GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VWA_3 - von Willebrand factor type A domain
Pfam: PF13768 (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: 155
Sequences: 11581
Seq/Len: 74.72
HH_delta: 0.062 (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
9_T41_A1.323343.033
80_L102_L1.234662.830
25_R69_K1.110882.546
4_V38_N1.020992.340
29_R65_L0.994652.280
99_A129_F0.988612.266
12_S105_D0.959882.200
87_A100_I0.901582.067
79_D82_A0.89412.049
86_A89_A0.784491.798
25_R65_L0.784181.798
32_P35_D0.77151.768
78_T106_G0.750381.720
46_V86_A0.71511.639
6_L83_A0.710641.629
5_I24_L0.709641.627
8_D12_S0.699031.602
139_A143_R0.694331.592
117_D121_R0.691121.584
60_N63_E0.683371.566
6_L87_A0.674881.547
6_L100_I0.673261.543
84_L100_I0.670711.537
78_T105_D0.669111.534
85_R118_L0.656451.505
5_I101_I0.654991.501
86_A90_L0.652851.496
4_V40_I0.645611.480
83_A87_A0.621251.424
13_M20_V0.620091.421
38_N52_G0.61971.420
4_V90_L0.60981.398
82_A85_R0.597651.370
100_I128_I0.596031.366
9_T43_G0.582321.335
91_L98_R0.581751.334
26_A30_S0.571411.310
18_E21_K0.56431.294
19_L22_D0.55961.283
40_I86_A0.558771.281
88_L124_G0.557121.277
85_R89_A0.5541.270
12_S78_T0.549021.258
4_V87_A0.54731.255
7_V20_V0.545371.250
22_D26_A0.543571.246
113_E117_D0.542181.243
130_T142_L0.540561.239
93_R96_C0.536891.231
84_L88_L0.533851.224
62_Q66_Q0.533361.223
103_L133_I0.526821.208
99_A127_R0.521341.195
40_I90_L0.521171.195
57_T60_N0.503921.155
118_L121_R0.502211.151
7_V24_L0.500381.147
3_V99_A0.498961.144
48_P51_P0.494091.133
41_A71_L0.487611.118
114_E117_D0.470251.078
6_L40_I0.46171.058
108_P141_F0.460981.057
19_L23_A0.460381.055
63_E66_Q0.458351.051
40_I83_A0.447731.026
61_R64_A0.445071.020
80_L108_P0.442531.014
5_I37_F0.437621.003
20_V24_L0.436891.001
132_G142_L0.436131.000
132_G137_A0.434920.997
114_E118_L0.434490.996
28_L61_R0.431680.990
21_K25_R0.431110.988
116_L119_V0.427250.979
116_L120_R0.427090.979
44_S79_D0.42370.971
11_G76_G0.423340.970
117_D120_R0.421090.965
140_D144_E0.418780.960
66_Q70_S0.418020.958
42_F80_L0.417120.956
97_V127_R0.416850.956
42_F83_A0.416310.954
11_G105_D0.415090.951
14_S17_K0.413910.949
22_D25_R0.41340.948
41_A49_L0.41240.945
25_R29_R0.410490.941
138_D141_F0.404590.927
101_I129_F0.403030.924
118_L122_A0.402410.922
84_L102_L0.397440.911
88_L122_A0.395150.906
65_L69_K0.394790.905
48_P86_A0.393490.902
101_I131_F0.388140.890
43_G79_D0.387150.887
128_I145_L0.386210.885
103_L131_F0.386010.885
14_S73_A0.385770.884
46_V83_A0.382830.878
115_I119_V0.379190.869
92_Q98_R0.378220.867
6_L42_F0.376570.863
116_L144_E0.371630.852
82_A86_A0.37030.849
84_L87_A0.369850.848
102_L130_T0.36980.848
81_L85_R0.369290.846
119_V123_R0.366040.839
140_D143_R0.365030.837
120_R123_R0.363760.834
81_L108_P0.362940.832
44_S76_G0.361120.828
13_M73_A0.360460.826
52_G55_P0.357760.820
5_I27_I0.356910.818
21_K68_I0.35560.815
4_V98_R0.355350.815
23_A27_I0.354110.812
98_R126_I0.35250.808
87_A91_L0.352490.808
40_I87_A0.351930.807
104_T142_L0.351520.806
28_L37_F0.34910.800
3_V37_F0.348690.799
26_A29_R0.348040.798
63_E67_W0.345290.791
108_P111_G0.344920.791
3_V101_I0.340160.780
65_L70_S0.338270.775
16_E19_L0.337940.775
44_S77_G0.337570.774
112_E115_I0.334760.767
38_N90_L0.333810.765
66_Q69_K0.330150.757
9_T47_R0.329970.756
88_L118_L0.328040.752
13_M17_K0.326840.749
113_E118_L0.322790.740
55_P60_N0.321220.736
18_E22_D0.320520.735
98_R125_H0.319050.731
40_I46_V0.315090.722
41_A47_R0.314810.722
114_E121_R0.31340.718
48_P90_L0.313190.718
46_V82_A0.311560.714
102_L128_I0.310040.711
85_R121_R0.309990.711
31_L35_D0.308520.707
23_A26_A0.308030.706
48_P52_G0.307970.706
141_F144_E0.307370.705
67_W70_S0.303040.695
42_F78_T0.302780.694
88_L126_I0.300730.689
8_D13_M0.299360.686
12_S104_T0.298880.685
62_Q65_L0.298580.684
118_L123_R0.297750.683
4_V91_L0.294840.676
124_G127_R0.293650.673
10_S13_M0.29310.672
107_Q138_D0.292610.671
37_F64_A0.291190.667
10_S106_G0.290410.666
119_V122_A0.290290.665
81_L115_I0.287520.659
49_L67_W0.284810.653
104_T130_T0.284080.651
6_L102_L0.283540.650
11_G14_S0.283180.649
134_G137_A0.283130.649
85_R114_E0.282190.647
29_R61_R0.281660.646
80_L104_T0.281470.645
135_S140_D0.280860.644
9_T13_M0.280110.642
84_L128_I0.277340.636
45_S82_A0.276730.634
68_I71_L0.276150.633
9_T71_L0.27480.630
10_S104_T0.274060.628
93_R98_R0.272140.624
78_T104_T0.270560.620
80_L84_L0.269380.617
8_D105_D0.268170.615
19_L27_I0.267940.614
115_I120_R0.267310.613
31_L37_F0.264940.607
5_I28_L0.263460.604
49_L52_G0.26330.604
38_N41_A0.259570.595
42_F104_T0.259570.595
4_V100_I0.258410.592
61_R65_L0.258410.592
42_F102_L0.258360.592
24_L39_I0.258290.592
5_I39_I0.257590.590
8_D104_T0.256630.588
21_K28_L0.254690.584
39_I64_A0.253970.582
129_F133_I0.253830.582
20_V23_A0.253020.580
24_L68_I0.252850.580
129_F132_G0.252530.579
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
4fx5A0.993599.80.062
3k6sA0.980699.70.128
2odpA0.993599.70.131
3hrzD0.993599.70.144
3ibsA0.948499.70.16
1ijbA0.980699.70.163
4jduA0.948499.70.163
1mf7A0.967799.70.164
1n3yA0.967799.70.165
1atzA0.967799.70.166

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