GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VWA_2 - von Willebrand factor type A domain
Pfam: PF13519 (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: 172
Sequences: 11828
Seq/Len: 68.77
HH_delta: 0.027 (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
8_N45_S1.308832.951
34_A64_K1.293922.917
30_N68_N1.168232.634
82_L105_L1.14962.592
3_V42_G1.110322.503
102_A130_Y1.038872.342
81_N84_D1.012332.282
11_S108_D1.011672.281
89_A103_I0.96142.168
30_N64_K0.931662.100
90_A122_L0.857951.934
42_G56_L0.82641.863
94_A125_Q0.808321.822
88_E91_K0.804881.815
131_T148_A0.801311.807
4_F104_V0.770311.737
5_V89_A0.747981.686
5_V103_I0.728381.642
80_T108_D0.727021.639
90_A125_Q0.704051.587
50_S88_E0.702581.584
12_M21_R0.683091.540
22_I26_K0.68121.536
80_T109_G0.680121.533
3_V44_V0.675161.522
4_F29_L0.666061.502
85_A89_A0.657661.483
45_S53_L0.654811.476
23_D26_K0.643581.451
6_L25_A0.627111.414
7_D11_S0.626341.412
3_V89_A0.622661.404
14_G21_R0.613511.383
93_L101_R0.612041.380
102_A128_T0.611191.378
3_V92_M0.610861.377
5_V85_A0.602271.358
8_N22_I0.598451.349
103_I129_I0.594641.341
64_K68_N0.588591.327
6_L29_L0.577621.302
145_Q155_Y0.575291.297
27_D31_E0.566261.277
8_N47_S0.56461.273
146_R150_A0.562751.269
60_K64_K0.55421.249
84_D87_Q0.548461.237
90_A118_A0.547061.233
59_D62_E0.546521.232
2_V102_A0.537191.211
118_A121_A0.52531.184
44_V88_E0.524931.183
61_D65_N0.520291.173
88_E92_M0.515121.161
12_M25_A0.512581.156
11_S80_T0.500781.129
31_E34_A0.49991.127
86_L103_I0.499111.125
87_Q118_A0.49561.117
62_E65_N0.490421.106
120_K150_A0.488891.102
31_E35_N0.484381.092
65_N69_K0.484291.092
44_V85_A0.478011.078
120_K124_Q0.474311.069
87_Q121_A0.468221.056
100_R128_T0.464861.048
133_G144_L0.462921.044
117_E120_K0.461941.041
145_Q149_E0.461451.040
4_F41_V0.459011.035
82_L111_D0.458211.033
52_T88_E0.453951.023
24_Q27_D0.453471.022
65_N68_N0.452011.019
44_V92_M0.451471.018
121_A124_Q0.444591.002
45_S51_R0.444331.002
54_S57_T0.442860.998
13_N72_P0.438140.988
54_S63_L0.437850.987
46_F82_L0.431380.973
142_E146_R0.430550.971
81_N112_N0.430070.970
105_L129_I0.429120.967
111_D143_F0.426420.961
87_Q91_K0.423220.954
45_S70_L0.420940.949
52_T55_P0.417960.942
44_V50_S0.416430.939
119_A123_K0.416220.938
10_G108_D0.414060.934
114_S117_E0.413570.932
10_G78_G0.411860.929
146_R149_E0.41130.927
86_L122_L0.408790.922
133_G155_Y0.406820.917
92_M95_S0.405760.915
106_I134_I0.40250.907
5_V44_V0.401320.905
3_V56_L0.400710.903
48_D79_G0.398910.899
129_I151_T0.396660.894
116_I146_R0.396050.893
33_L63_L0.392520.885
121_A125_Q0.389850.879
83_Y87_Q0.388350.876
33_L41_V0.385260.869
120_K123_K0.383690.865
23_D27_D0.374850.845
123_K150_A0.373760.843
52_T92_M0.373530.842
