GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2358 - Uncharacterized conserved protein (DUF2358)
Pfam: PF10184 (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: CL0051
Length: 113
Sequences: 4192
Seq/Len: 37.1
HH_delta: 0.204 (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
21_Y44_K1.315483.341
80_W98_G1.185453.010
25_D111_Y1.156722.937
103_T112_R1.139622.894
26_E40_L1.131972.875
66_L81_R0.937032.380
28_V43_Y0.898542.282
105_N111_Y0.779521.980
31_I36_S0.673761.711
25_D105_N0.668191.697
80_W100_S0.667991.696
81_R95_S0.663651.685
29_V38_K0.640031.625
83_R95_S0.625521.589
24_Y28_V0.622451.581
77_R101_T0.602141.529
31_I112_R0.596051.514
75_T103_T0.592441.505
69_E77_R0.587111.491
73_E103_T0.585861.488
29_V112_R0.581371.476
67_S79_R0.572541.454
64_E83_R0.557851.417
21_Y40_L0.556931.414
86_P90_W0.553141.405
40_L109_L0.508571.292
64_E81_R0.492671.251
76_I104_L0.487971.239
60_D85_V0.484191.230
68_I78_A0.483531.228
85_V93_R0.457531.162
24_Y43_Y0.457221.161
59_S85_V0.453821.152
83_R93_R0.447211.136
41_D45_R0.444161.128
44_K51_R0.441011.120
103_T111_Y0.440881.120
41_D44_K0.436841.109
39_G42_R0.434421.103
62_S83_R0.406971.034
105_N109_L0.401421.019
77_R99_T0.399971.016
26_E109_L0.399091.013
19_L22_S0.398891.013
82_L98_G0.396941.008
45_R51_R0.394661.002
70_Q76_I0.38680.982
82_L96_F0.386770.982
81_R97_D0.378020.960
67_S75_T0.375290.953
51_R55_R0.374550.951
78_A102_Y0.372470.946
18_D44_K0.370950.942
27_D111_Y0.367110.932
104_L110_I0.364390.925
30_F43_Y0.35850.910
50_L54_G0.352820.896
73_E105_N0.350050.889
68_I76_I0.34710.881
65_V78_A0.341670.868
28_V40_L0.340710.865
40_L44_K0.335290.851
79_R99_T0.325620.827
68_I77_R0.325420.826
30_F100_S0.309420.786
57_F86_P0.30940.786
29_V36_S0.306730.779
23_I102_Y0.30570.776
37_F42_R0.305140.775
75_T101_T0.304070.772
63_L80_W0.301120.765
21_Y41_D0.298120.757
65_V68_I0.297240.755
27_D105_N0.293830.746
86_P94_I0.291580.740
42_R45_R0.284470.722
30_F102_Y0.284120.722
28_V39_G0.2790.709
27_D39_G0.278370.707
26_E41_D0.277140.704
84_G94_I0.276770.703
79_R97_D0.27330.694
102_Y110_I0.273090.694
32_D96_F0.272470.692
76_I102_Y0.271040.688
25_D107_D0.265840.675
38_K73_E0.265790.675
82_L100_S0.265190.673
21_Y28_V0.265090.673
63_L82_L0.264890.673
25_D109_L0.262820.667
46_N50_L0.25640.651
24_Y80_W0.255650.649
32_D100_S0.252660.642
52_F57_F0.25250.641
45_R52_F0.252280.641
30_F50_L0.248170.630
28_V102_Y0.247150.628
66_L79_R0.244610.621
63_L98_G0.244350.621
20_D32_D0.243980.620
58_F84_G0.241870.614
84_G96_F0.239190.607
30_F82_L0.23860.606
43_Y50_L0.23150.588
30_F34_I0.227960.579
71_D75_T0.225530.573
69_E75_T0.223220.567
61_P82_L0.219220.557
24_Y32_D0.216160.549
80_W96_F0.215790.548
20_D23_I0.214360.544
30_F46_N0.213950.543
38_K42_R0.212030.538
50_L53_L0.211710.538
72_G111_Y0.210140.534
32_D82_L0.21010.534
37_F46_N0.20990.533
43_Y46_N0.209130.531
24_Y110_I0.207190.526
86_P92_P0.206690.525
24_Y50_L0.204870.520
75_T104_L0.204070.518
58_F86_P0.203960.518
67_S71_D0.202740.515
30_F37_F0.202440.514
69_E79_R0.202220.514
85_V91_R0.200610.509
54_G96_F0.199890.508
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
4h3uA0.938199.50.204
3kkgA0.946999.40.218
3f9sA0.946999.40.22
2f99A0.946999.40.227
2gexA0.946999.40.228
3hk4A0.938199.40.236
3k0zA0.920499.40.236
3dm8A0.938199.40.246
2geyA0.938199.40.248
3fgyA0.938199.30.258

Page generated in 0.0124 seconds.