GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UPF0081 - Uncharacterised protein family (UPF0081)
Pfam: PF03652 (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: 135
Sequences: 5005
Seq/Len: 37.07
HH_delta: 0.228 (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
54_G91_I1.086182.894
44_K84_R1.071082.854
78_A92_L0.931542.482
44_K85_F0.78022.079
29_E42_E0.769552.050
42_E45_K0.740551.973
19_D23_I0.738091.967
67_E75_R0.719011.916
76_K79_E0.718231.914
3_I54_G0.678981.809
78_A82_K0.654751.745
79_E83_K0.647781.726
15_I29_E0.641311.709
40_I84_R0.631271.682
45_K49_E0.626581.669
12_R32_P0.625231.666
54_G89_P0.615531.640
44_K48_E0.600571.600
12_R30_T0.587031.564
67_E71_A0.567641.512
48_E85_F0.565891.508
41_E84_R0.562781.499
80_E84_R0.554081.476
62_N66_S0.52651.403
21_L24_I0.518141.381
33_R39_D0.509421.357
7_D14_G0.505961.348
55_I82_K0.498371.328
63_M97_L0.480481.280
76_K80_E0.47611.269
37_E41_E0.474421.264
64_D67_E0.47291.260
5_G56_V0.47271.259
58_G98_T0.470341.253
55_I88_I0.469721.252
4_L52_I0.464471.238
34_R38_K0.463171.234
5_G58_G0.462241.232
15_I46_L0.453121.207
17_V50_Y0.451481.203
55_I85_F0.445811.188
40_I80_E0.444371.184
37_E84_R0.438611.169
68_S71_A0.437511.166
40_I81_L0.435221.160
93_V97_L0.434331.157
10_T70_Q0.43321.154
29_E49_E0.432311.152
10_T73_R0.423821.129
8_Y77_F0.420281.120
98_T101_E0.411741.097
79_E82_K0.407261.085
100_K104_R0.394031.050
75_R80_E0.390661.041
101_E105_R0.389621.038
7_D11_K0.381861.017
75_R92_L0.370190.986
17_V52_I0.361510.963
10_T33_R0.360870.962
80_E83_K0.360730.961
8_Y39_D0.356420.950
57_V81_L0.341980.911
93_V98_T0.341960.911
6_L15_I0.340290.907
13_I33_R0.340180.906
82_K87_G0.340050.906
47_I55_I0.33970.905
57_V78_A0.332790.887
7_D58_G0.332450.886
18_S22_G0.332350.886
44_K47_I0.332280.885
8_Y57_V0.330260.880
101_E104_R0.327380.872
41_E45_K0.323330.861
59_L92_L0.316510.843
94_D97_L0.31570.841
16_A24_I0.315220.840
37_E83_K0.312120.832
4_L47_I0.310350.827
70_Q73_R0.309110.824
13_I39_D0.308630.822
63_M96_R0.306590.817
95_E99_T0.304030.810
9_G14_G0.301230.803
5_G16_A0.300310.800
58_G94_D0.299630.798
62_N70_Q0.296150.789
29_E45_K0.291620.777
70_Q74_V0.289840.772
10_T95_E0.286640.764
8_Y13_I0.284460.758
38_K41_E0.282670.753
78_A90_V0.28090.748
38_K42_E0.280710.748
48_E84_R0.280590.748
82_K89_P0.277420.739
14_G99_T0.275440.734
31_I42_E0.275270.733
47_I85_F0.274530.731
59_L75_R0.273050.728
97_L100_K0.272990.727
11_K33_R0.267750.713
13_I77_F0.26510.706
56_V91_I0.264180.704
87_G90_V0.261640.697
48_E51_Q0.261030.695
45_K48_E0.2610.695
9_G58_G0.260280.693
103_E106_L0.259970.693
59_L63_M0.258490.689
84_R87_G0.258210.688
64_D68_S0.257780.687
7_D95_E0.25550.681
43_L81_L0.254180.677
27_P50_Y0.253910.677
65_G68_S0.250490.667
62_N69_E0.250260.667
4_L55_I0.249360.664
85_F88_I0.248910.663
31_I45_K0.244950.653
59_L67_E0.244150.651
62_N71_A0.242930.647
7_D94_D0.242230.645
8_Y18_S0.238790.636
57_V92_L0.237590.633
9_G95_E0.236730.631
15_I27_P0.235910.629
61_L68_S0.234980.626
13_I60_P0.234560.625
3_I20_P0.23440.625
62_N67_E0.234390.625
14_G30_T0.234140.624
8_Y59_L0.232750.620
102_A105_R0.227830.607
66_S71_A0.225810.602
94_D98_T0.224810.599
102_A106_L0.224210.597
49_E83_K0.224140.597
65_G78_A0.223310.595
59_L99_T0.220960.589
69_E73_R0.219410.585
82_K90_V0.219360.584
64_D100_K0.217740.580
12_R60_P0.216790.578
13_I99_T0.216210.576
20_P25_A0.215730.575
27_P49_E0.215550.574
42_E49_E0.214850.572
36_R80_E0.212840.567
97_L101_E0.212690.567
47_I52_I0.211850.564
3_I18_S0.21170.564
7_D16_A0.210750.562
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
1vhxA0.992699.90.228
1nu0A0.992699.90.253
3epqA0.96399.70.401
2gupA0.970499.60.437
4htlA0.96399.60.445
3mcpA0.96399.60.456
3vglA0.96399.60.459
3vovA0.955699.60.463
3r8eA0.970499.60.463
2hoeA0.948199.60.465

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