GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PilN - Fimbrial assembly protein (PilN)
Pfam: PF05137 (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: CL0331
Length: 78
Sequences: 1022
Seq/Len: 13.1
HH_delta: 0.722 (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
29_S73_T0.425952.423
13_G37_S0.407772.320
42_L74_I0.375432.136
30_G38_V0.340651.938
30_G72_F0.310071.764
35_Y39_A0.291071.656
18_S29_S0.282431.607
15_W33_D0.275461.567
5_E48_S0.270951.541
21_I39_A0.26921.531
27_S73_T0.254591.448
5_E9_A0.247631.409
42_L56_L0.239731.364
36_Q40_A0.235141.338
4_D8_R0.23331.327
35_Y56_L0.226681.290
14_V37_S0.225431.282
31_Y71_S0.215131.224
14_V70_V0.208821.188
14_V32_A0.208231.185
39_A43_R0.205031.166
63_E68_S0.199511.135
13_G33_D0.198411.129
48_S51_F0.197511.124
38_V70_V0.197371.123
51_F76_A0.194591.107
8_R23_G0.19231.094
35_Y42_L0.191691.090
10_L14_V0.189541.078
27_S38_V0.183091.042
20_S27_S0.182861.040
26_L76_A0.182671.039
3_L21_I0.178761.017
35_Y70_V0.17761.010
35_Y59_I0.174570.993
32_A60_S0.174510.993
42_L46_E0.174510.993
40_A44_N0.174080.990
45_L75_T0.172930.984
23_G29_S0.171660.977
31_Y40_A0.168530.959
5_E8_R0.168270.957
60_S73_T0.167690.954
30_G42_L0.167550.953
54_V76_A0.166680.948
10_L41_F0.166330.946
2_L7_A0.165720.943
17_T31_Y0.165470.941
15_W31_Y0.16480.938
3_L46_E0.164680.937
16_L41_F0.163570.931
11_P41_F0.161790.920
36_Q60_S0.160570.913
56_L59_I0.1590.905
14_V41_F0.156560.891
15_W61_R0.155250.883
39_A54_V0.155110.882
15_W39_A0.154560.879
19_L76_A0.153360.872
2_L6_L0.151220.860
12_E34_S0.150180.854
39_A70_V0.149220.849
62_Q71_S0.146750.835
9_A50_F0.146230.832
63_E67_N0.145360.827
70_V76_A0.144340.821
47_Q52_S0.14280.812
18_S57_S0.142350.810
32_A56_L0.142340.810
11_P48_S0.141640.806
15_W56_L0.14120.803
7_A38_V0.140810.801
9_A16_L0.140550.800
46_E52_S0.140410.799
23_G33_D0.139850.796
30_G59_I0.139130.791
34_S37_S0.138480.788
14_V62_Q0.137970.785
63_E71_S0.137340.781
27_S75_T0.137190.780
39_A56_L0.136940.779
25_T73_T0.136060.774
45_L52_S0.136060.774
39_A42_L0.135490.771
4_D29_S0.135260.769
2_L46_E0.134930.768
15_W41_F0.133410.759
26_L69_L0.133210.758
22_N27_S0.132310.753
41_F45_L0.132170.752
9_A44_N0.132160.752
25_T29_S0.132040.751
55_S75_T0.131860.750
15_W59_I0.130690.743
43_R46_E0.129920.739
14_V30_G0.128970.734
49_P58_S0.128730.732
57_S68_S0.127260.724
22_N63_E0.126980.722
8_R67_N0.126960.722
57_S75_T0.126910.722
28_I74_I0.126730.721
18_S52_S0.12670.721
12_E44_N0.12630.718
20_S52_S0.125390.713
42_L70_V0.125330.713
25_T75_T0.124480.708
18_S74_I0.123960.705
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
2w7vA0.935984.90.722
2rjzA0.961550.60.782
1uv7A0.948740.10.795
1ulrA0.897421.40.82
3trgA0.897420.30.822
2bjdA0.910317.70.827
2kxyA0.884617.60.827
1w2iA0.910317.40.827
2fhmA0.923116.20.829
3d7aA0.935914.40.833
If you are interested in a protein containing this domain,
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