GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF883 - Bacterial protein of unknown function (DUF883)
Pfam: PF05957 (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: CL0406
Length: 94
Sequences: 820
Seq/Len: 8.72
HH_delta: 0.764 (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
69_V76_S0.294092.129
82_G86_L0.283132.050
80_A84_G0.281042.034
69_V77_V0.269571.951
66_E70_R0.266321.928
77_V81_A0.221131.601
72_N75_Q0.212271.537
55_R59_R0.21121.529
13_D24_L0.203081.470
88_G92_R0.192751.395
10_L17_L0.189431.371
76_S80_A0.185971.346
29_A33_R0.18391.331
7_L11_R0.179461.299
77_V92_R0.179121.297
68_Y74_W0.17851.292
69_V72_N0.177251.283
11_R21_A0.169891.230
18_A21_A0.169011.223
49_D56_E0.168851.222
19_R22_A0.166471.205
83_V91_L0.164611.192
65_T68_Y0.162081.173
43_A67_D0.161791.171
57_Q65_T0.161021.166
6_E10_L0.160561.162
70_R78_G0.160481.162
85_F88_G0.158171.145
68_Y75_Q0.157021.137
72_N85_F0.155961.129
33_R44_R0.15441.118
52_D79_I0.152351.103
69_V73_P0.151541.097
51_A54_A0.150461.089
15_E18_A0.150241.088
5_A8_E0.148041.072
73_P80_A0.147721.069
34_D38_E0.146861.063
36_A41_D0.146321.059
70_R74_W0.145211.051
71_E82_G0.144561.046
30_D77_V0.144271.044
51_A56_E0.143851.041
65_T92_R0.14181.026
66_E74_W0.141291.023
25_A29_A0.141111.021
73_P76_S0.140041.014
36_A50_A0.139891.013
7_L19_R0.139731.012
28_K31_E0.138891.005
34_D87_L0.137270.994
23_D31_E0.134770.976
6_E19_R0.134660.975
24_L32_A0.134390.973
18_A74_W0.13240.958
6_E13_D0.131940.955
31_E35_R0.131610.953
85_F91_L0.130140.942
81_A89_L0.129730.939
89_L92_R0.129580.938
16_D20_S0.129410.937
6_E18_A0.129250.936
36_A80_A0.12820.928
14_L21_A0.126710.917
86_L91_L0.126180.913
16_D54_A0.12570.910
47_A51_A0.125680.910
79_I83_V0.125670.910
30_D37_E0.125450.908
41_D44_R0.125280.907
6_E59_R0.125130.906
67_D87_L0.124190.899
30_D38_E0.122580.887
36_A44_R0.121760.881
52_D56_E0.121260.878
54_A80_A0.120620.873
26_G79_I0.120220.870
9_Q52_D0.120210.870
51_A78_G0.120080.869
58_A72_N0.119950.868
36_A39_A0.119870.868
13_D17_L0.118230.856
29_A87_L0.117460.850
62_A85_F0.117260.849
45_D83_V0.115660.837
23_D45_D0.115470.836
26_G30_D0.115410.835
38_E53_Q0.115360.835
14_L17_L0.115120.833
29_A40_L0.114850.831
55_R58_A0.114550.829
70_R77_V0.114140.826
46_R72_N0.114110.826
9_Q48_E0.113970.825
24_L28_K0.113440.821
54_A58_A0.113020.818
53_Q57_Q0.112990.818
32_A44_R0.112810.817
10_L89_L0.112780.816
7_L36_A0.112490.814
80_A85_F0.112380.814
26_G33_R0.112160.812
5_A9_Q0.111960.810
74_W88_G0.11080.802
11_R18_A0.110670.801
45_D48_E0.109590.793
62_A92_R0.109310.791
26_G75_Q0.10930.791
22_A29_A0.107790.780
12_A78_G0.107610.779
42_D46_R0.107050.775
44_R71_E0.106960.774
15_E69_V0.106930.774
56_E60_E0.106620.772
35_R60_E0.106010.767
74_W90_L0.105980.767
23_D64_Q0.105510.764
34_D63_E0.105410.763
47_A62_A0.104640.757
69_V74_W0.104060.753
35_R48_E0.103760.751
46_R49_D0.103680.751
76_S81_A0.103580.750
27_E56_E0.103520.749
47_A64_Q0.102910.745
36_A42_D0.102830.744
5_A43_A0.102460.742
29_A37_E0.102210.740
8_E12_A0.102050.739
11_R36_A0.10190.738
22_A25_A0.101730.736
72_N79_I0.101480.735
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
1gs9A0.797987.50.764
2a01A0.76686.50.767
3r2pA0.723486.10.769
1nfnA0.840483.10.777
2l7bA0.744782.20.779
1gs9A0.680981.40.781
1nfnA0.723475.80.791
2a01A0.88374.10.794
2lemA0.787270.60.799
2l7bA0.861767.60.803
If you are interested in a protein containing this domain,
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