GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VirE - Virulence-associated protein E
Pfam: PF05272 (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: CL0023
Length: 198
Sequences: 3442
Seq/Len: 17.38
HH_delta: 0.547 (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_D74_P0.61163.150
95_G135_E0.519532.676
26_P74_P0.469472.418
155_D158_G0.447222.303
127_R134_P0.445932.297
92_Q99_V0.392072.019
54_V119_I0.384471.980
77_F99_V0.365691.883
69_F144_I0.35311.818
100_E146_T0.35021.804
69_F100_E0.347411.789
123_T135_E0.344731.775
90_L135_E0.338131.741
62_G160_R0.337011.736
116_K120_T0.308981.591
86_D93_L0.308011.586
157_T160_R0.306411.578
95_G139_R0.301631.553
127_R132_R0.299061.540
19_D25_D0.298571.538
66_S102_D0.294391.516
85_D129_P0.28531.469
86_D91_E0.283281.459
48_G139_R0.279191.438
116_K119_I0.278561.435
56_V145_G0.274881.416
26_P29_N0.270141.391
40_A44_A0.262551.352
76_Y80_S0.262071.350
79_D92_Q0.255051.314
40_A55_L0.254371.310
67_T70_R0.250431.290
149_D152_F0.244931.261
76_Y100_E0.240711.240
98_I144_I0.236231.217
36_W39_G0.231171.191
70_R121_R0.231171.191
43_R46_E0.230361.186
81_I85_D0.229191.180
86_D90_L0.226811.168
58_V149_D0.224661.157
154_K157_T0.221151.139
49_C139_R0.220951.138
103_E148_N0.215511.110
71_K74_P0.215021.107
87_K91_E0.21281.096
77_F84_F0.211461.089
88_D91_E0.210771.085
86_D89_F0.210081.082
28_Y31_Y0.209331.078
105_D113_E0.20791.071
82_N86_D0.207151.067
117_S120_T0.207081.066
58_V150_D0.206821.065
26_P30_R0.206821.065
52_D160_R0.205641.059
87_K93_L0.20531.057
27_E30_R0.205291.057
67_T71_K0.20461.054
69_F146_T0.203441.048
123_T136_E0.203211.047
125_T134_P0.203171.046
129_P132_R0.199971.030
39_G42_A0.199511.027
150_D158_G0.199381.027
126_Y137_F0.199111.025
24_E30_R0.198831.024
20_Y25_D0.198791.024
34_R37_L0.196021.010
56_V147_T0.195441.007
93_L135_E0.194951.004
38_V41_V0.194841.003
84_F107_L0.194441.001
57_L67_T0.193980.999
46_E98_I0.190190.979
72_L144_I0.189870.978
123_T138_P0.189290.975
26_P75_E0.188770.972
151_D155_D0.188530.971
52_D62_G0.186980.963
54_V101_L0.186720.962
125_T135_E0.186430.960
46_E49_C0.186420.960
32_V45_Y0.183870.947
45_Y124_D0.18360.946
25_D30_R0.181490.935
44_A142_V0.181460.935
103_E116_K0.180430.929
90_L93_L0.179750.926
44_A50_K0.178370.919
57_L72_L0.177520.914
82_N85_D0.176650.910
128_P135_E0.175340.903
111_D116_K0.17530.903
59_G65_K0.172890.890
107_L115_L0.172660.889
28_Y32_V0.171530.883
67_T117_S0.171290.882
79_D84_F0.171030.881
29_N32_V0.17060.879
131_G135_E0.167770.864
98_I142_V0.167720.864
61_Q159_N0.16730.862
43_R49_C0.165150.851
127_R133_D0.16440.847
92_Q127_R0.163970.844
27_E31_Y0.16370.843
148_N160_R0.163430.842
147_T150_D0.163220.841
77_F81_I0.162190.835
103_E146_T0.162020.834
31_Y35_K0.16170.833
25_D32_V0.161680.833
78_S82_N0.161240.830
24_E95_G0.161210.830
111_D120_T0.160760.828
114_A117_S0.160370.826
104_L145_G0.160.824
58_V147_T0.159810.823
113_E116_K0.159370.821
120_T127_R0.159310.820
93_L99_V0.158830.818
102_D115_L0.158290.815
40_A53_T0.158230.815
70_R74_P0.157710.812
156_P159_N0.157580.812
24_E27_E0.15730.810
27_E32_V0.157140.809
107_L112_V0.156720.807
83_D89_F0.155550.801
92_Q151_D0.155390.800
125_T136_E0.155370.800
76_Y82_N0.154870.798
77_F85_D0.154460.795
83_D86_D0.154190.794
88_D92_Q0.15360.791
153_L158_G0.153420.790
77_F80_S0.153210.789
124_D127_R0.152660.786
46_E52_D0.15260.786
48_G124_D0.152560.786
128_P137_F0.151920.782
152_F158_G0.15160.781
77_F92_Q0.151080.778
132_R139_R0.150620.776
61_Q120_T0.150580.775
127_R131_G0.150540.775
47_P50_K0.149980.772
62_G102_D0.149410.769
66_S146_T0.14930.769
70_R145_G0.149270.769
110_K114_A0.148520.765
48_G51_N0.148370.764
149_D155_D0.148210.763
114_A120_T0.148030.762
48_G52_D0.146920.757
39_G43_R0.146920.757
99_V127_R0.146580.755
25_D47_P0.145390.749
91_E127_R0.144980.747
148_N153_L0.144940.746
127_R135_E0.144890.746
126_Y129_P0.144550.744
104_L107_L0.144410.744
45_Y155_D0.144060.742
95_G133_D0.143590.739
91_E129_P0.143560.739
81_I101_L0.143130.737
99_V141_A0.1430.736
116_K155_D0.141460.729
94_Q97_W0.141180.727
20_Y74_P0.141010.726
64_G68_F0.140940.726
32_V74_P0.140750.725
26_P32_V0.139720.720
43_R72_L0.139010.716
71_K156_P0.138960.716
35_K39_G0.138420.713
122_R126_Y0.138220.712
45_Y49_C0.13790.710
61_Q148_N0.137570.708
25_D41_V0.137350.707
37_L68_F0.137330.707
35_K45_Y0.137220.707
24_E32_V0.136680.704
24_E29_N0.136260.702
114_A119_I0.13560.698
117_S126_Y0.135150.696
59_G64_G0.135050.696
66_S93_L0.134940.695
94_Q137_F0.13470.694
37_L72_L0.134640.693
56_V154_K0.134260.691
27_E60_K0.133890.690
127_R149_D0.133850.689
20_Y48_G0.133750.689
71_K85_D0.133630.688
106_G113_E0.132620.683
47_P109_K0.131510.677
111_D119_I0.13150.677
121_R129_P0.13140.677
62_G66_S0.13140.677
110_K117_S0.131070.675
50_K94_Q0.130840.674
114_A118_F0.130790.674
58_V100_E0.128740.663
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
1u0jA0.919299.50.547
4akgA0.939499.50.563
1tueA0.919299.50.563
3m6aA0.939499.40.571
3k1jA0.919299.40.586
3u61B0.823299.40.587
3pvsA0.828399.40.59
3f9vA0.964699.40.595
3pxiA0.924299.30.596
1xwiA0.868799.30.598
If you are interested in a protein containing this domain,
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