GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ACBP - Acyl CoA binding protein
Pfam: PF00887 (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: 87
Sequences: 953
Seq/Len: 10.95
HH_delta: -0.006 (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
50_D53_G0.970113.796
40_D65_G0.83923.284
61_K64_K0.826083.233
45_R58_D0.78283.063
66_M74_E0.670262.623
40_D64_K0.577272.259
31_A63_L0.500841.960
29_L79_V0.490641.920
7_A11_F0.450461.763
73_R77_E0.442731.733
28_E78_L0.441371.727
57_W61_K0.41911.640
35_Q39_G0.413191.617
43_T57_W0.390131.527
68_K72_M0.381921.495
22_S25_D0.365931.432
70_E74_E0.361451.414
28_E32_L0.352781.381
80_E83_I0.340721.333
63_L66_M0.32941.289
70_E73_R0.320321.254
10_E13_S0.318911.248
25_D85_K0.318761.247
11_F83_I0.311261.218
41_C57_W0.311251.218
23_N26_K0.308491.207
48_F54_R0.305351.195
25_D78_L0.301251.179
54_R58_D0.301181.179
69_E72_M0.300191.175
15_L21_L0.290191.136
28_E62_A0.289511.133
33_Y75_Y0.288631.129
38_H42_D0.284781.114
78_L81_E0.280781.099
67_S70_E0.279321.093
6_E10_E0.275441.078
3_E7_A0.272671.067
12_V79_V0.270851.060
28_E63_L0.266121.041
21_L26_K0.265561.039
51_I54_R0.253820.993
34_K75_Y0.252220.987
30_Y56_K0.252070.986
36_A72_M0.249810.978
5_F12_V0.249120.975
80_E84_P0.247520.969
3_E6_E0.241190.944
35_Q63_L0.240460.941
46_P57_W0.238360.933
79_V82_L0.233270.913
47_G51_I0.231160.905
74_E77_E0.225890.884
45_R57_W0.22580.884
27_L30_Y0.216790.848
4_E73_R0.216650.848
4_E8_A0.213220.834
77_E81_E0.206670.809
11_F26_K0.206020.806
47_G53_G0.205480.804
41_C61_K0.20540.804
23_N52_E0.205220.803
30_Y33_Y0.202430.792
47_G50_D0.201220.787
58_D62_A0.200760.786
9_V12_V0.199420.780
48_F53_G0.195650.766
28_E81_E0.192090.752
39_G60_W0.189690.742
13_S55_A0.189630.742
81_E85_K0.187810.735
35_Q68_K0.187260.733
39_G63_L0.186370.729
28_E48_F0.183210.717
33_Y37_T0.18020.705
32_L74_E0.179820.704
9_V29_L0.178010.697
45_R54_R0.176780.692
8_A79_V0.173130.678
41_C45_R0.173080.677
9_V16_P0.17030.666
21_L25_D0.170070.666
52_E62_A0.169610.664
51_I55_A0.168540.660
20_Q26_K0.168330.659
34_K56_K0.16820.658
17_K21_L0.16780.657
22_S82_L0.166530.652
35_Q65_G0.165580.648
48_F51_I0.164430.643
30_Y34_K0.163990.642
8_A11_F0.161540.632
11_F21_L0.159750.625
32_L63_L0.157970.618
16_P26_K0.157620.617
41_C64_K0.157160.615
12_V26_K0.156650.613
67_S71_A0.156390.612
30_Y75_Y0.156160.611
3_E83_I0.156050.611
16_P21_L0.153510.601
42_D61_K0.152050.595
29_L78_L0.151760.594
13_S17_K0.151390.592
9_V33_Y0.151010.591
44_P84_P0.149890.587
17_K66_M0.148970.583
42_D68_K0.148910.583
25_D52_E0.148390.581
56_K75_Y0.147830.578
11_F14_N0.147320.577
27_L56_K0.146330.573
43_T58_D0.145690.570
79_V83_I0.144610.566
54_R57_W0.143440.561
74_E78_L0.142660.558
4_E72_M0.141260.553
23_N78_L0.140460.550
55_A59_A0.14030.549
67_S83_I0.140040.548
7_A10_E0.139410.546
27_L47_G0.138130.541
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
1hbkA1100-0.006
1st7A0.977100-0.005
2copA0.977100-0.002
3epyA0.97799.90.003
2cquA0.97799.90.01
3flvA199.90.021
2cb8A0.97799.90.025
2lbbA0.97799.90.027
3fp5A199.90.028
2wh5A199.90.038

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