GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VIT - Vault protein inter-alpha-trypsin domain
Pfam: PF08487 (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: 118
Sequences: 691
Seq/Len: 5.86
HH_delta: 0.771 (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
25_Q39_Y0.376223.113
36_E75_Y0.307522.545
66_K74_E0.277542.297
78_A85_A0.268752.224
71_A75_Y0.254342.105
72_K89_E0.253072.094
44_P47_A0.220521.825
51_G62_E0.220121.822
28_E109_E0.199851.654
6_K109_E0.197931.638
85_A103_N0.190631.578
12_V21_T0.186931.547
77_E81_Q0.184831.530
3_V27_F0.182711.512
105_P108_E0.181931.506
65_V106_P0.18081.496
78_A82_G0.17241.427
104_I110_V0.172251.425
21_T48_A0.171641.420
78_A103_N0.169751.405
82_G85_A0.169541.403
57_G108_E0.169381.402
53_S60_T0.166421.377
71_A78_A0.165231.367
34_P106_P0.164581.362
6_K28_E0.156021.291
24_T113_E0.154971.282
37_A104_I0.154841.281
82_G103_N0.151391.253
9_H15_I0.149031.233
53_S113_E0.147131.218
26_T111_T0.14191.174
5_L27_F0.139161.152
90_Q93_P0.138491.146
67_E70_E0.137731.140
27_F42_P0.137681.139
68_K75_Y0.137241.136
66_K70_E0.136731.132
21_T116_Y0.134211.111
48_A67_E0.133341.103
70_E73_Q0.133251.103
17_R112_I0.133031.101
20_R50_S0.132161.094
72_K76_E0.128361.062
84_S105_P0.127821.058
90_Q104_I0.126871.050
28_E60_T0.126681.048
92_D95_V0.12551.039
103_N110_V0.125111.035
67_E75_Y0.122431.013
44_P54_M0.121351.004
32_S107_N0.120420.997
50_S61_I0.120320.996
20_R115_T0.119960.993
69_E73_Q0.119790.991
75_Y85_A0.119670.990
71_A85_A0.119610.990
38_V99_T0.118490.981
14_I19_A0.117390.971
34_P69_E0.117080.969
12_V19_A0.116770.966
10_V30_P0.116570.965
27_F112_I0.11650.964
13_T70_E0.11640.963
64_E70_E0.115910.959
65_V108_E0.115830.959
50_S114_L0.115260.954
32_S60_T0.114760.950
73_Q77_E0.112980.935
31_S34_P0.112080.928
88_L100_V0.111990.927
23_V44_P0.111360.922
55_W60_T0.111150.920
77_E83_K0.111070.919
55_W73_Q0.111030.919
27_F34_P0.110810.917
24_T99_T0.110630.916
74_E77_E0.110530.915
3_V107_N0.110060.911
10_V115_T0.10860.899
25_Q112_I0.108270.896
69_E77_E0.106060.878
53_S100_V0.10540.872
10_V32_S0.105360.872
52_F100_V0.105150.870
4_P34_P0.104210.862
78_A84_S0.103880.860
22_T52_F0.10360.857
10_V23_V0.103280.855
3_V62_E0.103180.854
62_E72_K0.103140.854
53_S107_N0.102960.852
26_T30_P0.10230.847
11_K33_E0.101910.843
22_T113_E0.101650.841
57_G73_Q0.101530.840
66_K103_N0.101360.839
87_L102_V0.10130.838
47_A116_Y0.100960.835
55_W113_E0.100610.833
35_L76_E0.100340.830
3_V8_V0.100330.830
14_I112_I0.099250.821
17_R80_A0.099120.820
11_K24_T0.099080.820
85_A110_V0.0990.819
14_I114_L0.098820.818
30_P106_P0.098730.817
42_P112_I0.098310.814
13_T57_G0.09830.813
84_S103_N0.097760.809
7_S109_E0.097630.808
12_V109_E0.097540.807
61_I82_G0.096890.802
7_S114_L0.096370.798
32_S51_G0.095430.790
76_E107_N0.095330.789
46_G100_V0.095080.787
9_H111_T0.09490.785
56_I68_K0.094660.783
18_F46_G0.09460.783
71_A79_V0.094310.780
42_P89_E0.094170.779
69_E101_S0.09360.775
7_S26_T0.09330.772
52_F67_E0.093280.772
22_T45_E0.093220.771
25_Q42_P0.092940.769
50_S115_T0.092050.762
53_S62_E0.091450.757
63_G71_A0.09130.756
59_R104_I0.091060.754
73_Q104_I0.090960.753
24_T111_T0.090670.750
55_W58_G0.090640.750
56_I65_V0.090610.750
72_K102_V0.090580.750
50_S100_V0.089990.745
52_F98_F0.089840.743
12_V17_R0.089780.743
72_K87_L0.089740.743
33_E99_T0.089170.738
12_V115_T0.089050.737
7_S111_T0.089040.737
16_D52_F0.08890.736
13_T53_S0.088210.730
14_I116_Y0.088180.730
54_M86_A0.088170.730
28_E32_S0.0880.728
63_G67_E0.087640.725
55_W111_T0.087240.722
36_E89_E0.08710.721
25_Q41_F0.086970.720
62_E100_V0.086710.718
43_L100_V0.086670.717
93_P110_V0.086430.715
38_V68_K0.086220.714
49_I98_F0.086160.713
17_R102_V0.08610.713
7_S107_N0.08550.708
48_A112_I0.085030.704
41_F88_L0.08480.702
17_R44_P0.084540.700
51_G60_T0.084450.699
10_V44_P0.08440.698
54_M94_N0.084260.697
72_K107_N0.084160.696
16_D43_L0.084080.696
25_Q61_I0.084020.695
5_L8_V0.0840.695
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
4g2aA0.864497.30.771
3u9wA0.7881340.903
1w3fA0.983129.80.906
2x3cA0.788121.90.912
4eibA0.771221.50.912
3j26N0.898315.70.917
2j42A0.703413.80.919
3isyA0.720311.70.921
3tewA0.711910.90.922
2ia7A0.381410.80.922
If you are interested in a protein containing this domain,
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