101_R127_I0.373120.841
2_V41_V0.372190.839
2_V104_V0.370340.835
42_G92_M0.368990.832
83_Y111_D0.368460.831
90_A94_A0.367770.829
5_V105_L0.366080.825
49_S84_D0.365030.823
104_V130_Y0.36180.816
148_A153_G0.361690.815
86_L129_I0.360180.812
47_S81_N0.359180.810
105_L131_T0.359060.810
4_F32_L0.358470.808
62_E66_A0.356330.803
131_T144_L0.354450.799
104_V132_V0.35420.799
25_A134_I0.349450.788
30_N34_A0.348150.785
117_E121_A0.346650.782
119_A122_L0.342610.772
50_S85_A0.341260.769
33_L36_L0.340350.767
5_V46_F0.338170.762
33_L60_K0.337920.762
7_D12_M0.337890.762
3_V93_L0.336320.758
131_T155_Y0.333220.751
90_A121_A0.332930.751
103_I127_I0.332760.750
21_R25_A0.332190.749
107_T144_L0.331290.747
91_K95_S0.330190.744
46_F80_T0.32940.743
118_A122_L0.328850.741
44_V52_T0.326210.735
41_V63_L0.324660.732
13_N21_R0.324330.731
142_E145_Q0.322720.728
25_A28_A0.32170.725
136_S139_D0.321620.725
48_D81_N0.321250.724
59_D63_L0.319430.720
46_F85_A0.317640.716
21_R24_Q0.316650.714
83_Y118_A0.31450.709
57_T60_K0.312390.704
90_A93_L0.312240.704
3_V103_I0.311650.703
44_V89_A0.311540.702
143_F146_R0.311210.702
63_L66_A0.30990.699
6_L43_L0.309550.698
130_Y154_R0.309150.697
27_D30_N0.308630.696
123_K126_G0.307770.694
9_S107_T0.307420.693
3_V101_R0.307160.693
133_G138_S0.30650.691
134_I158_V0.306050.690
40_R56_L0.3030.683
26_K67_L0.300770.678
115_D119_A0.29920.675
107_T131_T0.298950.674
86_L89_A0.297560.671
69_K72_P0.296450.668
24_Q28_A0.296370.668
50_S84_D0.29530.666
119_A126_G0.295040.665
86_L90_A0.294340.664
84_D88_E0.29250.659
22_I25_A0.291720.658
144_L155_Y0.29150.657
66_A69_K0.290150.654
101_R126_G0.28760.648
132_V156_F0.28670.646
90_A127_I0.286540.646
129_I147_L0.284740.642
22_I72_P0.283010.638
106_I132_V0.278310.627
148_A151_T0.276580.624
110_E139_D0.276040.622
10_G13_N0.275740.622
22_I28_A0.274580.619
61_D64_K0.273620.617
130_Y151_T0.273240.616
46_F107_T0.271540.612
86_L105_L0.268980.606
154_R157_H0.267280.603
25_A29_L0.266550.601
60_K63_L0.265790.599
79_G112_N0.265520.599
144_L147_L0.264450.596
43_L63_L0.264280.596
139_D142_E0.263610.594
116_I120_K0.262320.591
125_Q128_T0.26110.589
72_P77_G0.259050.584
87_Q90_A0.25890.584
36_L39_D0.258590.583
11_S109_G0.258030.582
6_L70_L0.25760.581
135_G139_D0.256420.578
28_A134_I0.255990.577
67_L70_L0.255950.577
122_L129_I0.254850.575
4_F106_I0.254630.574
82_L86_L0.254510.574
34_A60_K0.2530.570
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
4jduA0.994299.90.027
3ibsA199.90.039
3hrzD0.959399.80.087
4fx5A0.93699.80.096
1rrkA0.959399.80.104
2odpA0.965199.80.111
4hqfA0.965199.80.112
3k6sA0.947799.80.112
4hqoA0.959399.80.116
1ijbA0.947799.80.117

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