GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PPC - Bacterial pre-peptidase C-terminal domain
Pfam: PF04151 (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: 70
Sequences: 1325
Seq/Len: 18.93
HH_delta: 0.192 (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
8_T63_T0.815033.154
6_S63_T0.807663.126
43_D54_I0.683622.646
27_D52_E0.53872.085
19_L26_A0.459251.777
7_F15_L0.4431.714
4_Y67_R0.437671.694
25_D52_E0.408771.582
32_D36_N0.39761.539
31_Y40_S0.396861.536
22_G50_N0.388581.504
10_P13_G0.388341.503
30_L56_F0.382511.480
21_G24_G0.382491.480
41_Y44_S0.379571.469
19_L68_V0.375251.452
32_D60_A0.360121.394
10_P61_A0.353341.367
38_L69_Y0.342821.327
26_A52_E0.334541.295
9_V13_G0.329041.273
30_L54_I0.322931.250
29_Y37_S0.318641.233
16_T55_T0.302631.171
9_V58_A0.302441.170
12_G59_P0.300051.161
25_D42_D0.292471.132
59_P62_G0.28961.121
33_S65_Y0.288451.116
9_V61_A0.285521.105
31_Y42_D0.282751.094
43_D52_E0.278061.076
18_D53_S0.275821.067
17_I66_I0.260451.008
31_Y37_S0.256540.993
32_D62_G0.246530.954
31_Y34_N0.245710.951
58_A61_A0.24530.949
32_D35_G0.241070.933
29_Y67_R0.234730.908
9_V59_P0.2330.902
4_Y35_G0.227270.880
31_Y67_R0.226930.878
19_L46_Q0.226590.877
6_S65_Y0.223780.866
37_S40_S0.22270.862
27_D43_D0.221080.856
12_G61_A0.216240.837
45_S54_I0.213770.827
59_P64_Y0.213380.826
46_Q49_G0.213080.825
13_G59_P0.211740.819
56_F59_P0.210110.813
25_D50_N0.20960.811
11_A61_A0.209410.810
17_I30_L0.201620.780
7_F64_Y0.194810.754
27_D42_D0.194080.751
5_Y64_Y0.193840.750
4_Y31_Y0.192380.744
25_D43_D0.192120.743
26_A68_V0.191510.741
26_A50_N0.191380.741
15_L24_G0.189390.733
4_Y65_Y0.186880.723
64_Y67_R0.184530.714
20_S26_A0.183360.710
3_D68_V0.18330.709
4_Y38_L0.182840.708
3_D65_Y0.181780.703
20_S57_T0.179930.696
29_Y52_E0.178630.691
27_D44_S0.177140.686
38_L67_R0.176760.684
4_Y69_Y0.174770.676
35_G38_L0.173630.672
16_T53_S0.171360.663
14_T58_A0.170670.660
41_Y45_S0.169780.657
13_G62_G0.169540.656
27_D50_N0.167620.649
24_G27_D0.165670.641
7_F17_I0.165110.639
7_F66_I0.164930.638
20_S51_D0.164370.636
28_L54_I0.163990.635
21_G26_A0.163920.634
8_T11_A0.161610.625
40_S69_Y0.158850.615
3_D32_D0.158810.615
41_Y52_E0.158770.614
45_S69_Y0.158640.614
14_T20_S0.158230.612
11_A34_N0.15720.608
11_A49_G0.156580.606
33_S60_A0.15640.605
12_G57_T0.155450.602
14_T55_T0.153860.595
18_D51_D0.153070.592
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
2luwA199.10.192
3jqwA0.942998.50.369
1nqjA0.957198.40.376
3afgA0.957197.70.508
1wmdA197.60.518
4g9sB0.942997.50.528
4dzgA0.957197.40.536
3osvA0.9857880.718
3payA181.70.74
3prxB0.9143770.75

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