GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BiPBP_C - Penicillin-Binding Protein C-terminus Family
Pfam: PF06832 (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: 89
Sequences: 614
Seq/Len: 6.9
HH_delta: 0.558 (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
50_D73_H0.458653.575
45_V77_V0.304932.377
36_L47_W0.26442.061
49_V75_L0.241251.881
23_A27_G0.224511.750
36_L77_V0.206381.609
47_W67_P0.192281.499
35_V64_F0.191651.494
27_G32_Q0.181951.418
74_T86_S0.180141.404
48_F53_P0.171721.339
53_P78_V0.168831.316
20_A27_G0.157841.230
34_L85_A0.153421.196
24_L32_Q0.151741.183
17_P20_A0.15071.175
34_L47_W0.144971.130
39_A75_L0.144131.124
21_V32_Q0.143851.121
15_S22_L0.143331.117
35_V62_Q0.143211.116
14_T74_T0.140861.098
23_A70_P0.139171.085
13_I38_A0.137151.069
31_R66_Q0.136191.062
40_G85_A0.136121.061
14_T42_R0.133541.041
69_R73_H0.132711.035
80_A83_R0.132631.034
17_P53_P0.132221.031
10_P41_G0.131111.022
79_D83_R0.13041.017
48_F76_T0.130211.015
33_P86_S0.129541.010
58_Q63_L0.12871.003
33_P76_T0.12740.993
17_P21_V0.126470.986
69_R72_E0.126340.985
10_P52_E0.124290.969
51_G74_T0.123350.962
36_L65_W0.12310.960
23_A26_P0.122480.955
46_Y53_P0.121770.949
23_A65_W0.121390.946
16_P54_L0.120890.942
57_T60_G0.11850.924
22_L34_L0.118180.921
18_D36_L0.1180.920
47_W61_H0.116940.912
34_L75_L0.11680.910
38_A45_V0.116750.910
10_P15_S0.115720.902
21_V26_P0.115590.901
20_A43_G0.114640.894
57_T84_S0.113990.889
64_F73_H0.113290.883
11_L22_L0.113180.882
53_P63_L0.112670.878
11_L82_G0.11250.877
78_V82_G0.111490.869
19_G70_P0.111370.868
51_G72_E0.111270.867
49_V72_E0.111110.866
14_T78_V0.110380.860
34_L67_P0.109960.857
49_V54_L0.109960.857
50_D53_P0.10970.855
39_A57_T0.109360.852
11_L80_A0.109260.852
43_G51_G0.109260.852
13_I18_D0.108770.848
56_T74_T0.108680.847
11_L83_R0.107510.838
34_L77_V0.107090.835
39_A70_P0.107060.835
31_R77_V0.106460.830
38_A41_G0.105710.824
79_D82_G0.105350.821
47_W65_W0.105010.819
46_Y61_H0.104710.816
22_L35_V0.104180.812
38_A65_W0.103550.807
33_P37_K0.103550.807
52_E56_T0.103030.803
50_D55_G0.10290.802
52_E66_Q0.102180.797
26_P32_Q0.102080.796
55_G74_T0.101230.789
37_K80_A0.100330.782
54_L63_L0.100220.781
18_D52_E0.10010.780
10_P70_P0.100070.780
36_L67_P0.099940.779
19_G67_P0.099780.778
13_I16_P0.099460.775
22_L46_Y0.099360.775
45_V49_V0.099080.772
11_L15_S0.098420.767
14_T37_K0.09840.767
52_E58_Q0.098110.765
47_W53_P0.098030.764
22_L42_R0.097980.764
37_K66_Q0.097920.763
32_Q70_P0.097420.759
11_L53_P0.097340.759
44_P79_D0.096820.755
25_D32_Q0.096610.753
10_P50_D0.096550.753
11_L78_V0.096250.750
24_L65_W0.096120.749
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
3pe9A0.842798.10.558
3pddA0.853997.90.59
3pddA0.943897.10.661
2lvcA0.8989940.741
3shsA0.842793.40.748
3fn9A0.8876900.77
2e6qA0.910189.90.771
3knbA0.8876870.782
1waaA0.8876860.785
2lqrA0.921385.50.787
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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