GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VWD - von Willebrand factor type D domain
Pfam: PF00094 (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: 159
Sequences: 1762
Seq/Len: 11.08
HH_delta: 0.746 (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
146_D151_D1.240188.274
33_C139_C0.989946.605
130_V138_T0.424422.832
1_C142_C0.415452.772
68_H83_N0.367682.453
41_F45_N0.366332.444
48_C57_C0.343912.294
12_F30_A0.296591.979
50_C57_C0.294641.966
11_T17_Y0.279681.866
21_G25_Y0.277751.853
135_K147_G0.277441.851
144_N151_D0.26461.765
15_K152_D0.260511.738
143_G152_D0.246691.646
110_F113_G0.239471.598
138_T144_N0.237241.583
5_G8_H0.2371.581
30_A41_F0.236931.581
5_G21_G0.234741.566
39_F45_N0.234191.562
112_S115_R0.230631.539
115_R118_V0.223981.494
26_I31_Q0.217541.451
30_A138_T0.215281.436
41_F48_C0.212681.419
5_G23_C0.208691.392
6_D20_P0.20761.385
61_V126_V0.202261.349
119_N122_G0.197231.316
70_I82_V0.191631.278
24_T62_T0.191561.278
131_P134_Y0.190491.271
8_H19_F0.188291.256
141_L153_F0.187231.249
15_K153_F0.187171.249
45_N48_C0.186231.242
31_Q139_C0.182471.217
5_G19_F0.181331.210
143_G146_D0.180221.202
72_I108_V0.180171.202
130_V134_Y0.180131.202
17_Y153_F0.180081.201
10_T16_S0.179421.197
45_N58_T0.178931.194
1_C13_D0.178361.190
32_D139_C0.172771.153
140_G143_G0.172571.151
8_H13_D0.172441.150
96_G100_R0.168431.124
26_I30_A0.168131.122
19_F25_Y0.163771.093
111_S114_V0.163591.091
3_V58_T0.161931.080
13_D146_D0.160541.071
7_P20_P0.160161.069
82_V87_V0.160141.068
149_P152_D0.158581.058
9_I23_C0.158011.054
29_L126_V0.157891.053
96_G102_S0.153721.026
8_H18_S0.152621.018
144_N154_T0.150941.007
41_F47_N0.150381.003
105_F127_Y0.14850.991
8_H21_G0.148220.989
9_I19_F0.147570.985
143_G151_D0.147260.982
148_E152_D0.145190.969
29_L128_V0.144690.965
39_F44_E0.144250.962
9_I12_F0.143540.958
51_G54_G0.142950.954
47_N50_C0.142150.948
98_I102_S0.14170.945
139_C144_N0.140570.938
24_T44_E0.140370.936
31_Q42_S0.139690.932
110_F115_R0.139430.930
146_D152_D0.138480.924
58_T126_V0.137650.918
20_P55_T0.136620.911
110_F114_V0.13590.907
109_V115_R0.135460.904
12_F29_L0.135380.903
148_E156_P0.13510.901
114_V118_V0.133760.892
46_K50_C0.133530.891
62_T71_E0.131640.878
43_V63_I0.130850.873
80_V83_N0.130120.868
71_E81_T0.129950.867
142_C145_F0.129270.862
80_V87_V0.129070.861
9_I21_G0.128790.859
70_I74_P0.128690.859
17_Y141_L0.128630.858
138_T158_G0.127420.850
118_V128_V0.127180.849
64_R69_E0.127030.847
66_G95_G0.125510.837
101_Y136_G0.125490.837
113_G118_V0.124610.831
3_V29_L0.12380.826
100_R106_V0.123740.826
80_V90_P0.123410.823
18_S55_T0.122610.818
118_V122_G0.121690.812
72_I90_P0.121560.811
106_V110_F0.121480.810
83_N87_V0.121060.808
63_I110_F0.120430.803
144_N149_P0.119930.800
70_I100_R0.118740.792
