GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
T2SS-T3SS_pil_N - Pilus formation protein N terminal region
Pfam: PF13629 (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: CL0159
Length: 72
Sequences: 626
Seq/Len: 8.69
HH_delta: 0.634 (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
27_G52_T0.577213.585
33_D47_K0.42452.636
23_R57_W0.416042.584
7_L46_G0.40342.505
25_A57_W0.296571.842
28_D48_K0.294281.828
30_E48_K0.272481.692
12_S43_Y0.246831.533
19_G58_D0.244371.518
17_L21_I0.240271.492
35_T45_T0.223531.388
17_L56_V0.220651.370
11_Q68_D0.21521.336
10_G28_D0.214581.333
24_V36_V0.204561.270
58_D64_I0.199941.242
34_V38_S0.194411.207
11_Q43_Y0.193941.204
32_A44_I0.191311.188
23_R41_E0.185411.151
11_Q14_I0.183431.139
32_A46_G0.176811.098
41_E57_W0.167081.038
7_L35_T0.166411.033
19_G62_R0.164591.022
20_P40_N0.162981.012
17_L65_Q0.160020.994
42_V55_I0.159480.990
7_L71_V0.158880.987
13_R68_D0.156570.972
5_L44_I0.156050.969
26_V52_T0.155970.969
23_R37_L0.154760.961
58_D62_R0.152070.944
27_G53_T0.150290.933
54_L69_V0.149880.931
5_L65_Q0.149810.930
15_L69_V0.147480.916
31_I39_P0.146960.913
28_D52_T0.146810.912
6_T13_R0.14620.908
12_S45_T0.143420.891
12_S31_I0.14270.886
12_S64_I0.141490.879
25_A43_Y0.141480.879
4_S61_G0.141150.877
23_R64_I0.140770.874
6_T69_V0.140170.871
16_R41_E0.139590.867
37_L70_R0.139540.867
19_G60_D0.139040.863
25_A45_T0.137530.854
7_L45_T0.13680.850
26_V65_Q0.136710.849
5_L67_Y0.136610.848
29_P70_R0.136070.845
6_T51_T0.135830.844
29_P33_D0.135670.843
37_L54_L0.135640.842
8_T63_V0.134980.838
3_Q7_L0.13420.833
18_P22_T0.132690.824
12_S66_T0.13040.810
19_G24_V0.13010.808
61_G64_I0.129220.803
49_P62_R0.128680.799
36_V39_P0.127820.794
42_V47_K0.12770.793
42_V56_V0.127690.793
21_I38_S0.127170.790
31_I44_I0.127070.789
55_I63_V0.126940.788
12_S61_G0.12670.787
8_T36_V0.125760.781
25_A64_I0.125040.777
41_E63_V0.124880.776
32_A36_V0.124670.774
21_I67_Y0.124610.774
4_S26_V0.122580.761
7_L67_Y0.122370.760
43_Y55_I0.122020.758
6_T70_R0.121970.757
32_A35_T0.120440.748
64_I71_V0.119870.744
25_A34_V0.119350.741
9_V48_K0.118510.736
17_L55_I0.118080.733
44_I63_V0.117650.731
21_I57_W0.117450.729
59_K70_R0.117430.729
26_V62_R0.115690.718
25_A41_E0.115590.718
26_V70_R0.114810.713
53_T69_V0.114780.713
10_G64_I0.114720.712
27_G43_Y0.114680.712
45_T66_T0.114170.709
13_R23_R0.114020.708
20_P39_P0.113960.708
6_T42_V0.113880.707
37_L57_W0.113720.706
10_G49_P0.11350.705
26_V54_L0.113290.704
34_V41_E0.112980.702
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
2l04A0.986196.90.634
1f1sA0.902895.90.68
4aq1A0.972279.90.778
3ncxA0.930677.40.782
3r8sD0.416758.90.808
2ftcC0.416753.60.814
2wgnB152.20.815
3j3wD0.430651.70.816
2h7wA149.70.818
4i3gA0.777848.10.82
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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