GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Vpu - Vpu protein
Pfam: PF00558 (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: 81
Sequences: 2512
Seq/Len: 31.01
HH_delta: 0.491 (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
8_A12_L1.350493.594
27_Y34_K1.020752.717
2_Q5_E1.016612.706
29_E32_K1.001262.665
44_E47_R0.944592.514
72_M75_D0.931762.480
76_N79_F0.86672.307
5_E8_A0.852052.268
30_Y33_I0.79572.118
26_V33_I0.770652.051
36_Q40_D0.698491.859
74_F79_F0.690311.837
34_K37_R0.636561.694
11_A18_I0.61631.640
3_S7_L0.601071.600
63_E66_S0.591111.573
70_E73_G0.588111.565
75_D79_F0.571571.521
73_G78_M0.548841.461
5_E15_A0.527361.403
27_Y30_Y0.527121.403
7_L11_A0.509521.356
62_E66_S0.505431.345
61_E76_N0.491181.307
16_L20_I0.485941.293
69_V78_M0.477191.270
40_D43_I0.475171.265
74_F77_P0.459931.224
2_Q6_I0.458971.221
24_T27_Y0.449141.195
66_S69_V0.444471.183
1_M5_E0.425541.132
2_Q7_L0.423151.126
19_A26_V0.420691.120
61_E66_S0.417091.110
30_Y34_K0.417061.110
15_A18_I0.406031.081
11_A15_A0.398361.060
31_R34_K0.391851.043
62_E67_A0.382841.019
18_I33_I0.373340.994
68_L74_F0.365740.973
75_D78_M0.365440.973
61_E65_L0.353020.939
15_A25_I0.351120.934
24_T28_I0.34860.928
69_V72_M0.346970.923
19_A33_I0.344690.917
12_L16_L0.333940.889
61_E67_A0.327980.873
38_K66_S0.31410.836
22_V25_I0.304530.810
61_E74_F0.301260.802
3_S6_I0.297620.792
59_G73_G0.292290.778
69_V76_N0.288750.768
34_K41_R0.288030.767
70_E76_N0.285170.759
8_A15_A0.283440.754
5_E27_Y0.271660.723
66_S75_D0.269240.717
16_L61_E0.265110.706
16_L34_K0.261630.696
6_I10_I0.26150.696
47_R50_A0.25750.685
3_S10_I0.257120.684
7_L18_I0.256940.684
72_M78_M0.25530.679
10_I14_V0.255020.679
70_E77_P0.252250.671
28_I32_K0.251570.670
1_M4_L0.25040.666
27_Y41_R0.249720.665
62_E69_V0.249390.664
15_A19_A0.247840.660
67_A76_N0.245620.654
68_L76_N0.242760.646
44_E48_E0.237030.631
59_G72_M0.230640.614
45_R52_D0.229320.610
60_D66_S0.228650.609
47_R61_E0.226880.604
63_E69_V0.22660.603
69_V75_D0.22570.601
74_F78_M0.225690.601
49_R52_D0.225340.600
16_L27_Y0.223370.594
39_I43_I0.218380.581
7_L27_Y0.218360.581
38_K43_I0.216950.577
60_D63_E0.21650.576
58_D66_S0.215620.574
63_E72_M0.213320.568
18_I36_Q0.212360.565
18_I21_V0.211890.564
41_R68_L0.209960.559
6_I9_I0.209620.558
68_L78_M0.208960.556
45_R48_E0.208020.554
5_E9_I0.207460.552
15_A21_V0.206160.549
42_L47_R0.204910.545
30_Y44_E0.204420.544
8_A27_Y0.204270.544
8_A16_L0.203430.541
3_S8_A0.201950.537
41_R44_E0.200830.534
61_E72_M0.200160.533
49_R59_G0.199240.530
37_R40_D0.198870.529
10_I13_I0.197080.524
19_A22_V0.195920.521
23_W56_E0.194640.518
67_A70_E0.192970.514
7_L10_I0.191410.509
8_A19_A0.191240.509
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
1vpuA0.530999.60.491
1pi7A0.444499.10.618
2yiuB0.493844.90.904
1zrtD0.469136.80.909
1q55A0.96336.40.909
2w1kA0.395133.10.911
2ks1B0.432131.70.911
2kogA0.333329.10.913
3kg2A0.518527.10.914
1pp9D0.543225.40.915

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