GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Penicillinase_R - Penicillinase repressor
Pfam: PF03965 (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: CL0123
Length: 115
Sequences: 19185
Seq/Len: 166.83
HH_delta: 0.084 (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
102_S105_E2.126872.545
19_T22_E1.742332.085
5_E48_K1.740912.083
66_I69_E1.729622.070
46_V53_R1.525431.826
108_E112_L1.496931.791
108_E111_K1.495151.789
54_E64_P1.49031.784
101_L112_L1.422331.702
52_T64_P1.368351.638
5_E44_R1.344291.609
8_I41_L1.331021.593
17_E64_P1.281471.534
65_L69_E1.265881.515
13_W73_A1.25541.502
11_I26_A1.245631.491
15_S26_A1.239731.484
20_V35_Y1.222241.463
109_L112_L1.191111.425
8_I38_V1.185261.418
5_E41_L1.17021.400
36_S39_Q1.164931.394
56_I62_Y1.138311.362
43_N47_E1.110491.329
20_V42_L1.101031.318
37_T40_T1.065561.275
43_N46_V1.065321.275
24_H35_Y1.051731.259
57_G63_S1.045481.251
19_T60_Y1.043811.249
39_Q43_N1.042121.247
52_T63_S1.039791.244
68_R72_L1.029781.232
105_E108_E1.026821.229
15_S18_A1.004181.202
4_L41_L0.95421.142
71_Y75_E0.948481.135
43_N53_R0.930271.113
21_R35_Y0.905141.083
103_P107_E0.899121.076
13_W70_E0.892241.068
55_K61_V0.885741.060
37_T41_L0.883061.057
21_R25_E0.87611.048
22_E26_A0.872861.045
68_R71_Y0.865511.036
106_L110_R0.855431.024
7_E11_I0.855331.024
90_Q93_A0.853651.022
9_M13_W0.849591.017
13_W65_L0.848561.016
22_E25_E0.842281.008
52_T66_I0.818930.980
11_I27_L0.818720.980
8_I23_I0.818470.980
59_A63_S0.815470.976
40_T44_R0.810520.970
17_E54_E0.808410.967
70_E74_Q0.806430.965
57_G60_Y0.802080.960
56_I60_Y0.801830.960
20_V39_Q0.797710.955
105_E111_K0.794780.951
105_E112_L0.789190.944
92_V95_L0.788890.944
75_E78_Q0.787750.943
53_R61_V0.785950.941
67_S71_Y0.784770.939
11_I18_A0.766870.918
40_T43_N0.765170.916
73_A77_R0.758790.908
7_E27_L0.758060.907
101_L105_E0.757060.906
12_L51_L0.738410.884
20_V38_V0.736330.881
104_E108_E0.736150.881
49_G68_R0.731480.875
72_L75_E0.731260.875
11_I15_S0.729360.873
46_V51_L0.728170.871
18_A22_E0.725350.868
53_R60_Y0.719720.861
44_R47_E0.717550.859
89_P93_A0.714030.855
67_S70_E0.706340.845
44_R48_K0.683140.818
56_I61_V0.682710.817
24_H38_V0.679410.813
94_A97_E0.668930.801
98_S101_L0.66760.799
4_L44_R0.666960.798
12_L18_A0.662540.793
42_L51_L0.658810.788
107_E111_K0.657680.787
35_Y39_Q0.653030.782
79_F90_Q0.651280.779
56_I59_A0.639760.766
10_E14_E0.639520.765
90_Q94_A0.638610.764
4_L40_T0.62380.747
18_A26_A0.622510.745
54_E63_S0.615590.737
11_I23_I0.61450.735
42_L63_S0.614140.735
45_L50_F0.612150.733
93_A97_E0.608510.728
39_Q53_R0.606680.726
46_V52_T0.603790.723
50_F72_L0.594320.711
13_W16_G0.588290.704
38_V42_L0.587430.703
9_M50_F0.587330.703
4_L37_T0.577080.691
17_E63_S0.577080.691
98_S102_S0.575870.689
96_V106_L0.569580.682
23_I38_V0.562680.673
23_I42_L0.560960.671
3_D6_L0.558420.668
21_R24_H0.557610.667
12_L16_G0.556890.666
3_D7_E0.555070.664
36_S40_T0.553020.662
6_L73_A0.552490.661
20_V36_S0.540680.647
102_S106_L0.533880.639
42_L46_V0.533570.639
13_W77_R0.530320.635
104_E107_E0.52980.634
107_E110_R0.526080.630
6_L76_L0.525390.629
65_L68_R0.514420.616
37_T44_R0.514130.615
6_L10_E0.51360.615
69_E72_L0.511550.612
71_Y74_Q0.51130.612
19_T56_I0.508970.609
92_V96_V0.49950.598
16_G70_E0.498780.597
101_L106_L0.486810.583
7_E10_E0.484760.580
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
1sd4A199.50.084
1okrA0.982699.50.089
2g9wA0.973999.40.145
4em2A0.878399.40.178
3k0lA0.878399.40.184
3echA0.878399.40.185
3s2wA0.878399.40.187
2fxaA0.878399.40.187
3e6mA0.878399.40.188
3jw4A0.878399.40.19

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