GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PilX_N - PilX N-terminal
Pfam: PF14341 (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: 51
Sequences: 1594
Seq/Len: 31.25
HH_delta: 0.524 (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
3_A7_V0.437981.786
37_R41_Q0.437561.784
42_A46_A0.433071.766
7_V11_I0.406691.658
43_F47_E0.404191.648
19_G23_M0.394581.609
30_E34_G0.367521.498
38_D41_Q0.362351.477
15_L19_G0.346571.413
27_T31_R0.344641.405
14_V17_L0.344611.405
39_S42_A0.319351.302
17_L21_A0.31671.291
24_R28_L0.315631.287
34_G38_D0.311841.271
28_L31_R0.305741.246
18_L21_A0.299841.222
35_N39_S0.295921.206
41_Q44_Q0.290751.185
17_L34_G0.273111.113
41_Q48_A0.270561.103
4_A7_V0.267261.090
30_E37_R0.25971.059
40_Q44_Q0.257671.050
4_A13_L0.247491.009
11_I48_A0.238930.974
15_L48_A0.238440.972
35_N38_D0.236160.963
36_Q39_S0.235950.962
10_I15_L0.234360.955
18_L25_S0.232250.947
13_L22_A0.229470.936
23_M27_T0.229150.934
40_Q48_A0.226760.924
8_A34_G0.223470.911
22_A47_E0.222910.909
23_M35_N0.222140.906
3_A8_A0.221940.905
32_M35_N0.215860.880
29_E32_M0.214160.873
20_V37_R0.21310.869
29_E33_A0.212510.866
30_E44_Q0.210760.859
7_V18_L0.208460.850
4_A8_A0.204320.833
28_L34_G0.204210.833
34_G37_R0.2040.832
16_T19_G0.200540.818
32_M49_G0.19870.810
14_V46_A0.197110.804
2_G18_L0.195230.796
28_L35_N0.19480.794
20_V25_S0.193870.790
6_V18_L0.192750.786
5_L22_A0.192020.783
36_Q40_Q0.191150.779
29_E36_Q0.19110.779
3_A33_A0.185710.757
28_L38_D0.185510.756
6_V22_A0.184420.752
38_D43_F0.183310.747
37_R44_Q0.182290.743
29_E44_Q0.180250.735
41_Q45_A0.177930.725
21_A26_S0.17750.724
1_R44_Q0.177070.722
17_L39_S0.175960.717
26_S44_Q0.174430.711
12_L45_A0.173390.707
45_A49_G0.172480.703
37_R40_Q0.172030.701
26_S29_E0.171780.700
6_V14_V0.169840.692
22_A36_Q0.169240.690
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
2hi2A0.941286.60.524
3sokA0.941286.50.525
1oqwA0.941284.40.537
3ci0K0.607874.70.578
4ainA140.10.657
2retA0.509811.40.732
3ci0I0.47068.50.746
3rlfF0.98043.10.791
3um7A0.94122.50.8
2kseA12.50.8
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