GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lactamase_B_2 - Beta-lactamase superfamily domain
Pfam: PF12706 (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: CL0381
Length: 194
Sequences: 9927
Seq/Len: 51.17
HH_delta: 0.27 (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
133_F148_I1.43323.588
59_P90_I1.39423.490
97_E104_R1.126862.821
99_E104_R1.088552.725
126_E131_K1.087042.721
124_V131_K1.057362.647
149_D187_K1.011312.532
3_I32_A1.008652.525
181_A189_V0.961272.406
32_A59_P0.942872.360
32_A61_Y0.942092.358
104_R126_E0.933232.336
5_I36_T0.877112.196
97_E106_T0.864832.165
150_L190_I0.844832.115
106_T126_E0.832772.085
179_E183_E0.819682.052
67_K71_R0.816032.043
34_F123_F0.801912.007
152_I192_I0.776751.944
2_R31_D0.751611.881
132_I152_I0.738541.849
181_A186_A0.72841.823
93_S96_D0.694331.738
153_L172_M0.663381.661
64_P68_E0.654531.638
34_F105_I0.650241.628
59_P88_D0.643251.610
5_I134_Y0.642731.609
127_P130_K0.63651.593
179_E182_K0.634331.588
2_R29_D0.630051.577
64_P93_S0.618451.548
33_V46_L0.615291.540
107_P123_F0.60011.502
176_E179_E0.599571.501
5_I125_I0.595961.492
133_F145_L0.582981.459
67_K91_E0.579141.450
62_G66_T0.570961.429
62_G67_K0.563461.410
124_V148_I0.558531.398
63_P66_T0.546551.368
131_K149_D0.535961.342
99_E102_D0.534571.338
148_I151_L0.534151.337
143_E146_K0.518481.298
135_S153_L0.511571.281
151_L186_A0.509131.274
131_K148_I0.506441.268
113_G170_G0.484391.213
4_L30_I0.478781.198
7_C35_I0.469651.176
130_K149_D0.464821.164
108_F124_V0.457641.146
37_H137_D0.45171.131
61_Y92_I0.448161.122
110_A135_S0.447251.120
135_S154_E0.447131.119
48_S52_A0.444981.114
36_T134_Y0.44461.113
40_P44_A0.444291.112
173_T176_E0.444181.112
64_P91_E0.441441.105
155_C177_A0.436521.093
112_H137_D0.428911.074
61_Y90_I0.42841.072
3_I103_F0.427451.070
175_E179_E0.426451.067
94_P109_P0.424981.064
174_L178_L0.424391.062
39_H42_H0.423061.059
188_K191_L0.417081.044
139_N176_E0.412471.032
150_L188_K0.411391.030
92_I107_P0.409871.026
5_I34_F0.407671.020
105_I123_F0.407641.020
157_Y173_T0.40611.017
10_G45_G0.403171.009
19_Q23_E0.3980.996
67_K89_I0.39510.989
178_L182_K0.39450.988
142_F183_E0.394150.987
92_I98_F0.393380.985
134_Y192_I0.388490.972
111_N139_N0.386610.968
68_E71_R0.38580.966
19_Q22_Q0.381680.955
3_I34_F0.378740.948
155_C191_L0.378520.948
35_I46_L0.373620.935
105_I125_I0.371860.931
140_Y183_E0.370750.928
34_F61_Y0.370430.927
38_S66_T0.368170.922
37_H42_H0.367390.920
106_T124_V0.365280.914
143_E183_E0.363790.911
124_V133_F0.361390.905
147_N185_K0.360050.901
43_I70_L0.355790.891
38_S69_F0.354410.887
33_V60_I0.351190.879
32_A100_I0.350080.876
134_Y152_I0.349910.876
39_H112_H0.349320.874
173_T177_A0.3460.866
42_H137_D0.343720.860
186_A189_V0.340770.853
50_I60_I0.331710.830
42_H193_H0.331690.830
46_L50_I0.331670.830
110_A138_T0.324530.812
97_E100_I0.321090.804
111_N138_T0.320360.802
172_M180_L0.319430.800
133_F151_L0.319090.799
