GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1233 - Putative excisionase (DUF1233)
Pfam: PF06806 (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: 72
Sequences: 2654
Seq/Len: 36.86
HH_delta: 0.301 (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
15_L62_I1.086042.465
25_T29_Y0.976362.216
58_N61_E0.953632.164
18_I63_D0.907942.060
9_W56_W0.849771.928
8_K59_R0.792691.799
15_L26_I0.776521.762
12_E27_K0.710031.611
64_Q68_N0.663911.507
59_R63_D0.650681.477
38_R65_W0.641041.455
30_R40_Y0.625551.420
7_N60_P0.59881.359
18_I59_R0.59661.354
11_T56_W0.582491.322
26_I57_Y0.547731.243
16_M26_I0.540331.226
64_Q67_E0.528521.199
12_E16_M0.526851.196
28_R31_K0.520341.181
9_W41_K0.518971.178
13_E23_P0.514261.167
30_R57_Y0.512461.163
21_L29_Y0.511111.160
12_E57_Y0.510391.158
21_L26_I0.47831.085
14_L20_G0.459041.042
16_M23_P0.457641.039
10_V59_R0.450951.023
30_R55_I0.444911.010
10_V14_L0.437490.993
19_T66_I0.429730.975
24_G27_K0.423340.961
9_W66_I0.411280.933
40_Y57_Y0.406550.923
23_P27_K0.399240.906
11_T54_E0.395650.898
61_E64_Q0.390350.886
22_S25_T0.388370.881
10_V18_I0.384110.872
21_L25_T0.38030.863
10_V15_L0.379680.862
39_H61_E0.377480.857
11_T14_L0.368670.837
37_G40_Y0.350810.796
57_Y62_I0.348250.790
62_I65_W0.34440.782
24_G28_R0.341680.775
14_L17_A0.329090.747
18_I66_I0.326770.742
7_N67_E0.32140.729
16_M19_T0.319660.725
41_K58_N0.317020.719
9_W58_N0.310580.705
7_N63_D0.306790.696
12_E26_I0.3040.690
15_L18_I0.302350.686
6_P59_R0.294810.669
13_E17_A0.290520.659
18_I62_I0.290380.659
8_K63_D0.286130.649
43_V56_W0.282520.641
8_K60_P0.278850.633
16_M22_S0.272280.618
11_T43_V0.271730.617
12_E30_R0.269190.611
10_V62_I0.268670.610
60_P64_Q0.268540.609
44_S53_S0.267940.608
37_G65_W0.267410.607
12_E55_I0.26560.603
15_L57_Y0.261650.594
28_R32_K0.257630.585
8_K31_K0.255240.579
25_T28_R0.249510.566
7_N58_N0.24890.565
27_K55_I0.248810.565
42_K55_I0.24510.556
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
1z4hA0.861198.90.301
2kvvA198.80.328
1j9iA0.777898.60.377
1y6uA0.875980.488
3qaoA0.791796.80.604
2kfsA0.847296.70.609
1r8eA0.819496.70.61
3hh0A0.805696.70.614
2zhgA0.861196.60.617
1r8dA0.777896.30.629

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