GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
XET_C - Xyloglucan endo-transglycosylase (XET) C-terminus
Pfam: PF06955 (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: 563
Seq/Len: 11.04
HH_delta: 0.092 (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
26_W30_N0.522022.483
10_N16_L0.428582.039
25_R29_R0.396461.886
43_F48_P0.389221.852
11_Q16_L0.372131.770
34_Y42_R0.332151.580
39_D42_R0.330681.573
20_Q24_M0.325311.548
17_S20_Q0.322111.532
10_N20_Q0.313061.489
28_R32_M0.298031.418
22_R30_N0.292831.393
7_S21_R0.26131.243
9_W22_R0.24971.188
27_V35_D0.244351.162
18_A49_P0.224671.069
48_P51_C0.22411.066
23_Q29_R0.214821.022
22_R49_P0.211521.006
33_I38_T0.197760.941
22_R40_T0.195340.929
39_D51_C0.192940.918
21_R31_Y0.189660.902
18_A21_R0.188030.895
20_Q32_M0.186370.887
16_L33_I0.185710.884
25_R28_R0.184740.879
7_S28_R0.18360.873
12_P16_L0.183490.873
7_S41_K0.183370.872
27_V33_I0.183270.872
24_M27_V0.180440.858
28_R40_T0.179850.856
9_W41_K0.178360.849
31_Y48_P0.175340.834
22_R31_Y0.175330.834
32_M38_T0.174740.831
7_S19_K0.174710.831
9_W21_R0.171620.816
34_Y39_D0.166560.792
40_T49_P0.165880.789
39_D50_E0.165810.789
28_R45_N0.16120.767
7_S18_A0.158910.756
44_P48_P0.157880.751
18_A38_T0.157320.748
11_Q24_M0.155860.741
8_W35_D0.155780.741
19_K22_R0.154540.735
11_Q20_Q0.154230.734
38_T45_N0.152470.725
19_K49_P0.14860.707
39_D48_P0.146070.695
29_R41_K0.144760.689
36_Y48_P0.144750.689
8_W12_P0.1440.685
32_M49_P0.143530.683
27_V41_K0.143170.681
43_F51_C0.142190.676
7_S24_M0.141910.675
6_K19_K0.140870.670
19_K23_Q0.139420.663
16_L20_Q0.138910.661
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
1umzA0.980499.60.092
2uwaA0.90299.50.201
3mwqA0.627590.88
1agiA0.647160.888
2jcqA0.86275.70.889
4aohA0.64715.10.892
3htnA0.50983.40.9
1rraA0.62753.30.901
1dy5A0.62753.30.901
1rnfA0.64713.20.901

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