GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PTS_IIB - PTS system LactoseCellobiose specific IIB subunit
Pfam: PF02302 (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: 90
Sequences: 3727
Seq/Len: 41.41
HH_delta: 0.082 (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
83_D86_E1.189373.492
17_A21_K1.107553.252
77_D83_D0.906582.662
23_A27_L0.881852.589
27_L85_E0.818362.403
6_C9_G0.810682.380
3_L48_A0.618041.814
18_N21_K0.612061.797
21_K25_K0.602531.769
26_E85_E0.584141.715
41_V46_D0.556661.634
22_K25_K0.55171.620
3_L36_G0.517281.519
18_N22_K0.509731.496
53_L57_I0.508811.494
42_E47_D0.471861.385
23_A26_E0.445951.309
41_V44_I0.441261.295
22_K26_E0.427791.256
50_L71_P0.422071.239
14_L17_A0.412941.212
6_C13_S0.412181.210
20_I52_L0.411281.207
23_A84_G0.403591.185
33_V37_S0.40071.176
74_P77_D0.395881.162
40_E43_E0.385541.132
44_I47_D0.372441.093
23_A85_E0.37141.090
24_L29_I0.369141.084
33_V36_G0.366861.077
6_C10_I0.366681.077
19_K84_G0.35451.041
41_V51_I0.353091.037
10_I13_S0.345851.015
42_E46_D0.344941.013
24_L88_L0.343141.007
9_G12_T0.341251.002
4_V20_I0.339230.996
6_C12_T0.3360.986
56_Q74_P0.330750.971
31_V34_S0.329610.968
4_V54_T0.32950.967
43_E47_D0.328160.963
73_I87_I0.314950.925
51_I66_A0.314070.922
52_L87_I0.313830.921
73_I83_D0.310820.913
23_A88_L0.308510.906
5_V57_I0.299060.878
76_E82_M0.293560.862
8_S37_S0.292110.858
58_A72_V0.291840.857
83_D87_I0.29040.853
39_L44_I0.284820.836
34_S48_A0.279520.821
36_G40_E0.278760.818
40_E44_I0.275070.808
16_V54_T0.271450.797
27_L88_L0.267990.787
24_L31_V0.266710.783
44_I48_A0.266370.782
67_G70_V0.265760.780
18_N25_K0.260930.766
53_L74_P0.260890.766
38_I44_I0.260770.766
17_A35_A0.258790.760
51_I70_V0.251770.739
15_M87_I0.249640.733
32_E36_G0.247510.727
82_M86_E0.246710.724
53_L58_A0.244970.719
20_I24_L0.242990.713
77_D86_E0.242710.713
32_E43_E0.242460.712
66_A71_P0.242360.712
37_S40_E0.237580.698
11_G14_L0.236250.694
9_G13_S0.235080.690
16_V79_Y0.2350.690
12_T79_Y0.232590.683
53_L72_V0.229510.674
73_I77_D0.226850.666
12_T15_M0.226230.664
16_V84_G0.225880.663
50_L73_I0.225420.662
4_V17_A0.224340.659
19_K79_Y0.224030.658
10_I54_T0.223440.656
84_G88_L0.222290.653
8_S13_S0.221750.651
11_G15_M0.219430.644
45_A48_A0.218720.642
42_E67_G0.216550.636
25_K28_G0.212710.624
38_I57_I0.212560.624
7_G57_I0.21250.624
11_G79_Y0.212170.623
8_S15_M0.211980.622
20_I33_V0.209840.616
39_L42_E0.209730.616
20_I87_I0.209710.616
71_P74_P0.209460.615
24_L54_T0.209030.614
5_V53_L0.207660.610
4_V7_G0.207250.608
4_V52_L0.205950.605
42_E45_A0.205890.604
53_L70_V0.201890.593
20_I84_G0.201550.592
58_A74_P0.201190.591
19_K22_K0.20060.589
29_I88_L0.20.587
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
1tvmA0.933399.20.082
1vkrA0.944499.20.119
3sqnA0.877899.10.143
3czcA0.966799.10.149
1e2bA0.9667990.174
2l2qA0.9778990.178
3nbmA0.977898.90.216
2m1zA0.977898.60.31
2kyrA0.977898.20.385
2r4qA0.966797.90.44

Page generated in 0.0322 seconds.