GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ricin_B_lectin - Ricin-type beta-trefoil lectin domain
Pfam: PF00652 (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: CL0066
Length: 124
Sequences: 2930
Seq/Len: 23.63
HH_delta: 0.104 (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
99_C116_C1.630764.724
14_C32_C1.520984.406
57_C74_C1.380864.000
15_L111_L0.888852.575
101_D114_W0.855572.478
16_D30_Y0.815122.361
59_D81_Q0.793092.297
59_D72_W0.67471.954
69_I100_L0.648821.879
114_W121_N0.619771.795
27_V58_L0.616381.785
68_K110_P0.594571.722
86_D92_R0.585381.696
16_D38_Q0.566861.642
23_N73_P0.560021.622
26_P68_K0.558141.617
98_L115_P0.550831.596
101_D121_N0.540061.564
29_L102_V0.522791.514
13_L107_D0.518651.502
93_N96_S0.50891.474
50_S53_N0.504151.460
31_P107_D0.501031.451
83_W100_L0.500971.451
66_G114_W0.497571.441
18_Q28_V0.48831.414
30_Y37_N0.485441.406
26_P110_P0.483531.401
83_W93_N0.479481.389
101_D122_Q0.461561.337
24_G72_W0.460881.335
13_L31_P0.442521.282
60_V69_I0.441351.278
117_N121_N0.439341.273
32_C57_C0.43871.271
64_S67_T0.43341.255
60_V113_L0.432171.252
33_D37_N0.428881.242
16_D37_N0.426481.235
103_K112_V0.420751.219
92_R99_C0.418361.212
32_C74_C0.41471.201
14_C57_C0.411441.192
17_V27_V0.407061.179
84_K94_K0.39031.131
120_P123_Q0.384351.113
90_R116_C0.383161.110
16_D28_V0.373611.082
32_C116_C0.366261.061
82_R94_K0.362581.050
74_C116_C0.357421.035
59_D75_D0.348891.011
40_W58_L0.346541.004
48_I52_N0.345421.001
86_D90_R0.343560.995
11_S29_L0.342710.993
14_C74_C0.339480.983
30_Y33_D0.338550.981
43_D47_Q0.332990.965
28_V37_N0.32240.934
85_F89_G0.321380.931
85_F91_I0.31570.914
18_Q26_P0.315280.913
63_S95_N0.315280.913
15_L100_L0.309340.896
16_D33_D0.305840.886
36_D39_L0.30540.885
84_K92_R0.303140.878
30_Y107_D0.302550.876
42_F85_F0.302340.876
27_V40_W0.300350.870
23_N72_W0.299980.869
48_I53_N0.297450.862
29_L109_N0.297340.861
13_L29_L0.296780.860
16_D35_S0.293640.851
88_D123_Q0.29280.848
61_D70_V0.283150.820
46_G49_R0.280090.811
75_D79_S0.272850.790
20_S71_L0.272690.790
103_K110_P0.271110.785
92_R97_G0.268710.778
95_N113_L0.265240.768
61_D68_K0.26490.767
17_V28_V0.262560.761
57_C99_C0.259780.753
59_D70_V0.258160.748
17_V71_L0.256550.743
47_Q51_N0.254920.738
74_C99_C0.25270.732
67_T113_L0.245960.712
72_W75_D0.245460.711
101_D112_V0.243730.706
57_C116_C0.243070.704
49_R52_N0.242870.704
76_S79_S0.241680.700
114_W117_N0.23890.692
45_D49_R0.237550.688
29_L113_L0.236990.686
64_S113_L0.235280.682
78_S82_R0.232190.673
14_C99_C0.231890.672
42_F48_I0.231690.671
30_Y108_G0.229980.666
29_L71_L0.225550.653
58_L100_L0.222710.645
43_D49_R0.222670.645
32_C99_C0.22220.644
63_S79_S0.215580.624
114_W119_S0.215060.623
15_L40_W0.21480.622
40_W50_S0.213740.619
48_I51_N0.213180.618
111_L124_W0.212270.615
93_N97_G0.211890.614
18_Q25_S0.211120.612
69_I113_L0.210950.611
91_I100_L0.210810.611
15_L29_L0.209320.606
98_L113_L0.20860.604
101_D119_S0.208580.604
46_G50_S0.207960.602
14_C116_C0.207890.602
17_V40_W0.204690.593
102_V111_L0.202170.586
96_S113_L0.201340.583
44_P47_Q0.200310.580
75_D81_Q0.200160.580
104_G108_G0.200120.580
102_V109_N0.200040.579
72_W77_N0.197760.573
35_S119_S0.196610.570
28_V33_D0.19560.567
17_V102_V0.192280.557
23_N107_D0.192270.557
90_R123_Q0.19050.552
22_K25_S0.189650.549
31_P115_P0.188710.547
61_D69_I0.188350.546
77_N119_S0.186680.541
70_V112_V0.1850.536
60_V93_N0.1850.536
76_S82_R0.184430.534
60_V96_S0.182280.528
25_S71_L0.181810.527
39_L47_Q0.179670.520
41_R51_N0.179320.519
45_D82_R0.17930.519
75_D78_S0.179160.519
39_L42_F0.178860.518
18_Q27_V0.177910.515
43_D46_G0.177340.514
59_D79_S0.1770.513
47_Q50_S0.175270.508
90_R99_C0.173630.503
49_R53_N0.173190.502
103_K111_L0.173060.501
41_R49_R0.172380.499
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
2d1zA0.967799.80.104
1xhbA0.943599.80.108
2d7iA0.951699.80.117
1abrB0.975899.80.122
1ggpB0.967799.80.122
3c9zA0.975899.80.127
3a21A0.967799.80.129
1vclA0.967799.80.131
2vlcA0.975899.80.14
2ffuA0.935599.80.14

Page generated in 0.0416 seconds.