GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mito_carr - Mitochondrial carrier protein
Pfam: PF00153 (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: 95
Sequences: 15233
Seq/Len: 160.35
HH_delta: 0.028 (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
48_Q52_K2.089072.473
51_R55_K1.894912.243
52_K56_E1.859442.201
54_Y62_L1.846682.186
53_I61_G1.61641.913
43_Y49_C1.575541.865
12_A74_I1.539591.822
28_I50_L1.454861.722
29_K33_Q1.444671.710
27_T31_R1.423381.685
44_Q48_Q1.420941.682
31_R57_E1.330441.575
50_L62_L1.329641.574
47_W51_R1.304991.545
45_G48_Q1.270331.504
57_E64_R1.258441.490
23_Y27_T1.257971.489
76_Y80_Y1.242541.471
20_L66_F1.224771.450
54_Y59_I1.21781.442
86_Y89_R1.208411.430
86_Y90_L1.198451.419
57_E61_G1.154741.367
79_I83_L1.074681.272
63_Y66_F1.046871.239
43_Y48_Q1.021881.210
73_S76_Y1.013511.200
48_Q51_R1.000251.184
59_I63_Y0.987631.169
7_N85_E0.980771.161
28_I49_C0.971841.150
8_F78_A0.958011.134
85_E88_K0.95151.126
13_L17_I0.950551.125
73_S77_T0.912531.080
26_D29_K0.908481.075
9_I12_A0.907431.074
83_L87_L0.892361.056
16_A70_L0.892191.056
9_I13_L0.880851.043
71_L75_P0.875591.036
15_G26_D0.87051.030
23_Y66_F0.866191.025
83_L86_Y0.861251.019
19_T23_Y0.86011.018
58_G61_G0.859871.018
6_A10_A0.857641.015
19_T69_S0.851811.008
51_R54_Y0.821020.972
82_G86_Y0.815610.965
19_T72_R0.814750.964
87_L91_L0.800880.948
52_K55_K0.792870.939
23_Y69_S0.780970.924
43_Y52_K0.766450.907
22_T69_S0.766250.907
5_F9_I0.756880.896
66_F70_L0.756170.895
73_S80_Y0.755410.894
47_W50_L0.751850.890
50_L54_Y0.750120.888
87_L90_L0.749640.887
6_A9_I0.743320.880
14_A18_S0.740020.876
88_K92_S0.738920.875
49_C52_K0.731180.866
23_Y63_Y0.729320.863
11_G78_A0.727610.861
84_Y88_K0.713620.845
30_T72_R0.707520.838
69_S81_F0.706620.836
27_T30_T0.701180.830
54_Y57_E0.694220.822
77_T80_Y0.693040.820
20_L70_L0.684840.811
10_A14_A0.682460.808
61_G64_R0.677950.803
28_I62_L0.674320.798
37_P40_K0.669140.792
69_S72_R0.667180.790
49_C53_I0.665260.787
23_Y30_T0.663720.786
27_T53_I0.662390.784
32_M49_C0.657110.778
38_S41_Q0.655570.776
16_A74_I0.653750.774
19_T22_T0.653190.773
18_S22_T0.649180.768
7_N89_R0.648420.768
28_I46_V0.645480.764
13_L16_A0.641220.759
44_Q52_K0.640850.759
23_Y73_S0.640650.758
22_T30_T0.637710.755
39_G42_P0.633940.750
80_Y84_Y0.625850.741
67_G70_L0.625350.740
78_A82_G0.621860.736
37_P41_Q0.619350.733
69_S77_T0.598830.709
67_G71_L0.596820.706
46_V49_C0.589480.698
69_S76_Y0.588370.696
8_F82_G0.586390.694
21_V24_P0.580150.687
72_R76_Y0.577280.683
23_Y26_D0.571720.677
11_G15_G0.56930.674
22_T25_L0.567770.672
30_T76_Y0.563440.667
23_Y72_R0.557020.659
42_P52_K0.544490.645
89_R92_S0.543970.644
46_V50_L0.543520.643
12_A78_A0.539160.638
45_G49_C0.536850.635
26_D30_T0.533370.631
69_S73_S0.532470.630
19_T73_S0.532140.630
16_A20_L0.528790.626
75_P79_I0.527760.625
60_R63_Y0.524510.621
54_Y60_R0.523790.620
31_R53_I0.518410.614
7_N86_Y0.517840.613
69_S80_Y0.515190.610
53_I57_E0.504160.597
72_R77_T0.499760.592
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
2lckA0.968499.70.028
2lckA199.60.065
1okcA199.60.069
1okcA199.60.075
3vocA0.7474150.863
3vjjA0.88427.60.878
2osoA0.54745.70.885
2izyA0.47374.10.891
4dinB0.652640.892
3tnpB0.46323.20.897

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