GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gemini_C4 - Geminivirus C4 protein
Pfam: PF01492 (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: 85
Sequences: 462
Seq/Len: 5.44
HH_delta: 0.893 (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
3_N6_S0.492522.818
53_R60_N0.423012.420
15_N18_A0.393752.253
2_G9_S0.307611.760
70_L75_N0.290281.661
59_S64_S0.284021.625
69_D75_N0.272991.562
74_V77_Q0.270051.545
82_T85_H0.266971.528
53_R58_P0.258041.476
71_L74_V0.251161.437
70_L77_Q0.247891.418
77_Q81_L0.243721.395
52_S62_E0.232591.331
59_S72_E0.224841.286
18_A23_S0.217421.244
69_D77_Q0.216991.242
6_S9_S0.216951.241
71_L82_T0.215541.233
19_R23_S0.215051.230
80_T84_R0.213031.219
33_H37_R0.21041.204
4_L9_S0.208381.192
70_L73_E0.206841.183
74_V82_T0.205651.177
54_R74_V0.204261.169
75_N82_T0.202691.160
43_N46_P0.19731.129
16_S23_S0.19661.125
73_E84_R0.19611.122
32_Q36_I0.194781.114
9_S56_E0.194281.112
3_N80_T0.189651.085
34_I37_R0.1891.081
34_I39_F0.187031.070
76_R82_T0.185261.060
31_G34_I0.183961.053
67_M75_N0.182551.045
11_N44_P0.182471.044
12_S69_D0.182271.043
32_Q37_R0.179761.029
71_L84_R0.17521.002
3_N27_Y0.175091.002
81_L85_H0.174330.997
54_R60_N0.17420.997
45_A61_G0.173990.996
11_N52_S0.173880.995
73_E82_T0.173450.992
16_S55_T0.172770.989
63_N73_E0.172760.988
29_Q39_F0.170740.977
21_T54_R0.168110.962
26_W29_Q0.167030.956
18_A21_T0.166790.954
17_S51_T0.166540.953
20_I26_W0.166480.953
21_T30_P0.165870.949
41_E46_P0.161860.926
7_M52_S0.161730.925
71_L81_L0.160710.920
27_Y30_P0.160260.917
20_I27_Y0.159980.915
49_S61_G0.157090.899
58_P74_V0.157090.899
63_N68_E0.156490.895
22_D84_R0.156390.895
70_L80_T0.154450.884
4_L12_S0.154290.883
72_E85_H0.153940.881
6_S62_E0.150420.861
33_H36_I0.149380.855
71_L80_T0.149210.854
27_Y33_H0.148950.852
52_S85_H0.148430.849
58_P61_G0.147880.846
28_P33_H0.14710.842
67_M85_H0.146770.840
32_Q35_S0.14670.839
68_E81_L0.14630.837
2_G10_S0.146260.837
49_S58_P0.145930.835
25_T31_G0.145530.833
67_M71_L0.145310.831
22_D65_R0.142220.814
6_S84_R0.1420.812
39_F44_P0.141710.811
64_S68_E0.140430.804
5_I8_C0.139830.800
20_I28_P0.138830.794
30_P43_N0.138570.793
22_D29_Q0.138440.792
22_D25_T0.13540.775
56_E60_N0.133560.764
77_Q82_T0.133280.763
54_R76_R0.132780.760
41_E49_S0.132510.758
25_T29_Q0.130790.748
2_G7_M0.130480.747
41_E45_A0.129650.742
59_S65_R0.129430.741
27_Y47_T0.129270.740
20_I85_H0.129220.739
26_W38_T0.128250.734
19_R68_E0.127870.732
10_S17_S0.127560.730
8_C19_R0.127330.729
48_S84_R0.126790.725
49_S70_L0.126110.722
14_G29_Q0.125150.716
75_N81_L0.124720.714
1_M12_S0.124580.713
56_E70_L0.124420.712
31_G40_R0.12360.707
44_P67_M0.123370.706
10_S39_F0.123070.704
58_P63_N0.122390.700
64_S69_D0.121940.698
2_G41_E0.121520.695
25_T81_L0.120910.692
14_G76_R0.120340.689
3_N51_T0.119980.687
33_H42_L0.119860.686
48_S51_T0.119270.682
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
1l2mA0.879.30.893
1m48A0.447116.70.93
4elnA19.60.937
3rvcA0.35293.80.947
1nh1A0.74123.70.947
3d6rB0.42353.40.948
1knvA0.341230.949
3o0gD0.54122.90.95
2pbyA0.41182.50.951
1mkiA0.41182.50.951
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