GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SecE - SecESec61-gamma subunits of protein translocation complex
Pfam: PF00584 (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: 57
Sequences: 1751
Seq/Len: 30.72
HH_delta: -0.025 (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
43_F47_L0.89492.899
21_R25_L0.710552.302
4_N8_E0.679952.203
3_K7_R0.626262.029
25_L29_I0.578931.876
29_I33_V0.571081.850
51_W55_L0.541491.754
41_F45_V0.51251.660
10_K14_K0.507351.644
40_L44_L0.497741.613
22_K26_K0.481011.558
50_S54_N0.473861.535
20_S23_E0.473021.533
52_L55_L0.434181.407
48_I51_W0.411561.333
51_W54_N0.390221.264
5_F9_V0.38891.260
47_L51_W0.37641.220
32_L36_I0.365711.185
35_V50_S0.362681.175
23_E27_S0.359411.164
48_I52_L0.35881.162
12_E16_V0.350691.136
6_F10_K0.341561.107
34_F39_G0.337681.094
13_L16_V0.329371.067
12_E31_V0.324271.051
21_R44_L0.314641.019
27_S42_F0.309111.001
33_V37_I0.305550.990
36_I40_L0.290130.940
26_K29_I0.285960.926
5_F45_V0.283460.918
24_L27_S0.278090.901
16_V34_F0.276860.897
22_K25_L0.275350.892
35_V39_G0.27350.886
44_L47_L0.272990.884
51_W56_I0.271340.879
17_T38_F0.268330.869
44_L48_I0.261790.848
3_K44_L0.259930.842
9_V24_L0.24810.804
15_K46_D0.247610.802
11_K31_V0.244460.792
25_L28_T0.242220.785
4_N10_K0.242190.785
24_L42_F0.236470.766
29_I56_I0.227180.736
18_W39_G0.227160.736
52_L56_I0.225920.732
34_F42_F0.221160.717
11_K15_K0.22090.716
9_V16_V0.218810.709
14_K40_L0.218420.708
17_T20_S0.218380.708
45_V49_F0.216830.703
47_L54_N0.214610.695
15_K38_F0.213190.691
27_S37_I0.21310.690
32_L39_G0.211050.684
38_F42_F0.207730.673
9_V26_K0.204790.664
39_G42_F0.203260.659
17_T46_D0.201070.651
13_L38_F0.198790.644
20_S37_I0.194220.629
28_T31_V0.193550.627
47_L52_L0.189080.613
7_R53_L0.188130.610
42_F49_F0.185750.602
26_K33_V0.184190.597
8_E17_T0.184060.596
3_K6_F0.183320.594
24_L34_F0.183320.594
26_K38_F0.182980.593
25_L44_L0.180930.586
28_T37_I0.180580.585
12_E15_K0.180340.584
5_F11_K0.180110.584
15_K21_R0.179560.582
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
3j01B199.4-0.025
3dl8C199.4-0.023
3dinD199.4-0.023
2zjsE199.30.021
3bo0B0.947498.80.234
2ww9B197.80.453
2wwbB197.80.453
1rh5B197.60.476
3mp7B0.964997.40.505
2oarA0.877234.10.795

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