GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FtsX - FtsX-like permease family
Pfam: PF02687 (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: CL0404
Length: 121
Sequences: 16394
Seq/Len: 135.49
HH_delta: 0.806 (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
30_I47_F1.754523.314
39_S42_Q1.447032.733
59_I98_F1.291692.440
26_R50_E1.247742.357
34_R40_K1.24642.354
110_L114_R1.107362.092
51_A109_S1.107162.091
44_R114_R1.106462.090
114_R118_K1.089772.059
90_S93_S1.014681.917
33_L38_A1.010851.910
33_L46_M0.988871.868
55_A105_S0.970991.834
58_G62_G0.943231.782
62_G66_G0.903691.707
19_I51_A0.82781.564
92_W96_I0.823721.556
68_L71_I0.819211.548
68_L72_F0.806291.523
38_A42_Q0.805271.521
71_I75_N0.798321.508
113_I117_L0.788731.490
42_Q45_K0.753871.424
55_A101_I0.752751.422
95_L99_I0.738411.395
26_R29_E0.721281.363
40_K117_L0.709211.340
55_A59_I0.708891.339
91_P95_L0.70541.333
7_L14_I0.681971.288
31_A35_A0.68081.286
27_R119_I0.666331.259
70_I87_F0.659781.246
41_R45_K0.655731.239
17_N21_S0.644611.218
92_W95_L0.641021.211
88_T91_P0.637031.203
24_R27_R0.637011.203
64_L68_L0.634821.199
59_I101_I0.632831.195
115_R119_I0.625881.182
45_K49_Y0.62391.179
70_I74_I0.605921.145
72_F76_F0.604641.142
30_I43_I0.600681.135
61_I64_L0.597591.129
7_L11_A0.589581.114
12_I108_A0.588811.112
10_I14_I0.572141.081
66_G70_I0.569141.075
63_I98_F0.562541.063
72_F75_N0.5561.050
108_A112_P0.551081.041
96_I99_I0.550661.040
60_L64_L0.545091.030
89_I94_F0.542511.025
59_I105_S0.534121.009
99_I103_L0.533861.008
16_F20_S0.530481.002
65_L68_L0.529371.000
44_R113_I0.526580.995
67_I94_F0.525420.993
55_A109_S0.523270.988
51_A105_S0.519620.982
49_Y53_L0.514690.972
57_I60_L0.512930.969
52_L106_I0.509790.963
26_R47_F0.506330.956
105_S108_A0.496930.939
67_I71_I0.493960.933
109_S113_I0.49040.926
28_R32_I0.48590.918
64_L67_I0.48390.914
88_T92_W0.478770.904
63_I94_F0.476070.899
93_S97_V0.472390.892
34_R43_I0.468080.884
71_I74_I0.466080.880
14_I17_N0.460330.870
56_L102_L0.458980.867
50_E53_L0.449550.849
44_R110_L0.449050.848
44_R117_L0.447590.846
67_I89_I0.446270.843
113_I116_I0.4420.835
103_L107_I0.438950.829
114_R117_L0.438610.829
40_K118_K0.436040.824
100_I103_L0.434550.821
14_I33_L0.432510.817
96_I100_I0.430590.813
51_A55_A0.425550.804
14_I21_S0.423390.800
17_N20_S0.417760.789
32_I35_A0.417690.789
59_I63_I0.417680.789
98_F102_L0.41520.784
23_I30_I0.410840.776
29_E33_L0.410490.775
23_I116_I0.409760.774
97_V101_I0.408980.773
74_I86_P0.407250.769
65_L69_L0.406230.767
29_E32_I0.405490.766
111_I114_R0.405260.766
100_I104_I0.403670.763
112_P116_I0.401110.758
49_Y52_L0.394190.745
29_E50_E0.39380.744
19_I22_S0.390920.738
63_I67_I0.390650.738
38_A43_I0.389350.735
53_L57_I0.387450.732
102_L106_I0.387120.731
115_R118_K0.386720.731
111_I115_R0.386670.730
12_I104_I0.386250.730
56_L59_I0.385230.728
48_L106_I0.378020.714
89_I92_W0.372320.703
22_S26_R0.372190.703
16_F108_A0.371950.703
18_I22_S0.371390.702
101_I105_S0.368720.697
70_I73_L0.367320.694
93_S96_I0.361750.683
84_S88_T0.360940.682
11_A101_I0.35980.680
89_I93_S0.358930.678
4_S7_L0.358660.678
27_R115_R0.358550.677
24_R115_R0.357030.674
19_I23_I0.356670.674
40_K44_R0.355180.671
46_M49_Y0.35470.670
21_S25_E0.353210.667
94_F98_F0.350440.662
16_F111_I0.349810.661
48_L52_L0.348270.658
16_F24_R0.34360.649
23_I47_F0.34330.649
18_I23_I0.339780.642
5_V9_L0.33960.642
41_R44_R0.33890.640
35_A112_P0.338370.639
18_I46_M0.329180.622
44_R48_L0.325320.615
18_I33_L0.324190.612
59_I102_L0.323370.611
60_L98_F0.321360.607
34_R38_A0.320710.606
53_L56_L0.317820.600
117_L120_N0.316220.597
20_S24_R0.315590.596
20_S25_E0.314920.595
102_L105_S0.31350.592
33_L36_L0.311270.588
91_P94_F0.309650.585
11_A14_I0.308660.583
4_S8_L0.306920.580
51_A108_A0.302540.572
107_I111_I0.301750.570
10_I18_I0.299260.565
101_I108_A0.297940.563
35_A46_M0.297510.562
48_L110_L0.297460.562
47_F50_E0.297180.561
45_K52_L0.296520.560
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
3tuiA153.50.806
3rlfF0.991718.30.847
3rlfG110.40.862
4il3A0.91747.50.87
2onkC0.98355.80.876
4aw6A0.91745.20.878
4he8L0.92565.20.879
3d31C0.98354.70.881
4av3A0.78513.80.886
4humA0.88433.60.888
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0359 seconds.