GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Flagellin_C - Bacterial flagellin C-terminal helical region
Pfam: PF00700 (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: 86
Sequences: 2589
Seq/Len: 30.1
HH_delta: -0.082 (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
43_L47_E1.056523.809
44_S48_D0.984313.549
53_E57_N0.823072.967
49_A54_A0.783592.825
14_A17_Q0.61972.234
65_L69_L0.546011.968
36_S40_T0.519511.873
59_T62_Q0.51031.840
6_N10_Q0.469491.693
78_L84_N0.453241.634
17_Q21_R0.443921.600
58_L62_Q0.439241.584
28_A32_L0.430741.553
35_Q39_L0.429051.547
30_D33_S0.424581.531
41_A45_N0.405631.462
57_N61_A0.401131.446
69_L81_S0.400991.446
2_D6_N0.395191.425
70_S74_Q0.383991.384
69_L72_T0.369221.331
33_S36_S0.363871.312
5_D9_D0.36171.304
9_D13_S0.360561.300
34_N37_E0.358221.291
3_K6_N0.349721.261
78_L81_S0.342241.234
55_I58_L0.339921.225
55_I59_T0.334251.205
62_Q66_Q0.329961.190
8_I12_S0.326911.179
51_M55_I0.324491.170
81_S84_N0.313771.131
40_T43_L0.311881.124
37_E41_A0.309291.115
10_Q13_S0.298471.076
5_D8_I0.28721.035
60_Q64_Q0.280681.012
6_N9_D0.276180.996
57_N60_Q0.274790.991
39_L42_S0.271940.980
9_D12_S0.271860.980
54_A57_N0.271860.980
65_L78_L0.270780.976
39_L43_L0.262770.947
34_N38_N0.259170.934
21_R28_A0.25630.924
69_L78_L0.254730.918
10_Q14_A0.254350.917
33_S37_E0.251870.908
20_A23_N0.24810.894
6_N17_Q0.247080.891
28_A31_R0.245240.884
72_T76_N0.242060.873
72_T83_L0.241140.869
12_S16_A0.239670.864
13_S34_N0.237130.855
51_M82_L0.2370.854
22_Q26_E0.236080.851
76_N85_Y0.229690.828
13_S21_R0.229060.826
7_A14_A0.226890.818
70_S73_A0.226810.818
29_K33_S0.224410.809
64_Q67_A0.224230.808
68_A71_A0.221650.799
77_Q84_N0.220520.795
31_R63_T0.218630.788
6_N13_S0.215130.776
7_A10_Q0.210190.758
42_S46_I0.207020.746
2_D5_D0.204580.738
2_D17_Q0.20380.735
13_S53_E0.201440.726
15_R64_Q0.200990.725
65_L68_A0.20030.722
62_Q70_S0.199750.720
73_A86_L0.198280.715
62_Q74_Q0.198150.714
67_A86_L0.198150.714
58_L65_L0.197560.712
26_E30_D0.19720.711
30_D73_A0.195950.706
15_R52_A0.195780.706
31_R35_Q0.194750.702
49_A69_L0.194260.700
29_K32_L0.193760.699
13_S17_Q0.192080.692
19_G48_D0.192070.692
12_S58_L0.190690.687
59_T63_T0.18860.680
67_A70_S0.185980.670
48_D51_M0.185140.667
1_I5_D0.183970.663
31_R46_I0.183490.662
33_S53_E0.183460.661
57_N65_L0.182980.660
31_R34_N0.179730.648
14_A21_R0.179410.647
72_T85_Y0.179320.646
16_A20_A0.179010.645
24_R32_L0.178910.645
68_A72_T0.177960.642
18_L22_Q0.177760.641
21_R33_S0.176610.637
56_T68_A0.175980.634
24_R45_N0.175870.634
27_S30_D0.175780.634
9_D14_A0.174290.628
56_T59_T0.174110.628
14_A31_R0.17410.628
83_L86_L0.173180.624
9_D57_N0.172990.624
71_A74_Q0.172840.623
69_L82_L0.1720.620
73_A77_Q0.171330.618
2_D30_D0.170780.616
3_K9_D0.17030.614
2_D13_S0.169510.611
37_E44_S0.169480.611
71_A81_S0.169260.610
21_R75_I0.167330.603
60_Q71_A0.166840.601
25_L29_K0.165550.597
77_Q81_S0.164770.594
1_I41_A0.164470.593
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
1ucuA199.7-0.082
2d4xA0.627998.70.366
3pwxA0.697798.40.431
3v47C0.558198.30.451
1oryB0.627998.20.461
1io1A0.5980.504
3k8wA0.581497.10.599
2d4yA0.697755.40.801
4dndA0.558111.50.857
3a69A0.95358.30.865

Page generated in 0.0225 seconds.