GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LAB_N - Lipid A Biosynthesis N-terminal domain
Pfam: PF07578 (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: CL0141
Length: 72
Sequences: 1603
Seq/Len: 22.26
HH_delta: 0.873 (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
47_A55_F0.583782.510
18_I22_K0.581992.503
47_A56_I0.450491.937
19_Y23_A0.403651.736
48_I56_I0.400821.724
30_V34_Y0.363551.563
6_Q58_G0.359161.544
9_F39_G0.356091.531
28_V33_W0.321711.383
44_L48_I0.320741.379
40_S62_G0.320581.379
10_S62_G0.319731.375
44_L56_I0.316871.363
37_L63_L0.316441.361
44_L60_S0.316131.359
9_F12_R0.302031.299
5_G42_L0.301071.295
16_Q27_V0.296411.275
11_S15_V0.29261.258
61_F65_I0.290131.248
41_L45_I0.279651.203
20_S33_W0.26951.159
5_G43_L0.269031.157
3_F7_L0.26241.128
10_S13_F0.258071.110
46_Y50_R0.256631.104
10_S61_F0.246851.061
41_L63_L0.242021.041
45_I49_I0.236771.018
34_Y49_I0.23190.997
13_F20_S0.231690.996
43_L59_Q0.229370.986
6_Q29_P0.225810.971
10_S36_S0.221060.951
52_D62_G0.219220.943
4_I35_L0.218420.939
32_F62_G0.217120.934
35_L38_I0.216380.930
29_P33_W0.215750.928
31_A34_Y0.215260.926
11_S65_I0.214090.921
16_Q39_G0.212670.914
53_P56_I0.209630.901
15_V18_I0.209280.900
15_V19_Y0.207350.892
24_K57_L0.204660.880
43_L55_F0.20420.878
6_Q59_Q0.201540.867
18_I21_E0.200120.861
17_W65_I0.198840.855
31_A35_L0.198830.855
8_L11_S0.198270.853
13_F54_V0.198190.852
43_L47_A0.197850.851
21_E33_W0.197260.848
6_Q40_S0.19560.841
50_R56_I0.195270.840
39_G43_L0.194880.838
7_L51_K0.191550.824
38_I44_L0.191120.822
30_V61_F0.190940.821
23_A38_I0.188680.811
37_L48_I0.188610.811
58_G61_F0.188490.811
17_W33_W0.187610.807
30_V48_I0.186980.804
15_V35_L0.185020.796
26_S32_F0.183940.791
48_I60_S0.182190.783
17_W20_S0.181530.781
12_R39_G0.180570.776
49_I52_D0.180230.775
19_Y27_V0.179020.770
57_L60_S0.17780.765
11_S31_A0.176790.760
24_K38_I0.175720.756
17_W58_G0.175020.753
37_L40_S0.173160.745
13_F16_Q0.172870.743
9_F45_I0.172530.742
5_G61_F0.171680.738
58_G65_I0.167620.721
7_L64_F0.166880.718
45_I50_R0.16670.717
60_S64_F0.166480.716
26_S48_I0.16620.715
18_I54_V0.166070.714
35_L42_L0.165660.712
4_I45_I0.16510.710
6_Q17_W0.162720.700
52_D55_F0.162340.698
3_F65_I0.161890.696
44_L50_R0.161320.694
3_F57_L0.158820.683
9_F36_S0.157640.678
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:
PDB Cov Prob HH_delta
3o0rB0.3756.10.873
3ne5A0.41675.80.874
1xioA0.95832.80.89
4j4yA0.38892.70.892
4j4xA0.38892.60.893
3qrxB0.36112.20.896
3bzqA0.41672.20.896
2gw8A0.41672.10.897
2eg2A0.41671.90.899
2cfqA0.76391.90.899
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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