GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YukD - WXG100 protein secretion system (Wss) protein YukD
Pfam: PF08817 (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: CL0072
Length: 79
Sequences: 5102
Seq/Len: 64.58
HH_delta: -0.003 (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
29_I61_P1.677543.962
63_Q67_D1.084052.560
23_V27_E0.966012.282
63_Q68_A0.846982.000
23_V31_E0.820421.938
26_A30_P0.785461.855
20_P23_V0.757861.790
60_D63_Q0.750771.773
64_T67_D0.741611.752
21_A66_A0.740431.749
4_R18_A0.721441.704
24_P27_E0.655441.548
71_R74_D0.651131.538
4_R72_D0.643611.520
31_E35_L0.594331.404
33_V49_W0.590021.393
4_R16_D0.584341.380
27_E30_P0.581321.373
32_L51_L0.579171.368
26_A61_P0.574271.356
6_T14_Q0.572521.352
8_D75_V0.556031.313
49_W78_L0.547021.292
31_E34_E0.528751.249
52_A58_P0.524161.238
33_V40_G0.517541.222
65_L70_V0.516921.221
30_P34_E0.498541.177
64_T68_A0.479681.133
19_L23_V0.478281.130
6_T16_D0.477961.129
22_D66_A0.445181.051
5_V19_L0.433871.025
26_A62_D0.427221.009
59_L68_A0.423731.001
22_D64_T0.422010.997
54_A74_D0.410080.969
25_V65_L0.401110.947
23_V28_L0.400420.946
25_V68_A0.388060.917
15_V36_L0.38140.901
54_A57_R0.379080.895
50_V58_P0.376830.890
5_V28_L0.371370.877
8_D14_Q0.364180.860
8_D77_V0.361740.854
29_I49_W0.356390.842
9_A15_V0.355160.839
51_L76_L0.352340.832
7_V17_L0.351850.831
7_V78_L0.34890.824
7_V32_L0.346560.818
40_G49_W0.343370.811
64_T69_G0.342180.808
27_E31_E0.338020.798
6_T75_V0.336470.795
70_V76_L0.328380.776
52_A57_R0.327760.774
14_Q75_V0.327150.773
32_L78_L0.325860.770
28_L65_L0.324730.767
60_D68_A0.31550.745
52_A55_G0.311990.737
74_D77_V0.307820.727
17_L32_L0.303930.718
52_A77_V0.303150.716
48_Q60_D0.302890.715
5_V59_L0.302430.714
41_D48_Q0.296130.699
38_L78_L0.294860.696
6_T73_G0.294140.695
25_V51_L0.289580.684
7_V28_L0.284070.671
20_P27_E0.283090.669
33_V41_D0.27490.649
32_L49_W0.26570.628
24_P62_D0.265670.627
19_L28_L0.265080.626
49_W76_L0.264680.625
24_P30_P0.264330.624
13_R36_L0.260450.615
20_P64_T0.260330.615
38_L48_Q0.2550.602
13_R35_L0.254280.601
50_V71_R0.252040.595
15_V35_L0.250070.591
27_E62_D0.247650.585
30_P33_V0.246110.581
24_P65_L0.245110.579
52_A56_G0.244510.577
38_L41_D0.243220.574
15_V55_G0.242380.572
10_G37_G0.241590.571
19_L31_E0.241180.570
37_G40_G0.239670.566
54_A70_V0.238580.563
10_G50_V0.238140.562
55_G73_G0.235940.557
8_D11_N0.235290.556
59_L76_L0.234570.554
28_L36_L0.233250.551
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
4k95A0.911499.2-0.003
3pluA0.911499.20.009
1uh6A0.911499.10.023
3u5em0.886199.10.048
3u5cf0.886199.10.049
3m62B0.898799.10.05
3v6cB0.911499.10.053
3l0wB0.886199.10.054
3phxB0.911499.10.054
3m63B0.898799.10.054

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