GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CoA_binding_2 - CoA binding domain
Pfam: PF13380 (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: CL0063
Length: 116
Sequences: 36264
Seq/Len: 312.62
HH_delta: 0.083 (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
2_S29_E2.712312.546
4_A56_I2.591422.433
73_D97_A2.383592.238
50_A74_E2.300172.159
4_A52_I2.131992.002
48_S51_E2.068721.942
69_P93_E2.031271.907
2_S31_Y2.017961.894
95_I99_R1.922511.805
3_I23_L1.868631.754
90_E93_E1.834251.722
19_V60_V1.792551.683
73_D77_A1.7861.677
31_Y55_P1.72311.618
63_V71_I1.711721.607
96_E100_E1.647961.547
23_L60_V1.635441.535
2_S57_D1.633211.533
69_P73_D1.592251.495
3_I58_L1.576071.480
97_A100_E1.530411.437
12_P32_P1.523871.431
3_I28_Y1.489341.398
97_A101_A1.48691.396
52_I56_I1.480211.390
47_P51_E1.461571.372
67_K71_I1.445941.357
21_R25_A1.410561.324
50_A77_A1.376841.293
62_C87_P1.374931.291
69_P90_E1.363871.280
31_Y56_I1.358371.275
61_V84_W1.346631.264
18_R21_R1.329551.248
76_A101_A1.306711.227
92_E96_E1.296931.218
98_A103_I1.249481.173
73_D93_E1.243961.168
31_Y46_Y1.243741.168
81_K103_I1.238531.163
74_E77_A1.235861.160
23_L28_Y1.227081.152
79_G82_A1.212911.139
5_V20_L1.190241.117
5_V60_V1.172861.101
96_E99_R1.158531.088
93_E97_A1.152211.082
18_R22_N1.150051.080
21_R41_L1.149361.079
31_Y44_K1.143941.074
77_A97_A1.138981.069
91_S95_I1.121741.053
49_L74_E1.088881.022
19_V62_C1.08191.016
70_E74_E1.079391.013
4_A59_A1.060930.996
22_N25_A1.060610.996
76_A103_I1.04380.980
12_P17_Y1.020380.958
77_A101_A1.015750.954
3_I60_V0.990020.929
67_K70_E0.984520.924
58_L83_V0.979980.920
89_A93_E0.966390.907
63_V67_K0.962510.904
59_A75_A0.956070.898
93_E96_E0.955880.897
92_E95_I0.954010.896
78_L82_A0.936450.879
53_P56_I0.929580.873
29_E44_K0.926520.870
12_P34_N0.922470.866
6_V63_V0.914840.859
76_A98_A0.91440.858
17_Y21_R0.910840.855
76_A97_A0.906450.851
12_P20_L0.90350.848
46_Y52_I0.903360.848
15_F62_C0.894730.840
22_N26_A0.893250.839
46_Y51_E0.883610.830
60_V87_P0.88170.828
2_S55_P0.881410.827
6_V61_V0.879070.825
32_P46_Y0.874480.821
24_K43_I0.863830.811
98_A101_A0.861330.809
57_D79_G0.860.807
14_K17_Y0.858620.806
89_A92_E0.854790.802
32_P43_I0.851640.800
56_I80_V0.838150.787
34_N37_G0.837020.786
74_E78_L0.8350.784
70_E73_D0.824420.774
33_V49_L0.82340.773
63_V68_V0.818940.769
95_I98_A0.808640.759
17_Y40_I0.798130.749
57_D81_K0.778610.731
72_V94_L0.771410.724
16_G20_L0.770480.723
58_L81_K0.768510.721
14_K65_P0.763530.717
16_G62_C0.763420.717
69_P97_A0.757590.711
73_D76_A0.74850.703
71_I74_E0.737660.693
17_Y41_L0.727240.683
65_P68_V0.726940.682
82_A85_L0.72280.679
5_V16_G0.710110.667
7_G13_G0.707240.664
4_A33_V0.698310.656
19_V22_N0.69450.652
48_S52_I0.694020.652
51_E55_P0.693970.651
21_R24_K0.693310.651
24_K41_L0.692770.650
15_F65_P0.68970.647
6_V59_A0.684360.642
54_E80_V0.682930.641
49_L71_I0.679250.638
59_A80_V0.677520.636
16_G21_R0.670580.630
45_C48_S0.668740.628
36_K39_E0.667090.626
15_F18_R0.665890.625
64_P67_K0.665020.624
5_V19_V0.664060.623
50_A78_L0.661830.621
61_V72_V0.656880.617
20_L24_K0.646960.607
37_G45_C0.642340.603
72_V84_W0.641840.603
55_P80_V0.637690.599
54_E77_A0.636730.598
70_E90_E0.631410.593
14_K18_R0.631290.593
46_Y53_P0.62540.587
70_E93_E0.617930.580
85_L88_G0.616540.579
91_S94_L0.615050.577
44_K53_P0.609960.573
77_A100_E0.608320.571
72_V76_A0.602930.566
19_V23_L0.599250.563
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
1y81A199.70.083
2duwA199.70.086
2d59A199.70.106
1iukA199.60.111
2csuA199.60.163
3ff4A0.982899.60.165
2nu8A0.974199.50.196
1oi7A0.974199.50.21
2yv1A0.974199.40.229
2yv2A0.974199.40.229

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