GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_S74 - Chaperone of endosialidase
Pfam: PF13884 (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: 58
Sequences: 655
Seq/Len: 11.29
HH_delta: 0.175 (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
2_D50_Q0.989573.640
8_N28_N0.977523.595
23_K51_E0.667792.456
11_D25_V0.577622.124
3_R9_I0.518781.908
7_T30_K0.512411.885
29_Y44_H0.502691.849
15_A24_P0.444671.635
3_R50_Q0.432611.591
25_V48_I0.417251.535
1_S6_K0.396521.458
28_N43_R0.364241.340
5_L29_Y0.340241.251
22_L47_F0.315951.162
26_T45_I0.310331.141
39_D42_R0.305411.123
50_Q53_Q0.30481.121
9_I25_V0.301181.108
25_V51_E0.292921.077
10_K26_T0.28911.063
22_L52_V0.286231.053
26_T43_R0.284641.047
24_P47_F0.282171.038
27_Y44_H0.276331.016
2_D53_Q0.266790.981
3_R48_I0.265770.977
3_R51_E0.25660.944
11_D23_K0.250820.922
31_D39_D0.246710.907
14_N18_K0.243640.896
22_L55_V0.233410.858
53_Q57_P0.230450.848
12_I24_P0.229030.842
41_D44_H0.223160.821
14_N17_D0.220050.809
28_N44_H0.219070.806
30_K44_H0.21750.800
13_D42_R0.214760.790
51_E54_E0.212360.781
44_H47_F0.208320.766
2_D5_L0.206430.759
47_F52_V0.204820.753
39_D44_H0.202750.746
3_R7_T0.196760.724
19_I40_E0.195920.721
19_I28_N0.194580.716
8_N21_Q0.191340.704
14_N24_P0.1910.702
6_K9_I0.188610.694
11_D24_P0.188260.692
28_N42_R0.186090.684
19_I22_L0.184830.680
15_A19_I0.184710.679
1_S48_I0.182880.673
45_I56_F0.182620.672
27_Y46_G0.182380.671
7_T31_D0.181460.667
28_N41_D0.180880.665
12_I15_A0.178620.657
13_D55_V0.178580.657
10_K31_D0.175330.645
21_Q39_D0.172160.633
31_D40_E0.170420.627
16_L40_E0.16860.620
18_K52_V0.168420.619
44_H56_F0.168090.618
2_D52_V0.167710.617
20_M29_Y0.166030.611
5_L31_D0.164540.605
9_I48_I0.16420.604
20_M24_P0.159150.585
5_L39_D0.159130.585
4_R30_K0.158790.584
17_D45_I0.158580.583
4_R52_V0.157950.581
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
3gw6A0.982899.20.175
3gudA0.982898.90.291
7ahlA0.982813.30.849
2rreA0.637912.10.852
1yarO0.41388.90.86
3zx6A18.30.862
3uo9A0.82768.30.862
3l1wA0.63797.60.864
2iw0A17.50.864
2c71A0.98287.20.865

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