GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VWA - von Willebrand factor type A domain
Pfam: PF00092 (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: CL0128
Length: 178
Sequences: 10340
Seq/Len: 58.09
HH_delta: -0.04 (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
81_L109_L1.179922.898
8_T44_T1.123852.760
29_S65_L0.995272.444
3_V41_G0.926892.276
11_S112_D0.864122.122
88_A107_I0.863182.120
79_T112_D0.820422.015
80_N83_A0.817992.009
25_K70_D0.813121.997
4_F24_V0.768321.887
49_A87_F0.752851.849
41_G55_L0.741771.822
87_F90_E0.737911.812
137_I141_I0.724991.780
79_T113_G0.68661.686
84_A88_A0.681631.674
5_L107_I0.678941.667
5_L88_A0.674941.658
35_N38_T0.67111.648
146_N150_R0.658771.618
136_V141_I0.651451.600
25_K65_L0.641331.575
126_A129_K0.63061.549
5_L84_A0.615461.511
4_F108_I0.613381.506
60_S63_D0.612631.504
7_D11_S0.606371.489
85_L107_I0.604861.485
138_A141_I0.598881.471
125_A129_K0.59821.469
17_F21_K0.59681.466
81_L115_S0.581851.429
126_A130_K0.573881.409
135_K141_I0.557451.369
106_V137_I0.54831.347
92_L105_K0.548241.346
11_S79_T0.539971.326
3_V91_Q0.537571.320
6_V24_V0.528691.298
51_V87_F0.528551.298
51_V54_S0.52151.281
45_F81_L0.514711.264
83_A86_K0.513751.262
12_M16_N0.51151.256
18_E21_K0.507631.247
8_T17_F0.507541.246
87_F91_Q0.507451.246
3_V43_V0.505041.240
19_K22_Q0.501611.232
44_T52_L0.500141.228
123_E127_N0.496541.219
15_D18_E0.493531.212
124_E128_L0.488921.201
6_V20_A0.487961.198
12_M20_A0.484751.190
21_K25_K0.482651.185
160_G165_L0.477351.172
3_V88_A0.477231.172
115_S148_E0.474811.166
8_T46_S0.473331.162
22_Q26_S0.47011.154
43_V87_F0.468931.152
146_N164_Y0.465011.142
122_S125_A0.454781.117
145_D148_E0.449291.103
127_N130_K0.447651.099
138_A149_L0.444871.093
62_N66_N0.439531.079
125_A128_L0.438811.078
138_A153_A0.437251.074
46_S80_N0.431161.059
43_V91_Q0.425671.045
149_L153_A0.425231.044
26_S29_S0.420831.033
147_E151_E0.418651.028
5_L43_V0.41731.025
10_G77_G0.414071.017
43_V84_A0.412051.012
85_L89_R0.409331.005
10_G112_D0.407871.002
49_A84_A0.405250.995
86_K90_E0.40520.995
28_I40_V0.398710.979
107_I136_V0.394250.968
124_E127_N0.39240.964
115_S118_S0.391230.961
4_F40_V0.388770.955
63_D66_N0.385160.946
148_E151_E0.384930.945
150_R162_V0.382030.938
3_V55_L0.379910.933
2_I106_V0.378930.931
25_K71_S0.376250.924
25_K29_S0.375430.922
53_F56_T0.373250.917
47_D77_G0.371940.913
133_G141_I0.371450.912
114_N145_D0.36830.904
127_N131_S0.367570.903
61_K65_L0.366760.901
124_E129_K0.365980.899
9_S12_M0.365670.898
85_L109_L0.363510.893
82_G115_S0.36250.890
86_K124_E0.361430.888
16_N20_A0.354810.871
3_V92_L0.351910.864
47_D78_G0.351890.864
122_S126_A0.351520.863
16_N19_K0.349610.859
