GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PP-binding_2 - Acyl-carrier
Pfam: PF14573 (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: CL0314
Length: 96
Sequences: 12013
Seq/Len: 125.14
HH_delta: 0.169 (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
18_M61_E1.916182.605
37_E78_Q1.875812.550
39_R42_E1.474392.004
22_Y57_D1.421071.932
16_L36_E1.375791.870
47_D50_D1.342231.825
76_T79_E1.317881.792
74_I83_F1.248291.697
35_L38_S1.233311.677
15_I85_V1.219531.658
59_E65_T1.198411.629
70_T83_F1.167021.587
67_P70_T1.162511.580
18_M22_Y1.128341.534
20_K36_E1.124421.529
40_T46_W1.101791.498
23_L46_W1.061331.443
83_F87_E1.048871.426
20_K24_S1.030851.401
36_E78_Q1.025791.395
39_R75_K0.997361.356
22_Y25_E0.995631.354
55_V59_E0.974411.325
39_R43_D0.961191.307
25_E57_D0.940791.279
57_D61_E0.925491.258
74_I79_E0.922931.255
70_T87_E0.921121.252
14_Y17_G0.904081.229
46_W50_D0.866811.178
16_L81_A0.860391.170
27_E46_W0.855481.163
22_Y61_E0.850091.156
13_E36_E0.832441.132
18_M21_K0.821221.116
23_L77_V0.802551.091
70_T73_N0.801211.089
36_E77_V0.789431.073
14_Y18_M0.787791.071
17_G21_K0.771451.049
69_E73_N0.754051.025
18_M62_F0.734530.999
16_L20_K0.73230.996
83_F86_Q0.709330.964
24_S33_S0.69610.946
16_L78_Q0.687390.935
30_T33_S0.68250.928
22_Y54_F0.662960.901
13_E17_G0.66060.898
23_L54_F0.652070.887
19_L58_V0.651290.885
26_G57_D0.648450.882
51_T55_V0.638530.868
58_V84_V0.634790.863
78_Q82_D0.628110.854
75_K79_E0.62470.849
16_L77_V0.622240.846
77_V81_A0.620750.844
19_L77_V0.612840.833
50_D53_E0.610810.830
38_S43_D0.607940.827
13_E85_V0.601930.818
79_E82_D0.596570.811
81_A85_V0.595690.810
20_K34_K0.593830.807
24_S34_K0.592580.806
51_T71_A0.590990.803
15_I84_V0.584840.795
26_G53_E0.583570.793
52_V68_D0.583540.793
82_D85_V0.562780.765
20_K77_V0.543710.739
29_I33_S0.540730.735
53_E57_D0.532970.725
24_S29_I0.532590.724
21_K61_E0.528780.719
53_E56_L0.526190.715
85_V88_R0.524120.713
46_W54_F0.523630.712
19_L81_A0.519450.706
38_S44_R0.511760.696
54_F80_I0.497960.677
15_I81_A0.491090.668
46_W51_T0.488530.664
24_S30_T0.48120.654
64_V87_E0.480410.653
15_I18_M0.464620.632
51_T68_D0.461040.627
34_K40_T0.459660.625
57_D60_E0.45340.616
13_E16_L0.450990.613
26_G50_D0.450020.612
17_G20_K0.446780.607
40_T80_I0.443230.603
58_V62_F0.438750.596
59_E64_V0.436710.594
74_I80_I0.4350.591
42_E72_D0.433010.589
69_E72_D0.432150.588
51_T72_D0.428240.582
71_A80_I0.426790.580
56_L60_E0.424060.577
21_K25_E0.424020.576
29_I34_K0.417420.567
54_F58_V0.416690.567
36_E81_A0.416390.566
35_L40_T0.405940.552
55_V68_D0.403830.549
23_L80_I0.402790.548
66_I84_V0.400950.545
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
2ju1A0.9167990.169
4h2wC0.9688990.172
2l22A0.9896990.175
4h2vC0.9479990.175
2avaA0.8438990.177
2l22A0.9896990.179
2dnwA0.9583990.18
4i4dA0.9479990.181
1klpA0.9271990.183
2lteA0.9479990.184

Page generated in 0.0324 seconds.