GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF234 - Archaea bacterial proteins of unknown function
Pfam: PF03008 (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: CL0236
Length: 100
Sequences: 495
Seq/Len: 4.95
HH_delta: 0.792 (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
4_F27_E0.312642.404
40_C87_C0.277582.135
37_E88_K0.250051.923
37_E86_E0.242351.864
8_N11_L0.238461.834
12_I20_V0.222251.709
62_R69_E0.219941.691
57_F60_I0.203811.567
12_I40_C0.198041.523
41_R60_I0.190621.466
48_N57_F0.189291.456
33_G88_K0.183641.412
2_F6_Y0.179281.379
1_W5_V0.177661.366
28_L32_M0.174381.341
41_R45_R0.170281.309
39_I43_Y0.169591.304
19_A23_K0.165991.276
4_F33_G0.165671.274
33_G37_E0.163861.260
12_I89_W0.162911.253
5_V24_I0.162431.249
40_C43_Y0.162121.247
61_G75_V0.161611.243
64_W69_E0.161171.239
29_N33_G0.160561.235
55_F74_A0.159971.230
29_N89_W0.148711.144
3_R31_Y0.147491.134
2_F66_K0.146611.127
36_F65_D0.146151.124
37_E69_E0.146071.123
26_P72_I0.145441.118
74_A83_L0.145041.115
76_D79_G0.144391.110
83_L89_W0.14291.099
17_G20_V0.140561.081
69_E88_K0.140411.080
63_W74_A0.137821.060
33_G86_E0.137741.059
13_E59_E0.137361.056
32_M35_A0.135811.044
9_R14_R0.135431.041
72_I85_G0.135011.038
10_S21_Y0.134531.035
45_R60_I0.131721.013
63_W68_E0.131421.011
1_W55_F0.129480.996
41_R72_I0.129270.994
3_R27_E0.127880.983
71_D88_K0.126650.974
8_N24_I0.126270.971
12_I17_G0.125490.965
10_S14_R0.124080.954
6_Y19_A0.123810.952
71_D86_E0.122770.944
47_L78_D0.122590.943
61_G70_I0.122440.942
69_E86_E0.121910.937
2_F90_T0.120720.928
48_N83_L0.120390.926
65_D85_G0.119960.923
54_P87_C0.119510.919
37_E64_W0.119380.918
31_Y35_A0.119340.918
57_F69_E0.119010.915
25_K46_R0.117410.903
73_V84_F0.117350.902
16_R20_V0.116990.900
1_W70_I0.116690.897
45_R84_F0.1160.892
77_E84_F0.115810.891
3_R8_N0.115030.885
16_R19_A0.114240.879
9_R19_A0.112730.867
16_R21_Y0.111790.860
41_R85_G0.111730.859
29_N60_I0.111570.858
72_I87_C0.110540.850
41_R49_R0.109550.842
4_F31_Y0.108250.832
20_V25_K0.108250.832
1_W22_E0.107910.830
36_F40_C0.106570.820
33_G71_D0.104750.806
36_F91_N0.104650.805
24_I32_M0.104310.802
14_R45_R0.104160.801
32_M89_W0.104060.800
40_C89_W0.103960.799
45_R72_I0.103360.795
63_W67_N0.10260.789
37_E71_D0.102580.789
21_Y65_D0.102260.786
3_R30_Q0.10220.786
87_C91_N0.101750.782
38_E42_E0.100910.776
27_E31_Y0.100340.772
18_E47_L0.100050.769
36_F89_W0.099950.769
38_E46_R0.099660.766
6_Y27_E0.099290.764
42_E54_P0.09820.755
38_E62_R0.098170.755
10_S24_I0.097420.749
4_F42_E0.097070.746
9_R16_R0.095980.738
58_S84_F0.095660.736
58_S76_D0.095560.735
36_F43_Y0.095440.734
2_F76_D0.094960.730
62_R84_F0.094460.726
28_L31_Y0.094270.725
78_D90_T0.093910.722
35_A47_L0.093840.722
48_N54_P0.093190.717
68_E89_W0.09280.714
1_W4_F0.092170.709
14_R23_K0.092140.709
16_R38_E0.092060.708
6_Y9_R0.091620.705
67_N91_N0.091620.705
75_V91_N0.091540.704
29_N74_A0.091420.703
74_A85_G0.091140.701
13_E86_E0.090920.699
72_I82_I0.09090.699
57_F84_F0.090710.698
65_D87_C0.09070.697
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
1gefA0.5796.60.792
3fovA0.8196.60.794
1y88A0.7396.50.794
1ob8A0.696.20.802
1hh1A0.6695.90.808
2eo0A0.6795.90.809
2wcwA0.6594.80.823
4f0qA0.9888.20.853
2vldA0.7879.20.868
1xmxA0.9370.80.877
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