GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_hydro_65C - Glycosyl hydrolase family 65 C-terminal domain
Pfam: PF03633 (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: 54
Sequences: 634
Seq/Len: 11.74
HH_delta: 0.153 (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
32_V45_V0.675143.387
13_R22_E0.519262.605
10_L25_I0.437392.195
9_S24_E0.392821.971
42_T49_E0.371771.865
42_T51_T0.324581.629
21_L52_L0.316141.586
19_H41_L0.305671.534
34_L37_G0.30281.519
40_P51_T0.301861.515
34_L52_L0.279711.403
12_F23_V0.272381.367
13_R20_W0.271691.363
21_L32_V0.260341.306
11_S22_E0.247221.240
22_E35_L0.242651.217
10_L16_Y0.240561.207
2_R17_R0.234851.178
15_R20_W0.234461.176
2_R10_L0.22541.131
21_L41_L0.222581.117
7_W10_L0.21381.073
24_E31_T0.203821.023
8_S27_H0.200821.008
14_L34_L0.198620.997
24_E33_T0.197130.989
30_V46_Y0.194020.973
8_S25_I0.19180.962
6_Q46_Y0.18970.952
27_H33_T0.185770.932
17_R42_T0.185690.932
6_Q9_S0.184220.924
26_T29_K0.182850.917
2_R16_Y0.176020.883
19_H43_I0.175250.879
40_P53_K0.173930.873
3_L10_L0.172220.864
5_K18_G0.167150.839
47_G50_V0.161590.811
1_P7_W0.160940.808
28_E52_L0.159230.799
44_K49_E0.158670.796
18_G23_V0.15530.779
38_D44_K0.154860.777
2_R47_G0.154570.776
19_H37_G0.151990.763
32_V46_Y0.151880.762
19_H40_P0.150460.755
20_W35_L0.149620.751
12_F21_L0.148530.745
9_S27_H0.147960.742
12_F46_Y0.147910.742
16_Y52_L0.146890.737
17_R26_T0.14530.729
15_R36_S0.144770.726
7_W16_Y0.144330.724
7_W32_V0.143210.719
18_G42_T0.142090.713
7_W45_V0.14180.711
38_D48_E0.141610.711
26_T31_T0.141140.708
27_H35_L0.140990.707
27_H51_T0.140490.705
3_L23_V0.13810.693
20_W23_V0.135530.680
10_L20_W0.133780.671
42_T48_E0.131820.661
11_S23_V0.130860.657
49_E53_K0.129310.649
32_V43_I0.129230.648
31_T43_I0.129120.648
2_R19_H0.128670.646
16_Y30_V0.128430.644
16_Y22_E0.128030.642
6_Q31_T0.127870.642
14_L35_L0.127840.641
33_T42_T0.124540.625
5_K40_P0.124340.624
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
1h54A0.981598.90.153
2rdyA0.96397.90.392
3rrsA0.981597.20.498
3qdeA0.981596.80.53
2eabA0.9815950.604
1v7wA0.96393.90.625
3cihA0.944482.20.701
1ulvA0.833378.90.71
2okxA0.96377.60.713
2waoA0.851930.60.786

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