GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Bet_v_1 - Pathogenesis-related protein Bet v I family
Pfam: PF00407 (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: CL0209
Length: 151
Sequences: 4040
Seq/Len: 26.75
HH_delta: 0.21 (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
76_D80_K0.964143.047
16_A106_P0.914232.889
23_F104_K0.876162.769
107_K113_V0.846032.673
105_I115_K0.816242.579
11_E107_K0.789762.496
9_E113_V0.78132.469
104_K112_C0.767792.426
74_A81_T0.765162.418
105_I113_V0.74482.354
14_V19_L0.721112.279
9_E115_K0.717012.266
7_E115_K0.716792.265
21_K25_S0.677632.141
15_S18_K0.670272.118
11_E113_V0.628541.986
108_G111_G0.598341.891
20_W78_E0.593491.875
20_W75_I0.582421.840
11_E111_G0.577711.826
7_E117_T0.572941.811
13_K111_G0.553261.748
81_T103_Q0.55131.742
23_F102_I0.549931.738
12_V114_V0.526841.665
71_K85_T0.52311.653
83_T101_T0.517621.636
19_L104_K0.495921.567
73_E85_T0.494621.563
17_D78_E0.486571.538
107_K111_G0.482721.525
103_Q117_T0.470011.485
81_T101_T0.468071.479
74_A83_T0.466451.474
73_E99_K0.4611.457
5_K117_T0.459111.451
16_A80_K0.43421.372
48_G75_I0.418311.322
84_Y100_S0.417071.318
16_A112_C0.413421.306
76_D81_T0.409631.294
28_H32_K0.400251.265
50_P74_A0.399321.262
16_A78_E0.392931.242
83_T99_K0.384521.215
12_V19_L0.377791.194
16_A104_K0.376561.190
25_S28_H0.375111.185
21_K77_E0.365141.154
85_T99_K0.364351.151
50_P75_I0.364241.151
73_E83_T0.359661.137
17_D106_P0.352871.115
24_K77_E0.344451.088
24_K48_G0.342941.084
17_D21_K0.341661.080
106_P110_G0.338981.071
14_V18_K0.332621.051
103_Q115_K0.331721.048
5_K119_E0.330851.046
101_T119_E0.315670.998
46_G72_V0.314940.995
72_V75_I0.311490.984
97_S121_E0.311170.983
22_A28_H0.298360.943
71_K87_I0.295070.932
106_P111_G0.287320.908
100_S116_W0.287230.908
30_L34_L0.283850.897
45_E53_S0.282760.894
85_T97_S0.279420.883
86_V100_S0.276880.875
107_K110_G0.265590.839
100_S118_I0.264410.836
16_A20_W0.263950.834
104_K114_V0.258420.817
69_K88_E0.255910.809
84_Y102_I0.254270.804
82_I102_I0.252610.798
57_W67_Y0.24820.784
53_S69_K0.246820.780
18_K28_H0.240350.760
34_L41_V0.24010.759
102_I114_V0.235430.744
58_T62_G0.234640.741
14_V112_C0.233510.738
53_S71_K0.233020.736
86_V116_W0.232140.734
122_K125_E0.230990.730
96_K121_E0.230560.729
47_D53_S0.228350.722
98_F116_W0.227390.719
17_D77_E0.226350.715
106_P112_C0.221640.700
72_V84_Y0.22070.697
47_D50_P0.219060.692
75_I82_I0.216540.684
20_W24_K0.215760.682
45_E55_K0.214940.679
15_S19_L0.213280.674
23_F84_Y0.212950.673
11_E112_C0.212920.673
72_V100_S0.210220.664
10_V33_I0.210010.664
21_K28_H0.209930.663
56_K67_Y0.209680.663
33_I72_V0.208570.659
19_L114_V0.207080.654
20_W82_I0.206860.654
13_K110_G0.205040.648
17_D80_K0.202930.641
26_S31_P0.20050.634
40_S57_W0.200080.632
34_L98_F0.199910.632
96_K122_K0.194150.614
132_K135_D0.194080.613
86_V98_F0.192060.607
80_K105_I0.191060.604
23_F72_V0.190680.603
44_V71_K0.19060.602
54_I71_K0.189450.599
30_L36_H0.1890.597
36_H90_D0.18660.590
18_K21_K0.185990.588
132_K136_F0.183740.581
43_V46_G0.180960.572
121_E125_E0.180720.571
59_F63_G0.17910.566
70_E84_Y0.178590.564
44_V56_K0.177950.562
101_T117_T0.177790.562
68_V86_V0.176890.559
102_I116_W0.176520.558
84_Y116_W0.173160.547
40_S59_F0.171550.542
85_T100_S0.170730.540
90_D94_D0.169810.537
32_K35_P0.168570.533
49_G75_I0.166090.525
20_W133_Y0.165710.524
108_G113_V0.165240.522
54_I69_K0.16520.522
102_I118_I0.16480.521
20_W104_K0.16440.520
6_L10_V0.164010.518
55_K70_E0.162820.515
42_E45_E0.162710.514
30_L118_I0.162220.513
5_K18_K0.16140.510
31_P43_V0.161180.509
117_T126_D0.1610.509
23_F82_I0.160570.507
95_Y120_Y0.159960.505
71_K86_V0.159270.503
54_I72_V0.158820.502
42_E56_K0.158510.501
33_I36_H0.156760.495
55_K69_K0.156070.493
86_V118_I0.156030.493
8_V116_W0.155090.490
72_V102_I0.154920.490
50_P76_D0.153970.487
69_K89_G0.153520.485
98_F120_Y0.15250.482
58_T67_Y0.152420.482
69_K87_I0.150830.477
70_E118_I0.150570.476
73_E119_E0.150390.475
26_S70_E0.150350.475
70_E98_F0.149660.473
96_K103_Q0.149440.472
51_G72_V0.14870.470
98_F118_I0.148410.469
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
2vjgA0.986899.80.21
3putA0.973599.70.217
2qimA0.986899.70.22
3rwsA0.980199.70.221
2flhA0.980199.70.226
4a8uA0.986899.70.228
1e09A0.986899.70.229
3ie5A0.986899.70.235
3q64A0.973599.70.237
3rd6A0.973599.70.239

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