GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FliO - Flagellar biosynthesis protein FliO
Pfam: PF04347 (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: 84
Sequences: 384
Seq/Len: 4.57
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_T51_I0.323592.570
36_E39_G0.302992.406
40_R56_E0.27562.189
26_L44_L0.265132.106
18_I24_L0.262292.083
33_V46_V0.219281.742
74_F78_L0.218071.732
36_E41_Y0.207611.649
32_L35_V0.199541.585
35_V44_L0.187891.492
30_K48_D0.186741.483
32_L43_L0.184231.463
26_L32_L0.183381.456
42_L55_A0.183371.456
27_G45_G0.17271.372
47_T50_G0.169711.348
45_G54_L0.15581.237
2_W5_R0.154021.223
41_Y57_L0.152341.210
32_L44_L0.149461.187
18_I34_L0.149021.184
26_L53_L0.144341.146
40_R55_A0.142061.128
23_R48_D0.14191.127
40_R57_L0.139631.109
5_R75_A0.138471.100
44_L47_T0.136631.085
19_K24_L0.135471.076
45_G51_I0.135391.075
20_V52_T0.135381.075
4_L7_L0.135361.075
5_R30_K0.135331.075
58_D61_E0.133871.063
8_G42_L0.133331.059
77_V81_A0.132741.054
53_L56_E0.132321.051
5_R29_K0.131571.045
42_L53_L0.131421.044
32_L47_T0.129371.027
24_L54_L0.129281.027
22_E77_V0.126051.001
27_G51_I0.125590.997
41_Y60_A0.124770.991
9_G16_R0.124470.989
4_L9_G0.123080.978
38_G43_L0.122880.976
77_V80_K0.122480.973
31_S55_A0.122460.973
34_L79_K0.121330.964
57_L81_A0.120280.955
19_K36_E0.120260.955
19_K68_S0.118870.944
73_P76_S0.11850.941
64_E73_P0.116720.927
14_G19_K0.116610.926
21_V41_Y0.116570.926
28_P35_V0.115190.915
25_P75_A0.113930.905
33_V44_L0.113850.904
7_L10_G0.1130.897
40_R81_A0.112550.894
29_K43_L0.11190.889
57_L76_S0.110430.877
38_G79_K0.11030.876
1_A4_L0.108590.862
38_G41_Y0.105970.842
5_R60_A0.105630.839
12_R50_G0.105570.838
63_E67_A0.103980.826
13_S68_S0.103930.825
9_G21_V0.103260.820
21_V34_L0.103130.819
18_I60_A0.101970.810
27_G46_V0.101250.804
27_G31_S0.099910.793
31_S48_D0.099750.792
15_G22_E0.099520.790
48_D78_L0.098820.785
27_G30_K0.098810.785
9_G12_R0.098010.778
65_D69_S0.097790.777
28_P73_P0.097640.775
9_G18_I0.09760.775
22_E32_L0.097230.772
46_V51_I0.097220.772
59_P62_E0.096820.769
15_G81_A0.096810.769
65_D77_V0.096680.768
13_S61_E0.096270.765
11_R36_E0.096240.764
5_R50_G0.095730.760
4_L8_G0.09550.758
1_A79_K0.094760.753
61_E80_K0.094620.751
18_I39_G0.094460.750
5_R31_S0.094210.748
42_L54_L0.093470.742
7_L51_I0.093260.741
63_E82_L0.093240.741
13_S66_S0.093090.739
37_V41_Y0.093090.739
50_G67_A0.092910.738
14_G82_L0.092660.736
27_G36_E0.092230.733
67_A82_L0.091990.731
3_L67_A0.091790.729
21_V36_E0.091620.728
65_D68_S0.091450.726
28_P69_S0.09050.719
3_L52_T0.089790.713
21_V73_P0.089680.712
61_E64_E0.089570.711
65_D73_P0.0890.707
40_R59_P0.088950.706
26_L47_T0.088880.706
30_K41_Y0.08790.698
8_G36_E0.087440.694
9_G42_L0.087250.693
13_S79_K0.087250.693
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
2nvvA128.70.873
3vpzA0.738122.60.879
3eh7A0.940520.80.881
2g39A118.30.883
3p9dH0.845217.70.885
3e19A0.63117.50.885
3rtkA0.8095170.885
2qgmA0.952416.10.886
2h3gX0.583315.30.888
2h1vA0.916714.70.888
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