130_K150_L0.314080.786
39_H137_D0.31330.784
135_S138_T0.312520.782
135_S151_L0.312360.782
153_L180_L0.311890.781
51_P54_A0.309920.776
35_I43_I0.308890.773
108_F144_E0.308010.771
36_T39_H0.307550.770
62_G70_L0.303980.761
91_E94_P0.302360.757
180_L184_L0.301180.754
3_I100_I0.298220.747
124_V147_N0.297770.745
108_F118_G0.294290.737
111_N115_P0.290250.727
124_V146_K0.288410.722
3_I105_I0.28820.721
138_T153_L0.288040.721
37_H112_H0.287860.721
131_K147_N0.287150.719
146_K185_K0.286150.716
177_A180_L0.285730.715
181_A191_L0.285610.715
95_G108_F0.285510.715
24_L28_P0.284810.713
7_C33_V0.284230.711
35_I70_L0.283740.710
36_T123_F0.281870.706
26_D29_D0.280080.701
178_L181_A0.278850.698
4_L7_C0.274970.688
136_G193_H0.273730.685
62_G89_I0.27040.677
154_E172_M0.269930.676
151_L181_A0.268980.673
45_G48_S0.267140.669
155_C174_L0.266440.667
95_G109_P0.26640.667
158_I174_L0.265610.665
33_V49_L0.264960.663
100_I103_F0.264650.662
65_E68_E0.262920.658
2_R30_I0.26290.658
12_R48_S0.262430.657
110_A117_Y0.261380.654
152_I190_I0.260780.653
154_E171_H0.260390.652
22_Q25_E0.259570.650
47_P51_P0.259330.649
53_W56_H0.25850.647
37_H41_D0.257520.645
22_Q26_D0.256120.641
6_D37_H0.255260.639
96_D106_T0.255060.638
131_K187_K0.25430.637
116_S136_G0.251010.628
140_Y176_E0.250570.627
146_K183_E0.248990.623
96_D107_P0.248530.622
30_I33_V0.24780.620
49_L53_W0.246160.616
151_L154_E0.244350.612
4_L33_V0.244180.611
65_E115_P0.243870.610
62_G193_H0.242420.607
151_L189_V0.242030.606
92_I123_F0.241670.605
48_S51_P0.241390.604
38_S62_G0.239330.599
157_Y174_L0.239330.599
110_A118_G0.236650.592
92_I96_D0.236230.591
46_L49_L0.234710.588
139_N172_M0.233960.586
112_H154_E0.233440.584
71_R89_I0.232690.582
38_S43_I0.231830.580
110_A136_G0.230430.577
70_L89_I0.229030.573
36_T113_G0.228620.572
5_I123_F0.228140.571
145_L184_L0.226790.568
38_S65_E0.226730.568
177_A181_A0.225290.564
41_D137_D0.224350.562
106_T144_E0.224210.561
174_L177_A0.2240.561
6_D137_D0.223950.561
113_G139_N0.222590.557
180_L183_E0.221540.555
21_M25_E0.221470.554
30_I49_L0.221450.554
24_L27_L0.220080.551
177_A186_A0.219830.550
31_D59_P0.218440.547
108_F133_F0.21770.545
11_T51_P0.217460.544
151_L184_L0.217440.544
177_A189_V0.217370.544
111_N170_G0.216150.541
178_L191_L0.215960.541
145_L148_I0.214840.538
114_P117_Y0.214020.536
108_F113_G0.213390.534
36_T137_D0.213270.534
142_F180_L0.212930.533
65_E91_E0.212120.531
88_D94_P0.21190.530
63_P117_Y0.211460.529
38_S116_S0.210040.526
95_G106_T0.208150.521
25_E28_P0.208020.521
172_M176_E0.207690.520
139_N170_G0.207560.520
5_I132_I0.207140.519
4_L11_T0.206220.516
28_P56_H0.205310.514
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
3zwfA0.938199.90.27
1y44A0.938199.90.281
2cbnA0.938199.90.282
3jxpA0.938199.90.304
1zkpA0.891899.90.306
3md7A0.881499.90.31
2e7yA0.912499.90.317
3g1pA0.850599.90.327
2ycbA0.948599.80.353
3iekA0.953699.80.359

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