108_D0.500430.830
78_A82_L0.485530.805
73_W77_N0.485250.804
29_T33_G0.483310.801
117_R143_M0.482310.800
21_N24_D0.482240.799
28_L64_I0.478360.793
98_K102_Y0.478190.793
32_G61_A0.478130.793
138_L141_Q0.477250.791
61_A106_A0.47530.788
72_L109_E0.47480.787
26_D30_N0.474790.787
28_L60_E0.473340.785
53_D57_K0.467580.775
110_D113_N0.467040.774
61_A64_I0.460910.764
146_A149_S0.460250.763
29_T71_A0.459360.762
7_F11_R0.458190.760
59_E63_K0.454830.754
12_K16_A0.454060.753
96_F100_T0.453430.752
138_L152_S0.451490.748
36_L74_C0.450480.747
36_L41_F0.448810.744
102_Y105_K0.448230.743
14_A27_N0.446280.740
33_G36_L0.445790.739
52_E97_E0.439940.729
132_E136_Q0.438160.726
62_L75_L0.434120.720
36_L80_T0.433140.718
126_A132_E0.431560.715
28_L133_I0.430640.714
54_A58_F0.428730.711
80_T96_F0.427790.709
122_M125_K0.427120.708
36_L78_A0.426060.706
58_F78_A0.425410.705
120_L143_M0.425070.705
159_K162_S0.424160.703
99_A103_F0.423480.702
28_L72_L0.422510.700
148_S155_S0.420240.697
156_S159_K0.417230.692
8_E52_E0.417180.692
13_K20_K0.412350.684
8_E12_K0.408610.677
120_L136_Q0.407360.675
7_F37_E0.407320.675
158_K164_F0.406640.674
29_T68_K0.405330.672
14_A31_W0.40430.670
133_I155_S0.402920.668
56_S60_E0.401140.665
52_E56_S0.397420.659
57_K61_A0.395950.656
72_L133_I0.395210.655
15_E35_L0.3920.650
97_E101_E0.390850.648
131_M134_H0.39040.647
33_G37_E0.390150.647
54_A78_A0.386820.641
106_A109_E0.384850.638
63_K108_D0.377730.626
56_S150_S0.373420.619
25_A68_K0.369940.613
41_F82_L0.36840.611
120_L123_A0.367910.610
33_G58_F0.367880.610
119_S126_A0.36760.609
77_N81_S0.36760.609
33_G77_N0.366590.608
137_G148_S0.363130.602
70_D74_C0.360270.597
59_E79_Y0.359770.596
111_P114_E0.359280.596
147_S151_S0.357840.593
26_D131_M0.357180.592
80_T141_Q0.355460.589
28_L61_A0.354680.588
29_T70_D0.354680.588
102_Y106_A0.35350.586
27_N30_N0.352930.585
9_H13_K0.351670.583
11_R100_T0.349440.579
73_W76_G0.348410.578
137_G151_S0.348120.577
8_E11_R0.346410.574
158_K162_S0.346090.574
71_A132_E0.345770.573
32_G54_A0.345110.572
17_A24_D0.344870.572
115_L119_S0.343950.570
117_R121_E0.342810.568
135_K139_G0.342270.567
52_E55_I0.3420.567
65_N110_D0.341830.567
77_N80_T0.338910.562
60_E105_K0.337430.559
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
4gywA0.795799.70.287
2h6fA0.881799.60.331
4gywA0.801199.60.343
2h6fA0.881799.60.347
1zu2A0.779699.60.348
2pl2A0.881799.60.349
4ga2A0.758199.50.351
4abnA0.876399.50.353
2pziA0.790399.50.36
1w3bA0.838799.50.367

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