GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2201 - VWA-like domain (DUF2201)
Pfam: PF09967 (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: 126
Sequences: 8111
Seq/Len: 64.37
HH_delta: 0.363 (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
7_T38_Q1.193962.835
69_F88_Y1.12752.677
76_L86_V0.978432.323
28_R53_E0.877752.084
68_D71_P0.845552.008
10_S91_D0.83331.979
24_A57_R0.824521.958
75_Y79_N0.738521.754
2_V35_H0.7241.719
75_Y78_E0.701451.666
69_F94_G0.674641.602
4_A72_V0.674231.601
6_D10_S0.66731.585
3_V23_V0.657311.561
4_A86_V0.652861.550
11_I19_F0.62611.487
4_A76_L0.623531.481
11_I15_E0.615391.461
43_V75_Y0.604351.435
9_G65_G0.604111.435
71_P74_E0.599251.423
76_L80_R0.573281.361
18_R21_S0.572481.359
3_V87_I0.570591.355
7_T40_D0.5691.351
24_A53_E0.560941.332
37_I75_Y0.555771.320
35_H49_F0.553161.314
73_F86_V0.54721.299
67_T91_D0.541141.285
67_T92_G0.538431.279
68_D96_P0.533821.268
80_R84_S0.529921.258
16_L20_L0.528821.256
2_V37_I0.520461.236
5_I23_V0.515651.224
5_I19_F0.51351.219
74_E78_E0.513131.218
26_I30_F0.507961.206
72_V76_L0.505611.201
1_I85_V0.490531.165
10_S67_T0.488921.161
38_Q46_V0.48631.155
69_F73_F0.478781.137
17_R20_L0.478681.137
52_L55_E0.466751.108
43_V72_V0.461021.095
45_D75_Y0.451451.072
47_Q50_R0.450761.070
39_F69_F0.449751.068
70_R94_G0.447641.063
25_G28_R0.442831.052
94_G97_P0.433931.030
21_S25_G0.4281.016
16_L19_F0.427411.015
38_Q44_Q0.424291.008
25_G29_R0.416640.989
17_R21_S0.412280.979
15_E19_F0.400160.950
54_D57_R0.396680.942
3_V34_V0.396070.941
73_F88_Y0.394930.938
71_P75_Y0.393380.934
45_D48_V0.384270.912
7_T16_L0.3840.912
54_D58_D0.381540.906
2_V84_S0.380070.903
2_V76_L0.379320.901
73_F77_E0.374160.888
39_F88_Y0.373410.887
41_A68_D0.363880.864
70_R98_E0.360870.857
70_R96_P0.358950.852
39_F72_V0.357110.848
43_V71_P0.356230.846
37_I45_D0.356060.845
37_I43_V0.354020.841
2_V79_N0.353270.839
37_I79_N0.351160.834
15_E18_R0.348040.826
37_I72_V0.347790.826
37_I76_L0.346910.824
70_R74_E0.344250.817
5_I36_V0.339120.805
53_E57_R0.3390.805
2_V86_V0.338130.803
18_R22_E0.335670.797
21_S24_A0.33550.797
35_H45_D0.332110.789
24_A28_R0.331630.787
68_D94_G0.326170.775
20_L24_A0.325260.772
4_A88_Y0.323850.769
55_E58_D0.323410.768
40_D63_G0.322530.766
68_D95_W0.32240.766
14_E18_R0.322310.765
1_I87_I0.315250.749
35_H79_N0.314170.746
19_F22_E0.312940.743
20_L59_I0.311240.739
24_A59_I0.310210.737
35_H80_R0.310030.736
4_A37_I0.303790.721
35_H47_Q0.301950.717
3_V89_F0.301640.716
8_S92_G0.301250.715
1_I34_V0.300810.714
27_L52_L0.299630.711
66_G93_E0.299270.711
27_L34_V0.298910.710
8_S67_T0.289850.688
10_S92_G0.282730.671
8_S90_T0.281160.668
2_V49_F0.280810.667
74_E77_E0.279050.663
3_V85_V0.277310.658
82_R87_I0.276860.657
52_L56_L0.275240.654
7_T44_Q0.273680.650
12_S61_L0.273470.649
69_F90_T0.271030.644
33_E49_F0.270460.642
44_Q47_Q0.269310.640
66_G95_W0.269060.639
76_L79_N0.26840.637
40_D68_D0.268310.637
40_D64_G0.268180.637
7_T61_L0.267780.636
11_I16_L0.265690.631
3_V22_E0.265380.630
27_L32_A0.265280.630
16_L61_L0.265060.629
60_K78_E0.263690.626
6_D91_D0.262210.623
3_V26_I0.260120.618
6_D90_T0.258780.614
19_F23_V0.254160.604
1_I30_F0.253550.602
9_G12_S0.250870.596
68_D97_P0.250.594
23_V36_V0.249690.593
62_K77_E0.24860.590
72_V94_G0.24840.590
41_A65_G0.246210.585
45_D79_N0.244990.582
45_D83_P0.244450.580
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
3hrzD199.30.363
2odpA199.30.381
2xggA0.976299.20.393
4hqoA199.20.395
4hqfA199.20.398
1ijbA199.20.4
3zqkA0.992199.20.414
1rrkA199.10.417
4fx5A0.984199.10.418
3k6sA0.992199.10.42

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