GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CoA_binding - CoA binding domain
Pfam: PF02629 (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: 96
Sequences: 50886
Seq/Len: 530.06
HH_delta: 0.11 (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
7_I63_I3.555813.524
76_Q80_D2.450642.428
5_N29_G2.279192.259
5_N64_D2.152942.133
37_D40_K2.033612.015
53_S56_E1.958641.941
38_P42_G1.870551.854
80_D84_E1.833411.817
18_L67_I1.74211.726
5_N31_V1.703981.689
55_D81_E1.678671.663
6_V28_F1.648521.634
22_G67_I1.633451.619
6_V65_I1.552131.538
77_E81_E1.460361.447
35_D40_K1.385341.373
11_A33_V1.373911.361
31_V63_I1.373061.361
74_A78_V1.360811.348
4_T28_F1.359531.347
70_V78_V1.341251.329
63_I87_I1.31051.299
7_I57_L1.256181.245
68_I71_P1.25381.242
52_G56_E1.23681.226
74_A77_E1.228011.217
81_E85_A1.213351.202
5_N30_I1.208541.198
6_V22_G1.203861.193
6_V67_I1.134891.125
7_I66_A1.121021.111
4_T7_I1.113631.104
11_A35_D1.110881.101
34_F54_M1.110571.100
77_E80_D1.108921.099
18_L69_T1.079561.070
8_I19_L1.076281.067
32_A51_Y1.07211.062
68_I75_A1.070831.061
81_E84_E1.067671.058
80_D83_V1.061821.052
56_E59_E1.057581.048
11_A19_L1.044051.035
14_L69_T1.035831.026
70_V75_A1.024681.015
4_T65_I1.024491.015
17_A20_Y1.019661.010
21_N25_M1.004720.996
71_P74_A0.986940.978
38_P41_I0.984330.975
17_A21_N0.981270.972
39_E42_G0.972030.963
55_D59_E0.96580.957
35_D41_I0.94020.932
59_E85_A0.938920.930
13_N17_A0.935730.927
16_R20_Y0.935080.927
8_I67_I0.924260.916
72_A75_A0.923040.915
14_L17_A0.917730.909
66_A87_I0.912170.904
60_F63_I0.906690.898
7_I34_F0.90420.896
38_P52_G0.897940.890
13_N16_R0.879580.872
9_V78_V0.872940.865
57_L63_I0.870860.863
9_V66_A0.868380.861
64_D88_K0.862160.854
51_Y60_F0.835350.828
54_M81_E0.834740.827
4_T64_D0.828340.821
66_A82_L0.826070.819
9_V34_F0.823180.816
42_G45_I0.820560.813
56_E60_F0.81180.804
70_V74_A0.798490.791
9_V70_V0.797240.790
79_A83_V0.794640.787
5_N63_I0.786190.779
12_G15_G0.7860.779
51_Y56_E0.768870.762
44_E47_G0.767630.761
9_V68_I0.765260.758
14_L72_A0.763520.757
32_A60_F0.75560.749
79_A82_L0.74680.740
40_K43_K0.745820.739
68_I79_A0.74470.738
39_E43_K0.739630.733
11_A16_R0.72820.722
82_L89_G0.725470.719
49_P60_F0.710250.704
15_G19_L0.707740.701
41_I44_E0.701620.695
19_L33_V0.693440.687
32_A63_I0.688440.682
15_G20_Y0.686270.680
8_I15_G0.684130.678
78_V81_E0.674760.669
17_A69_T0.667250.661
58_E81_E0.664470.658
5_N32_A0.662060.656
54_M78_V0.657090.651
31_V49_P0.656070.650
20_Y23_F0.654170.648
20_Y46_G0.647850.642
58_E85_A0.643950.638
79_A89_G0.642270.636
7_I32_A0.634390.629
18_L22_G0.63140.626
75_A79_A0.627790.622
27_G30_I0.627490.622
31_V60_F0.620980.615
55_D58_E0.61780.612
25_M28_F0.609950.604
51_Y57_L0.608450.603
29_G32_A0.607410.602
85_A88_K0.607370.602
54_M57_L0.606030.601
37_D42_G0.603050.598
13_N72_A0.602150.597
57_L60_F0.592710.587
32_A49_P0.582070.577
16_R46_G0.581080.576
65_I88_K0.578610.573
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
3e82A198.80.11
3kuxA198.80.112
3fhlA198.80.118
3keoA198.80.126
3gdoA198.80.133
3e18A198.80.138
3db2A198.80.138
3rc1A198.80.139
3euwA198.70.144
3q2iA198.70.145

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