GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VWC - von Willebrand factor type C domain
Pfam: PF00093 (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: CL0451
Length: 57
Sequences: 1245
Seq/Len: 21.84
HH_delta: -0.015 (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
22_C31_C0.653682.851
17_D20_T0.622562.715
49_P56_V0.42681.862
41_C57_C0.391011.705
54_C57_C0.390461.703
9_Q12_E0.382461.668
36_C41_C0.375991.640
19_C24_C0.358191.562
13_S23_T0.344781.504
8_Y12_E0.334171.458
53_C57_C0.330921.443
36_C53_C0.325941.422
24_C31_C0.32121.401
31_C36_C0.314071.370
52_E56_V0.311351.358
19_C22_C0.30391.325
19_C36_C0.298231.301
2_S7_V0.287371.253
36_C54_C0.281571.228
26_D33_R0.273591.193
49_P52_E0.254211.109
10_N26_D0.251771.098
30_Q42_P0.246461.075
19_C53_C0.238451.040
13_S21_T0.235861.029
14_W27_G0.235021.025
48_K55_P0.230821.007
40_D44_P0.22810.995
34_I52_E0.218980.955
19_C41_C0.217510.949
8_Y14_W0.214470.935
47_V50_P0.208360.909
24_C36_C0.203670.888
1_C24_C0.201390.878
1_C22_C0.199560.870
37_P55_P0.197470.861
3_F18_P0.19650.857
25_Q37_P0.196360.856
19_C54_C0.192620.840
20_T33_R0.191640.836
10_N25_Q0.191410.835
8_Y29_V0.191150.834
13_S48_K0.19050.831
39_L44_P0.19030.830
7_V21_T0.187350.817
39_L57_C0.1870.816
3_F14_W0.185790.810
32_S42_P0.185570.809
28_E42_P0.182440.796
6_R43_N0.182440.796
11_G24_C0.180420.787
40_D52_E0.17910.781
28_E34_I0.178330.778
35_Q48_K0.178290.778
16_P23_T0.177380.774
44_P56_V0.174660.762
21_T32_S0.174140.760
47_V56_V0.173470.757
43_N48_K0.173370.756
29_V35_Q0.172970.754
1_C31_C0.172290.751
50_P53_C0.170540.744
2_S18_P0.168350.734
21_T38_P0.167550.731
8_Y23_T0.167210.729
28_E33_R0.166290.725
15_H20_T0.165050.720
7_V23_T0.165020.720
7_V50_P0.164860.719
1_C8_Y0.164090.716
1_C19_C0.160860.702
3_F40_D0.160480.700
24_C53_C0.160370.699
19_C31_C0.15980.697
10_N27_G0.159270.695
25_Q32_S0.158360.691
2_S5_G0.156790.684
50_P54_C0.15640.682
9_Q13_S0.155510.678
6_R21_T0.155060.676
14_W29_V0.153530.670
2_S9_Q0.149540.652
39_L56_V0.148830.649
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
1u5mA0.964999.1-0.015
3bk3C0.947498.60.18
1xhhA0.859675.40.694
2xttA0.61474.40.697
2cg7A0.596567.50.711
1gl0I0.596561.60.721
3ix0A160.80.723
1wo9A0.596550.50.738
1skzA0.7544470.743
3tvjI0.631644.30.748

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