GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VIT_2 - Vault protein inter-alpha-trypsin domain
Pfam: PF13757 (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: CL0029
Length: 78
Sequences: 613
Seq/Len: 7.86
HH_delta: 0.721 (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
34_L48_F0.544263.708
53_D56_A0.285131.942
60_G71_T0.268331.828
62_E69_I0.259781.770
30_T57_T0.254481.734
15_Q37_E0.246261.678
65_I74_V0.238231.623
29_G59_V0.234151.595
21_A30_T0.229861.566
18_R24_N0.218341.487
37_E69_I0.202961.383
64_D69_I0.195031.329
62_E71_T0.184181.255
57_T76_D0.183881.253
13_P36_Y0.181971.240
53_D63_A0.175391.195
72_V76_D0.172811.177
29_G48_F0.172291.174
36_Y43_P0.170581.162
25_G61_F0.169611.155
25_G68_R0.168981.151
19_V41_D0.16561.128
40_E43_P0.162571.107
27_S55_G0.162331.106
14_L36_Y0.160951.096
22_C62_E0.160941.096
36_Y51_P0.157981.076
21_A28_A0.156991.069
61_F76_D0.156891.069
32_A53_D0.156281.065
65_I77_R0.150121.023
16_S27_S0.149971.022
35_T39_P0.14861.012
20_T33_S0.148511.012
47_V77_R0.147771.007
12_L36_Y0.145470.991
13_P44_L0.144310.983
14_L17_S0.142650.972
41_D69_I0.141250.962
20_T42_R0.137380.936
21_A26_Y0.135380.922
28_A72_V0.135070.920
13_P43_P0.133250.908
40_E55_G0.133190.907
20_T24_N0.130680.890
25_G52_L0.129440.882
31_T61_F0.129250.881
22_C31_T0.128560.876
13_P41_D0.128430.875
46_G63_A0.128310.874
26_Y53_D0.128220.873
37_E41_D0.128170.873
59_V74_V0.127570.869
59_V70_V0.127130.866
24_N61_F0.125910.858
16_S29_G0.125450.855
64_D67_G0.125320.854
47_V56_A0.1250.852
19_V39_P0.124810.850
36_Y50_F0.123940.844
11_P14_L0.120840.823
31_T72_V0.119480.814
13_P49_V0.119130.812
46_G52_L0.119070.811
30_T49_V0.118710.809
25_G39_P0.117690.802
26_Y32_A0.117410.800
63_A76_D0.117370.800
34_L50_F0.116740.795
35_T56_A0.116730.795
59_V63_A0.116250.792
29_G54_E0.115380.786
17_S36_Y0.114920.783
17_S73_Q0.11480.782
46_G56_A0.114730.782
23_V28_A0.11380.775
34_L51_P0.113780.775
11_P40_E0.113670.774
60_G69_I0.113530.773
48_F74_V0.112980.770
54_E62_E0.112960.770
48_F70_V0.112060.763
20_T31_T0.111130.757
45_E71_T0.111010.756
31_T69_I0.110440.752
28_A32_A0.110290.751
34_L72_V0.110120.750
48_F72_V0.108930.742
11_P41_D0.108620.740
20_T77_R0.108080.736
27_S40_E0.107820.735
19_V32_A0.107590.733
19_V38_N0.107530.733
24_N68_R0.107370.731
22_C66_G0.106940.729
20_T27_S0.106650.727
18_R25_G0.106030.722
41_D60_G0.106030.722
18_R33_S0.105370.718
22_C72_V0.103880.708
26_Y59_V0.103870.708
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
4g2aA196.40.721
1ep5B0.4872110.889
1vcpA0.397410.70.89
4agkA0.487210.30.89
2kqvA0.974470.898
3hrzA0.88466.20.9
4hg6B0.94876.20.9
1svpA0.55.80.901
2yjgA0.38464.50.906
3qorA0.88464.30.907
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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