GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CHB_HEX_C_1 - Chitobiasebeta-hexosaminidase C-terminal domain
Pfam: PF13290 (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: CL0159
Length: 67
Sequences: 1104
Seq/Len: 16.48
HH_delta: 0.427 (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
22_T38_L0.850643.049
33_T36_S0.738322.646
26_T32_P0.644872.311
24_Y56_F0.59492.132
24_Y38_L0.553141.983
11_T44_T0.528731.895
26_T29_G0.493571.769
39_Y42_P0.49071.759
14_L23_I0.459781.648
23_I55_A0.449781.612
57_D61_N0.447291.603
16_T21_A0.436271.564
24_Y54_R0.402251.442
23_I53_A0.397841.426
31_E52_K0.391411.403
24_Y37_P0.387331.388
12_V51_V0.386231.384
57_D60_G0.362681.300
18_D21_A0.356291.277
11_T42_P0.339591.217
34_P56_F0.33071.185
43_I51_V0.329331.180
54_R62_S0.328981.179
45_I49_T0.328541.178
54_R63_S0.328141.176
41_G44_T0.309061.108
21_A55_A0.290991.043
29_G32_P0.281831.010
13_T39_Y0.281141.008
23_I39_Y0.278550.998
12_V43_I0.276050.989
31_E54_R0.269670.967
32_P52_K0.263030.943
18_D57_D0.262280.940
14_L53_A0.252360.905
31_E36_S0.243670.873
27_T51_V0.242220.868
25_Y39_Y0.232870.835
24_Y32_P0.229640.823
15_S18_D0.229520.823
9_N44_T0.225630.809
18_D59_D0.217760.780
15_S19_P0.215480.772
9_N46_T0.215210.771
16_T20_D0.213260.764
26_T52_K0.21130.757
12_V50_T0.210720.755
28_D32_P0.210640.755
26_T30_S0.208290.747
45_I51_V0.207770.745
21_A58_P0.194370.697
24_Y34_P0.189830.680
27_T50_T0.188260.675
9_N17_A0.187860.673
9_N49_T0.186160.667
10_T48_T0.186010.667
46_T58_P0.185250.664
10_T43_I0.184680.662
18_D55_A0.184220.660
10_T46_T0.182340.654
23_I63_S0.179070.642
21_A57_D0.178330.639
17_A20_D0.177770.637
17_A47_G0.176810.634
31_E44_T0.17460.626
53_A59_D0.173580.622
13_T40_T0.173450.622
34_P37_P0.171860.616
41_G58_P0.171770.616
12_V21_A0.171720.615
16_T55_A0.171290.614
13_T42_P0.170890.613
10_T45_I0.165560.593
20_D54_R0.165270.592
47_G50_T0.164040.588
11_T48_T0.16290.584
13_T17_A0.162660.583
15_S35_S0.160460.575
32_P54_R0.157490.564
10_T14_L0.157370.564
19_P35_S0.157190.563
34_P50_T0.154050.552
27_T49_T0.153740.551
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
1c7sA0.940398.20.427
3pe9A150.10.792
3pddA140.70.803
1e07A1350.809
1z7zI0.970123.30.824
1qlmA121.50.827
3o12A0.925418.10.833
2oz4A0.970116.40.835
3mepA0.925413.10.842
2v5mA112.10.845

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