42_S45_N0.118170.788
22_N35_S0.117960.787
1_C11_T0.117540.784
80_V89_L0.117330.783
109_V118_V0.117220.782
1_C12_F0.117170.782
107_V125_S0.117110.781
93_S96_G0.117060.781
13_D151_D0.115670.772
54_G64_R0.115410.770
45_N128_V0.115330.769
73_K81_T0.115270.769
91_Y97_S0.114820.766
49_P52_Q0.114360.763
13_D25_Y0.113160.755
5_G142_C0.112830.753
118_V121_D0.11180.746
115_R122_G0.111560.744
25_Y29_L0.111550.744
145_F155_T0.111460.744
132_P135_K0.111210.742
133_W148_E0.111070.741
68_H72_I0.110640.738
154_T158_G0.110530.737
24_T148_E0.109580.731
41_F46_K0.109540.731
135_K145_F0.109030.727
41_F44_E0.109010.727
63_I141_L0.108940.727
63_I108_V0.108860.726
4_Y16_S0.108850.726
3_V9_I0.108770.726
20_P122_G0.108620.725
113_G129_S0.108460.724
15_K154_T0.108030.721
79_Q82_V0.107950.720
42_S156_P0.107940.720
68_H87_V0.1070.714
47_N51_G0.106990.714
67_N90_P0.10660.711
107_V116_V0.10650.711
43_V49_P0.105910.707
107_V110_F0.105540.704
82_V91_Y0.105510.704
79_Q86_P0.105490.704
1_C29_L0.105430.703
118_V126_V0.105170.702
125_S129_S0.10490.700
36_D94_S0.103890.693
126_V145_F0.103790.692
102_S105_F0.103630.691
111_S118_V0.103610.691
151_D158_G0.103180.688
64_R68_H0.103150.688
88_S92_W0.10310.688
107_V115_R0.102860.686
74_P135_K0.102790.686
99_E102_S0.102690.685
36_D135_K0.102610.685
112_S118_V0.102290.682
3_V45_N0.102140.681
57_C127_Y0.101920.680
39_F49_P0.101860.680
90_P114_V0.101710.679
8_H25_Y0.101020.674
3_V117_Q0.101010.674
9_I18_S0.100570.671
106_V109_V0.100460.670
13_D144_N0.100110.668
89_L122_G0.100070.668
105_F132_P0.100010.667
85_Q88_S0.099920.667
43_V46_K0.099780.666
47_N55_T0.09970.665
73_K89_L0.099690.665
134_Y138_T0.099670.665
67_N100_R0.099350.663
91_Y134_Y0.098820.659
64_R67_N0.097850.653
48_C59_R0.097740.652
23_C62_T0.097360.650
24_T70_I0.097090.648
2_S12_F0.097060.648
32_D137_K0.096250.642
116_V128_V0.096040.641
100_R104_G0.095980.640
18_S87_V0.095740.639
119_N125_S0.095720.639
88_S97_S0.095610.638
126_V148_E0.095350.636
30_A128_V0.094970.634
125_S131_P0.094790.632
140_G152_D0.094650.631
107_V119_N0.09460.631
131_P147_G0.094320.629
58_T61_V0.0940.627
4_Y7_P0.093990.627
110_F147_G0.093980.627
46_K108_V0.093970.627
119_N145_F0.093770.626
145_F154_T0.093760.626
43_V47_N0.093640.625
107_V124_M0.093490.624
20_P47_N0.093310.623
79_Q85_Q0.093280.622
125_S153_F0.093230.622
11_T15_K0.092990.620
65_L112_S0.092750.619
9_I43_V0.092590.618
65_L110_F0.092530.617
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
1lshB0.371198.20.746
4bq6D0.905770.80.896
4ba0A0.754711.90.931
2c4bA0.30825.10.941
3goeA0.51574.30.943
3es6B0.49064.30.943
3uipD0.27673.30.946
1tuoA0.37743.30.946
3cpsA0.33332.90.948
3cmcO0.33332.60.949
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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