GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF948 - Bacterial protein of unknown function (DUF948)
Pfam: PF06103 (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: 90
Sequences: 483
Seq/Len: 5.37
HH_delta: 0.784 (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_G6_A0.426283.587
31_V35_I0.244622.058
62_D66_K0.232211.954
71_D74_F0.216061.818
23_K29_D0.210661.773
30_E36_D0.187551.578
28_L31_V0.179551.511
15_I19_K0.17581.479
56_T60_L0.169261.424
5_I11_A0.163461.376
66_K74_F0.155911.312
53_L57_N0.152291.282
2_A6_A0.151471.275
35_I38_L0.148311.248
10_F14_V0.144131.213
10_F13_L0.143551.208
48_E54_H0.143191.205
78_A81_G0.141091.187
24_L38_L0.140111.179
10_F70_V0.139251.172
30_E61_E0.139221.172
33_K36_D0.138061.162
55_N61_E0.136241.146
64_N71_D0.134151.129
3_G77_V0.134021.128
23_K73_V0.133591.124
34_T39_Q0.133381.122
28_L32_N0.133131.120
34_T38_L0.132631.116
59_L74_F0.131531.107
20_V23_K0.13031.096
50_N53_L0.129941.093
58_E61_E0.127851.076
6_A10_F0.12631.063
66_K71_D0.126261.062
17_L42_V0.126091.061
9_A12_V0.125831.059
36_D61_E0.123871.042
28_L36_D0.123751.041
44_P48_E0.1211.018
2_A76_A0.120531.014
22_K26_K0.119041.002
46_T71_D0.118991.001
3_G14_V0.11740.988
26_K35_I0.11660.981
20_V60_L0.11450.964
60_L63_V0.11360.956
19_K35_I0.112830.949
54_H73_V0.111790.941
52_L55_N0.111780.941
56_T67_L0.111670.940
4_L65_E0.11010.926
55_N59_L0.109880.925
8_I22_K0.109730.923
40_E49_I0.109190.919
66_K81_G0.109050.918
7_A27_T0.108340.912
32_N45_I0.106140.893
51_D57_N0.106070.893
45_I75_E0.105780.890
47_K51_D0.105690.889
9_A14_V0.105610.889
5_I16_F0.105510.888
49_I52_L0.105490.888
24_L47_K0.10540.887
73_V81_G0.104660.881
5_I15_I0.104440.879
32_N67_L0.104420.879
31_V52_L0.104310.878
2_A7_A0.104250.877
21_L62_D0.103970.875
59_L63_V0.102480.862
74_F78_A0.102270.861
48_E55_N0.102070.859
33_K37_T0.102020.858
21_L77_V0.101720.856
68_E71_D0.10070.847
46_T67_L0.099950.841
57_N61_E0.09930.836
59_L64_N0.09890.832
22_K38_L0.098860.832
53_L61_E0.098680.830
29_D75_E0.098660.830
19_K23_K0.098590.830
60_L64_N0.09840.828
50_N70_V0.098290.827
21_L35_I0.097960.824
59_L78_A0.097360.819
34_T41_Q0.0970.816
27_T32_N0.096780.814
26_K77_V0.096460.812
29_D77_V0.096270.810
23_K28_L0.095820.806
35_I58_E0.09570.805
45_I82_E0.095660.805
14_V59_L0.095590.804
65_E69_K0.095550.804
18_I80_L0.095510.804
55_N76_A0.095210.801
37_T73_V0.09520.801
49_I75_E0.094960.799
17_L63_V0.094740.797
10_F23_K0.093780.789
26_K56_T0.09360.788
40_E43_D0.092950.782
4_L8_I0.092850.781
11_A14_V0.092750.780
31_V68_E0.092660.780
13_L16_F0.092560.779
21_L25_K0.09240.778
29_D33_K0.091270.768
10_F80_L0.090980.766
55_N72_P0.090880.765
72_P78_A0.090520.762
48_E57_N0.090230.759
16_F66_K0.090050.758
13_L81_G0.089990.757
35_I57_N0.08970.755
32_N75_E0.089150.750
38_L42_V0.088990.749
8_I51_D0.088780.747
57_N64_N0.088750.747
73_V77_V0.088640.746
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
2ch7A0.811177.10.784
2f95B0.966766.10.8
2f95B164.50.802
2ch7A0.888962.60.805
3g67A160.80.807
4gycB0.744451.20.817
3zx6A0.8333470.821
3p8qA0.777845.80.822
1qu7A0.788945.10.823
3g67A0.788945.10.823
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