GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PduL - Propanediol utilisation protein PduL
Pfam: PF06130 (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: 71
Sequences: 595
Seq/Len: 8.38
HH_delta: 0.843 (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_A52_E0.589492.760
17_D56_L0.503782.359
15_P19_E0.469322.197
15_P52_E0.413211.935
17_D20_K0.407661.909
41_G68_L0.401821.881
31_V58_M0.400641.876
13_M56_L0.361381.692
24_Q27_Q0.346321.621
32_E44_E0.3341.564
44_E67_A0.328691.539
14_S55_A0.318351.490
39_R64_E0.310931.456
9_R64_E0.304371.425
23_G56_L0.299671.403
30_S44_E0.294841.380
14_S17_D0.290591.361
5_I8_A0.290521.360
43_F68_L0.287521.346
29_V47_R0.277241.298
17_D23_G0.271341.270
5_I33_V0.268271.256
16_E20_K0.266491.248
37_G69_G0.265251.242
5_I47_R0.264431.238
8_A64_E0.262541.229
33_V47_R0.253911.189
23_G48_V0.247321.158
8_A47_R0.241511.131
11_I29_V0.237321.111
51_P54_F0.231341.083
13_M48_V0.225671.057
3_G6_V0.223611.047
43_F67_A0.2161.011
28_F47_R0.213971.002
11_I58_M0.203330.952
55_A71_K0.200740.940
36_V42_I0.199250.933
23_G32_E0.195640.916
37_G45_N0.195420.915
2_E5_I0.194260.909
15_P50_V0.194020.908
18_A42_I0.190770.893
24_Q28_F0.189750.888
6_V62_T0.186670.874
46_V60_I0.1840.861
54_F67_A0.180070.843
5_I66_N0.178450.835
19_E52_E0.176620.827
11_I60_I0.175990.824
57_Q70_L0.171870.805
18_A65_A0.170360.798
32_E36_V0.167970.786
54_F63_D0.16760.785
21_L53_R0.165650.776
60_I66_N0.165450.775
20_K30_S0.165140.773
26_G30_S0.164610.771
45_N63_D0.163610.766
62_T65_A0.162070.759
27_Q47_R0.161010.754
31_V45_N0.16070.752
42_I65_A0.159740.748
28_F45_N0.158680.743
25_D60_I0.158320.741
48_V56_L0.157740.739
50_V53_R0.157180.736
4_V18_A0.156330.732
42_I62_T0.155340.727
21_L28_F0.154820.725
33_V45_N0.154790.725
2_E63_D0.154770.725
27_Q55_A0.153980.721
65_A71_K0.153730.720
27_Q53_R0.153350.718
48_V64_E0.152890.716
19_E55_A0.151550.710
24_Q47_R0.150930.707
27_Q30_S0.150810.706
8_A28_F0.150430.704
37_G70_L0.149750.701
23_G29_V0.149690.701
62_T71_K0.149350.699
13_M21_L0.148220.694
13_M23_G0.148180.694
62_T68_L0.148170.694
27_Q38_P0.146270.685
13_M22_F0.145350.681
8_A57_Q0.145270.680
36_V53_R0.145150.680
22_F53_R0.143550.672
19_E22_F0.14340.671
21_L26_G0.143210.670
9_R61_D0.142990.669
8_A39_R0.142560.667
16_E54_F0.142510.667
61_D67_A0.142290.666
21_L48_V0.142010.665
21_L37_G0.14070.659
47_R60_I0.139420.653
28_F52_E0.138870.650
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
4aayA0.915587.20.843
3ml1A0.915586.10.845
1tmoA0.915585.60.846
2iv2X0.915584.40.848
2napA0.915579.90.856
1g8kA0.915579.10.857
3i9v30.915578.90.857
1eu1A0.915578.30.858
2e7zA0.915577.80.858
2vpzA0.915577.30.859
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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