133_G136_V0.347060.852
86_K89_R0.346440.851
80_N116_N0.34440.846
110_I141_I0.342880.842
104_P135_K0.342060.840
49_A80_N0.341550.839
106_V135_K0.34090.837
123_E126_A0.33660.827
137_I161_H0.33540.824
2_I40_V0.33520.823
3_V105_K0.33510.823
82_G86_K0.334510.821
106_V133_G0.333720.820
7_D12_M0.332650.817
43_V51_V0.331970.815
117_D121_P0.32940.809
85_L88_A0.326310.801
91_Q94_S0.325090.798
89_R128_L0.324680.797
20_A24_V0.324230.796
160_G163_F0.324110.796
79_T111_T0.323930.796
53_F58_Y0.318220.781
83_A87_F0.317410.779
45_F111_T0.316350.777
18_E22_Q0.315770.775
80_N117_D0.315560.775
4_F27_I0.315430.775
140_G144_A0.313520.770
43_V49_A0.312670.768
51_V91_Q0.308930.759
28_I64_L0.30770.756
39_R55_L0.306660.753
17_F20_A0.306490.753
10_G75_S0.305780.751
60_S64_L0.304660.748
49_A83_A0.304620.748
41_G91_Q0.3040.747
22_Q25_K0.301590.741
45_F79_T0.300730.739
5_L45_F0.299810.736
41_G92_L0.298540.733
43_V88_A0.297340.730
47_D50_R0.296460.728
110_I139_I0.295310.725
28_I68_I0.29480.724
161_H165_L0.294370.723
111_T138_A0.287080.705
89_R93_F0.286990.705
80_N115_S0.286250.703
109_L138_A0.284810.699
45_F84_A0.284360.698
88_A91_Q0.28340.696
88_A92_L0.283350.696
38_T103_S0.28330.696
46_S75_S0.281470.691
11_S113_G0.279170.686
17_F75_S0.278940.685
53_F64_L0.278560.684
41_G108_I0.278090.683
121_P125_A0.277520.682
48_S83_A0.276190.678
23_F27_I0.276070.678
61_K64_L0.274940.675
12_M17_F0.273370.671
147_E150_R0.27320.671
64_L67_A0.272650.670
57_D61_K0.270320.664
121_P124_E0.269140.661
121_P126_A0.267040.656
75_S78_G0.266140.654
82_G117_D0.265070.651
39_R57_D0.265030.651
111_T149_L0.264660.650
34_S38_T0.262670.645
39_R95_S0.262180.644
83_A118_S0.26150.642
8_T50_R0.259810.638
135_K138_A0.257570.633
13_S74_S0.257240.632
13_S16_N0.257120.631
108_I139_I0.256970.631
20_A110_I0.256090.629
150_R153_A0.255680.628
140_G149_L0.255110.626
41_G44_T0.254920.626
5_L109_L0.254620.625
34_S40_V0.254560.625
135_K161_H0.253810.623
47_D80_N0.25130.617
78_G116_N0.250380.615
86_K127_N0.250130.614
90_E94_S0.249220.612
64_L68_I0.248650.611
120_S124_E0.247150.607
11_S78_G0.246680.606
58_Y63_D0.246670.606
125_A130_K0.246440.605
82_G124_E0.246250.605
118_S121_P0.245860.604
8_T75_S0.244930.601
138_A162_V0.244060.599
44_T50_R0.243410.598
161_H164_Y0.242950.597
109_L134_I0.24230.595
9_S111_T0.242230.595
81_L85_L0.241980.594
3_V107_I0.241720.594
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
3k6sA0.971999.9-0.04
1mf7A0.971999.90.009
1ijbA0.971999.90.015
3hrzD0.994499.90.034
3zqkA0.92799.90.039
4hqfA0.977599.80.046
2b2xA0.971999.80.046
1mjnA0.938299.80.047
4hqoA0.977599.80.05
1pt6A0.971999.80.051

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