GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
X_fast-SP_rel - Xylella fastidiosa surface protein related
Pfam: PF06669 (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: 70
Sequences: 334
Seq/Len: 4.77
HH_delta: 0.622 (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
9_K25_G0.449952.191
31_K55_N0.425182.070
45_I60_M0.420872.049
6_Q9_K0.401411.955
12_T21_H0.383351.867
47_T56_I0.381561.858
8_G23_K0.364011.772
14_A18_G0.337861.645
40_Y46_K0.32621.588
20_F28_L0.286511.395
51_Q54_G0.285671.391
34_A46_K0.281841.372
33_E46_K0.27841.356
6_Q25_G0.272391.326
7_I25_G0.271991.324
6_Q21_H0.270961.319
50_D54_G0.270761.318
14_A27_T0.267321.302
48_V59_Q0.258061.257
12_T23_K0.249411.214
60_M64_P0.231471.127
10_P21_H0.22291.085
29_T55_N0.221841.080
22_R54_G0.216641.055
36_T39_T0.216521.054
17_E49_V0.213581.040
15_G47_T0.213181.038
50_D55_N0.211741.031
10_P24_L0.209651.021
16_N40_Y0.208711.016
35_T38_G0.207781.012
14_A19_N0.206021.003
16_N33_E0.205811.002
26_Q54_G0.198630.967
14_A31_K0.194560.947
39_T63_S0.193760.943
15_G56_I0.189130.921
50_D57_E0.187850.915
62_D65_V0.186490.908
39_T62_D0.185110.901
22_R26_Q0.18510.901
43_K47_T0.183940.896
45_I58_I0.182360.888
31_K50_D0.181240.882
23_K26_Q0.180930.881
8_G21_H0.179850.876
9_K24_L0.179180.872
33_E40_Y0.177570.865
22_R49_V0.177350.864
20_F51_Q0.173110.843
33_E42_G0.172810.841
20_F49_V0.172560.840
36_T61_A0.170690.831
9_K12_T0.168040.818
43_K63_S0.166430.810
33_E41_S0.165650.807
14_A17_E0.162730.792
7_I21_H0.16110.784
22_R29_T0.157630.768
7_I23_K0.156830.764
29_T54_G0.156350.761
6_Q10_P0.1560.760
14_A29_T0.155160.755
36_T58_I0.153230.746
40_Y47_T0.153020.745
40_Y60_M0.152480.742
42_G57_E0.148070.721
22_R25_G0.147420.718
12_T25_G0.146380.713
47_T59_Q0.146380.713
44_N47_T0.142290.693
15_G30_I0.141370.688
20_F56_I0.141070.687
41_S47_T0.139820.681
45_I64_P0.139370.679
19_N39_T0.138270.673
13_F50_D0.136480.665
16_N43_K0.135650.660
35_T40_Y0.134210.653
8_G12_T0.133740.651
16_N46_K0.13090.637
31_K57_E0.130820.637
30_I58_I0.130580.636
12_T27_T0.130510.635
31_K45_I0.130310.634
16_N42_G0.130160.634
36_T40_Y0.127560.621
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
3d9xA0.885797.80.622
1qiuA0.921.40.87
1v1hA0.885714.80.878
3izoF0.914.70.878
3s6xA0.985712.80.881
3efcA0.971460.897
1s7mA0.95.10.9
3f83A0.957150.901
4je0A0.85714.90.901
4jdzB0.85714.80.901
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