GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
YajC - Preprotein translocase subunit
Pfam: PF02699 (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: 82
Sequences: 1525
Seq/Len: 18.6
HH_delta: 0.58 (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
65_I71_I0.882592.580
30_H34_L0.866612.533
5_L9_V0.762512.229
32_E36_S0.753522.202
50_Y74_E0.71272.083
29_E32_E0.69332.026
49_I71_I0.686752.007
62_V70_E0.61581.800
15_F19_M0.575331.682
32_E35_A0.568931.663
24_K28_K0.552481.615
25_K29_E0.537571.571
37_L53_V0.521341.524
8_L12_F0.520411.521
33_M81_V0.518261.515
50_Y60_T0.516631.510
43_V63_L0.512921.499
14_I18_L0.511341.495
46_I77_A0.487341.424
49_I65_I0.483791.414
66_A69_V0.481341.407
26_Q29_E0.480251.404
27_Q31_Q0.468971.371
56_I75_K0.46561.361
21_R25_K0.453951.327
16_Y22_P0.453361.325
62_V72_T0.439541.285
31_Q35_A0.435431.273
10_I13_V0.43111.260
4_M8_L0.424691.241
8_L11_I0.414891.213
54_V70_E0.410951.201
42_E52_T0.410361.199
49_I73_V0.404831.183
26_Q30_H0.404141.181
33_M36_S0.402711.177
6_I10_I0.390761.142
61_V78_I0.38951.138
57_D72_T0.386071.128
16_Y20_I0.384081.123
64_E67_P0.362651.060
12_F20_I0.356471.042
11_I15_F0.351771.028
7_P10_I0.34671.013
37_L78_I0.344761.008
19_M24_K0.343131.003
4_M10_I0.334170.977
17_F21_R0.333890.976
45_T63_L0.327150.956
38_K41_D0.325920.953
12_F15_F0.324710.949
50_Y55_E0.320.935
60_T72_T0.319870.935
65_I69_V0.319090.933
50_Y72_T0.319040.933
4_M7_P0.318930.932
23_Q27_Q0.310680.908
20_I24_K0.309910.906
51_G63_L0.305620.893
44_V50_Y0.300540.878
64_E68_G0.298360.872
52_T64_E0.293920.859
55_E62_V0.292570.855
74_E77_A0.290150.848
9_V12_F0.287930.842
58_D75_K0.284460.831
9_V13_V0.280580.820
10_I14_I0.278790.815
45_T73_V0.276440.808
3_S7_P0.275340.805
60_T74_E0.272170.796
5_L8_L0.270110.790
13_V17_F0.264430.773
3_S6_I0.263330.770
39_P55_E0.263290.770
42_E74_E0.254850.745
65_I73_V0.250730.733
24_K27_Q0.249820.730
34_L80_R0.24730.723
61_V81_V0.24130.705
23_Q30_H0.230720.674
53_V61_V0.227560.665
34_L76_S0.224330.656
42_E60_T0.224210.655
38_K81_V0.223850.654
64_E72_T0.220820.645
63_L73_V0.218040.637
22_P28_K0.217730.636
7_P12_F0.217110.635
23_Q26_Q0.214710.628
54_V62_V0.213410.624
46_I79_A0.208680.610
39_P54_V0.20780.607
51_G71_I0.207170.606
64_E69_V0.206220.603
53_V56_I0.205460.601
68_G76_S0.20530.600
43_V78_I0.201280.588
19_M22_P0.201080.588
45_T78_I0.20030.585
55_E70_E0.199350.583
66_A71_I0.198260.580
22_P33_M0.196260.574
7_P11_I0.1960.573
15_F22_P0.194580.569
47_G73_V0.193820.567
74_E80_R0.193720.566
21_R24_K0.19130.559
17_F23_Q0.191170.559
62_V67_P0.191160.559
42_E50_Y0.190920.558
51_G73_V0.187790.549
31_Q34_L0.187280.547
28_K32_E0.186050.544
6_I13_V0.185820.543
54_V75_K0.183770.537
64_E70_E0.183070.535
8_L15_F0.181750.531
60_T63_L0.181050.529
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
2rddB0.43998.90.58
3udcA0.914683.10.849
2e6zA0.634178.20.856
2vv5A0.914673.30.862
2jwaA0.341570.80.864
4hw9A0.914670.60.864
1dbgA0.963466.60.867
2l2tA0.3537640.87
2ks1B0.341560.30.872
2j5uA0.890257.90.874
If you are interested in a protein containing this domain,
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