GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Vps39_2 - Vacuolar sorting protein 39 domain 2
Pfam: PF10367 (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. )
Length: 109
Sequences: 874
Seq/Len: 8.02
HH_delta: 0.691 (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
84_C103_H0.350263.017
103_H106_C0.33062.848
96_F100_H0.27812.395
84_C106_C0.274562.365
81_C84_C0.269682.323
98_C102_V0.201891.739
91_S105_S0.199591.719
102_V107_I0.191371.648
55_K58_N0.185141.595
95_V101_V0.179141.543
100_H103_H0.174061.499
25_P28_D0.167021.439
61_L64_E0.154361.330
46_E53_L0.147871.274
15_D18_K0.147511.271
101_V104_Y0.146621.263
64_E68_L0.146571.263
33_L51_K0.144691.246
93_F102_V0.144571.245
55_K62_K0.143341.235
12_D15_D0.139391.201
66_V69_R0.139221.199
42_N46_E0.137951.188
16_V31_D0.135851.170
88_L92_V0.135771.169
94_V104_Y0.135531.167
59_L66_V0.135481.167
14_I26_L0.135291.165
27_S39_K0.134181.156
11_L74_V0.134031.154
13_P32_F0.132661.143
98_C107_I0.131981.137
100_H107_I0.130611.125
46_E50_E0.130471.124
18_K26_L0.129011.111
81_C106_C0.126451.089
99_G105_S0.126081.086
33_L61_L0.125991.085
29_L50_E0.125711.083
58_N61_L0.124031.068
43_R46_E0.123811.066
73_V95_V0.122111.052
17_L58_N0.121971.051
89_G92_V0.12011.035
49_I53_L0.119611.030
91_S95_V0.11881.023
27_S50_E0.118091.017
31_D34_C0.117861.015
96_F107_I0.117781.015
38_R42_N0.116931.007
98_C103_H0.115570.995
80_K87_P0.115460.995
19_L36_S0.115250.993
71_R95_V0.114620.987
88_L94_V0.114290.984
96_F102_V0.114010.982
62_K69_R0.113830.980
18_K29_L0.113310.976
35_K49_I0.110760.954
37_L59_L0.110170.949
59_L63_Y0.109430.943
81_C103_H0.108660.936
26_L42_N0.108480.934
11_L22_D0.107760.928
21_P88_L0.10770.928
93_F105_S0.107060.922
45_R48_Q0.105120.905
62_K67_K0.104830.903
41_S48_Q0.104740.902
26_L41_S0.104450.900
25_P55_K0.103780.894
80_K88_L0.103490.891
44_K48_Q0.102310.881
25_P32_F0.101990.879
24_W90_N0.101850.877
34_C41_S0.101790.877
11_L19_L0.101720.876
87_P92_V0.100740.868
13_P37_L0.100180.863
41_S45_R0.099790.860
99_G103_H0.098440.848
46_E52_N0.097890.843
44_K68_L0.097730.842
94_V105_S0.097450.839
60_Q94_V0.096850.834
10_R65_L0.096590.832
10_R102_V0.096530.831
21_P26_L0.09640.830
82_S87_P0.09630.829
24_W42_N0.095950.826
53_L61_L0.095930.826
35_K45_R0.095790.825
53_L59_L0.095780.825
52_N60_Q0.095310.821
16_V25_P0.095170.820
17_L50_E0.094770.816
20_L23_D0.094680.816
23_D87_P0.094520.814
41_S44_K0.094110.811
17_L45_R0.093790.808
21_P75_I0.093520.806
44_K82_S0.092690.798
25_P46_E0.092590.798
50_E53_L0.092550.797
54_L58_N0.09240.796
46_E70_S0.092120.793
10_R42_N0.092030.793
38_R69_R0.09190.792
46_E49_I0.091720.790
29_L71_R0.091670.790
16_V20_L0.091450.788
53_L57_E0.091340.787
37_L61_L0.091220.786
54_L61_L0.091120.785
46_E57_E0.091060.784
18_K36_S0.090620.781
29_L32_F0.09020.777
80_K97_P0.090130.776
21_P70_S0.089660.772
43_R85_G0.089630.772
94_V101_V0.089380.770
22_D67_K0.088960.766
36_S46_E0.088840.765
34_C50_E0.088610.763
52_N96_F0.088510.762
25_P70_S0.08830.761
57_E77_E0.088110.759
85_G105_S0.0880.758
97_P101_V0.087870.757
22_D41_S0.087840.757
104_Y107_I0.087640.755
79_T86_K0.087470.753
9_S12_D0.087290.752
46_E63_Y0.086370.744
9_S19_L0.086140.742
27_S57_E0.085920.740
19_L29_L0.085370.735
89_G105_S0.085320.735
102_V105_S0.085270.734
87_P91_S0.085150.733
86_K105_S0.085090.733
11_L54_L0.084740.730
25_P29_L0.084640.729
33_L37_L0.08460.729
63_Y85_G0.084450.727
42_N75_I0.084050.724
92_V97_P0.084040.724
91_S97_P0.083870.722
93_F97_P0.083760.721
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
4aycA0.752397.50.691
2kizA0.4128970.719
2l0bA0.6514970.719
1v87A0.5138970.72
3ng2A0.376196.80.73
1chcA0.321196.80.73
3fl2A0.743196.60.735
2eclA0.42296.60.735
2ectA0.42296.60.735
2ecmA0.330396.60.736
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0342 seconds.