GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TonB_C - Gram-negative bacterial TonB protein C-terminal
Pfam: PF03544 (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: CL0428
Length: 79
Sequences: 4014
Seq/Len: 50.81
HH_delta: -0.017 (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
38_S45_D1.271892.485
25_D31_S1.208022.360
25_D29_R1.149272.246
21_E34_R1.097522.144
21_E70_T1.067512.086
23_T32_D1.003981.962
47_A50_R0.977761.910
49_L53_K0.941511.840
33_V49_L0.906971.772
23_T70_T0.898861.756
25_D68_K0.882731.725
21_E36_I0.854451.670
21_E72_T0.825621.613
40_G45_D0.801081.565
61_P66_P0.796921.557
17_T76_R0.787851.539
33_V53_K0.782941.530
39_S45_D0.779711.523
19_V37_Q0.751351.468
14_I43_I0.743671.453
20_V52_V0.727081.421
26_P68_K0.721971.411
3_P51_A0.712691.393
19_V74_P0.692191.352
14_I41_P0.688531.345
30_V33_V0.683261.335
9_A43_I0.682061.333
8_E12_R0.661531.293
17_T74_P0.659751.289
29_R56_R0.644091.258
58_K61_P0.631441.234
20_V48_A0.624551.220
19_V72_T0.615971.204
35_V45_D0.605241.183
48_A77_F0.594571.162
7_E11_R0.587491.148
7_E10_R0.586461.146
3_P55_W0.571691.117
24_I57_F0.570851.115
36_I72_T0.564421.103
18_V35_V0.560741.096
60_A69_V0.560151.094
9_A14_I0.559761.094
39_S44_L0.546411.068
35_V49_L0.541361.058
71_Y74_P0.538511.052
64_G67_V0.537061.049
23_T68_K0.530481.037
31_S68_K0.528511.033
22_F33_V0.517691.012
33_V52_V0.510770.998
8_E43_I0.500260.977
6_P9_A0.48610.950
16_G44_L0.477910.934
19_V36_I0.475360.929
47_A51_A0.472150.923
15_E78_K0.458240.895
22_F52_V0.450450.880
50_R54_K0.442710.865
22_F73_V0.440720.861
42_P46_E0.434770.850
30_V57_F0.427670.836
60_A64_G0.42560.832
62_K65_K0.423420.827
20_V35_V0.409570.800
52_V55_W0.394360.771
18_V48_A0.391960.766
51_A75_I0.37790.738
51_A55_W0.375030.733
60_A67_V0.372540.728
46_E49_L0.370450.724
14_I40_G0.368920.721
46_E50_R0.368040.719
61_P64_G0.367330.718
5_Y9_A0.363570.710
5_Y16_G0.351740.687
52_V73_V0.351030.686
37_Q45_D0.347090.678
5_Y44_L0.341810.668
24_I60_A0.32570.636
10_R13_G0.315730.617
55_W75_I0.313030.612
5_Y14_I0.311160.608
17_T37_Q0.310770.607
55_W73_V0.306290.598
5_Y15_E0.304480.595
8_E42_P0.303560.593
35_V38_S0.302540.591
45_D49_L0.302490.591
23_T31_S0.30230.591
24_I28_G0.290920.568
24_I69_V0.286060.559
20_V33_V0.283840.555
39_S42_P0.28140.550
4_V7_E0.279640.546
9_A13_G0.278290.544
18_V45_D0.276410.540
9_A15_E0.275810.539
4_V47_A0.271070.530
57_F60_A0.264260.516
18_V39_S0.257940.504
48_A75_I0.25220.493
60_A66_P0.251720.492
38_S42_P0.250870.490
30_V55_W0.248820.486
59_P64_G0.242570.474
19_V54_K0.240320.470
6_P47_A0.23920.467
24_I58_K0.237810.465
6_P44_L0.237540.464
59_P62_K0.237440.464
12_R71_Y0.236760.463
24_I67_V0.236390.462
13_G16_G0.235730.461
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
2k9kA199.5-0.017
2m2kA199.30.051
2grxC0.936799.30.058
1u07A0.936799.20.098
1lr0A0.96298.70.295
1tolA0.911498.10.417
4g7xB0.949497.70.487
3dczA0.9747360.8
3a7rA0.96225.70.813
2yizA0.6709250.814

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