GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Vps51 - Vps51Vps67
Pfam: PF08700 (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: CL0295
Length: 87
Sequences: 624
Seq/Len: 7.17
HH_delta: 0.798 (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
6_F11_Y0.230141.899
35_I39_D0.223211.842
46_V60_I0.206911.707
29_N37_E0.195931.617
8_V12_F0.19281.591
49_N53_F0.192481.588
23_E30_K0.187431.547
20_S23_E0.18151.498
28_E32_R0.180241.487
44_K53_F0.159881.319
10_E15_L0.15921.314
8_V18_N0.158791.310
58_D64_E0.156311.290
47_Y56_A0.156111.288
68_S72_N0.152821.261
11_Y15_L0.148891.229
43_R49_N0.143571.185
72_N76_E0.143421.183
75_S79_Q0.142741.178
42_L53_F0.140291.158
26_Q33_Q0.140181.157
15_L46_V0.14011.156
14_D18_N0.13961.152
49_N52_D0.138311.141
68_S76_E0.138211.140
36_E42_L0.136051.123
72_N82_Q0.132861.096
5_N14_D0.132081.090
36_E39_D0.131071.082
16_L19_S0.130651.078
24_I41_E0.129471.068
57_S70_L0.128261.058
43_R56_A0.127941.056
25_R28_E0.12581.038
45_L63_M0.125191.033
51_R59_E0.124621.028
7_D10_E0.123691.021
38_K56_A0.123631.020
26_Q76_E0.122991.015
48_E65_N0.122881.014
5_N8_V0.122561.011
61_S74_L0.12221.008
56_A60_I0.122021.007
55_E61_S0.121611.003
43_R46_V0.12161.003
50_Y56_A0.121341.001
29_N41_E0.121261.001
65_N81_I0.119830.989
58_D63_M0.119590.987
46_V59_E0.118320.976
29_N36_E0.116330.960
14_D30_K0.116030.957
5_N40_E0.115290.951
59_E63_M0.114840.948
62_S81_I0.114790.947
76_E83_S0.114740.947
78_Q82_Q0.114180.942
16_L24_I0.113270.935
54_I64_E0.113160.934
25_R47_Y0.113110.933
51_R55_E0.112810.931
32_R42_L0.112770.931
50_Y57_S0.112570.929
47_Y52_D0.112450.928
19_S27_L0.112070.925
10_E72_N0.11180.923
24_I61_S0.111710.922
18_N37_E0.111370.919
21_I56_A0.109940.907
48_E51_R0.109660.905
70_L73_L0.109150.901
48_E52_D0.108560.896
24_I57_S0.108440.895
20_S77_L0.10740.886
47_Y60_I0.107030.883
11_Y19_S0.106770.881
34_E58_D0.106730.881
43_R47_Y0.105980.874
16_L51_R0.105860.874
38_K41_E0.104740.864
50_Y60_I0.104670.864
36_E79_Q0.104580.863
68_S71_R0.104510.862
29_N40_E0.104420.862
20_S36_E0.103320.853
69_E72_N0.101360.836
9_D14_D0.101310.836
45_L66_D0.101050.834
8_V14_D0.100810.832
69_E76_E0.099870.824
6_F26_Q0.099710.823
51_R57_S0.099410.820
48_E59_E0.099390.820
19_S65_N0.098790.815
45_L48_E0.098580.813
31_L57_S0.098330.811
26_Q75_S0.098260.811
25_R64_E0.098250.811
5_N10_E0.098080.809
39_D54_I0.097680.806
13_K17_K0.09720.802
51_R54_I0.096980.800
15_L19_S0.096810.799
40_E52_D0.095990.792
16_L23_E0.095940.792
78_Q83_S0.095610.789
53_F57_S0.095310.786
39_D46_V0.095180.785
38_K60_I0.095140.785
72_N75_S0.094770.782
40_E48_E0.094580.780
22_K72_N0.094550.780
32_R76_E0.093870.775
37_E48_E0.09320.769
76_E81_I0.093140.769
10_E18_N0.093040.768
26_Q54_I0.092980.767
43_R57_S0.092910.767
20_S27_L0.091830.758
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
2jqqA0.747166.40.798
3ghgA0.97755.40.81
1lwuB0.655246.30.82
1tohA0.873639.20.828
3errA0.747133.40.834
1lwuC0.632231.90.835
1ez3A0.827629.10.838
3t98B0.90827.90.84
1fzcB0.758626.60.841
3vkgA124.50.843
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