GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SmpB - SmpB protein
Pfam: PF01668 (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: 68
Sequences: 1447
Seq/Len: 21.28
HH_delta: -0.062 (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_S57_M1.164733.929
54_L57_M1.056333.563
45_V52_L0.950073.205
47_I52_L0.850322.868
33_I38_V0.846222.855
8_K12_N0.827592.792
46_R55_I0.81062.734
5_K10_R0.792172.672
10_R18_T0.693342.339
40_L57_M0.63742.150
28_T65_G0.588761.986
15_I18_T0.583231.967
30_V33_I0.527511.779
10_R15_I0.500761.689
35_A63_K0.476081.606
3_I34_R0.447551.510
8_K41_N0.439841.484
48_K55_I0.437591.476
2_I5_K0.427461.442
33_I59_I0.418611.412
35_A64_Q0.4031.359
37_K60_A0.378351.276
23_I52_L0.364191.229
44_Y55_I0.34171.153
4_A20_E0.327231.104
24_V51_E0.309961.046
62_Y65_G0.280480.946
4_A38_V0.278280.939
5_K56_N0.273530.923
39_S42_D0.266660.900
65_G68_F0.263020.887
28_T66_N0.261550.882
38_V57_M0.257590.869
39_S58_H0.253360.855
24_V30_V0.239550.808
16_L26_K0.23780.802
12_N41_N0.234770.792
28_T67_R0.224670.758
22_G27_G0.221120.746
28_T68_F0.220740.745
11_F14_E0.217120.732
37_K63_K0.214750.724
30_V36_G0.213750.721
43_S55_I0.21170.714
47_I61_P0.211440.713
24_V53_F0.209170.706
14_E19_F0.208310.703
26_K66_N0.207630.700
8_K64_Q0.204250.689
20_E49_N0.202320.682
41_N58_H0.201660.680
10_R14_E0.201620.680
32_S62_Y0.199370.673
7_K45_V0.199360.673
40_L56_N0.198920.671
12_N44_Y0.19660.663
28_T62_Y0.194530.656
46_R54_L0.194070.655
28_T34_R0.19340.652
24_V65_G0.191730.647
7_K41_N0.190970.644
45_V54_L0.189930.641
39_S61_P0.186910.631
5_K44_Y0.185050.624
11_F20_E0.184830.623
60_A63_K0.182550.616
48_K53_F0.18130.612
56_N61_P0.180880.610
7_K11_F0.179640.606
7_K50_G0.179140.604
23_I59_I0.178850.603
44_Y56_N0.176960.597
63_K66_N0.176440.595
30_V34_R0.175620.592
47_I50_G0.175450.592
38_V41_N0.173110.584
43_S58_H0.172580.582
26_K35_A0.172460.582
59_I62_Y0.170780.576
47_I51_E0.169140.571
21_A52_L0.168760.569
58_H63_K0.168620.569
3_I7_K0.1670.563
10_R13_Y0.166560.562
3_I20_E0.166240.561
14_E48_K0.164630.555
8_K11_F0.164490.555
6_N13_Y0.162650.549
21_A53_F0.162510.548
5_K18_T0.162450.548
37_K47_I0.157830.532
1_K49_N0.157510.531
8_K21_A0.156020.526
39_S64_Q0.15340.517
12_N68_F0.150850.509
14_E66_N0.150550.508
26_K55_I0.149620.505
41_N60_A0.148820.502
5_K55_I0.147840.499
25_L30_V0.147790.499
14_E67_R0.147610.498
60_A68_F0.147140.496
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
1j1hA199.9-0.062
1p6vA199.9-0.054
1wjxA199.9-0.051
2qnkA0.941236.50.88
1zvfA0.970610.20.906
1yfuA0.955910.10.906
3vupA0.47068.40.909
3mtwA0.60296.60.913
3nuhB0.72063.60.923
2vnuD0.95592.90.926

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