GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Beta-lactamase - Beta-lactamase
Pfam: PF00144 (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: CL0013
Length: 329
Sequences: 6866
Seq/Len: 20.87
HH_delta: 0.092 (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
162_K170_E1.304444.245
70_E171_N1.219023.967
24_N302_G1.19893.902
169_Q174_Q1.067453.474
74_D77_D1.059843.449
76_D97_R1.040723.387
77_D81_K0.996623.243
181_T223_S0.958883.120
66_Q171_N0.930633.029
63_A167_L0.855492.784
77_D82_Y0.817222.659
62_T231_F0.801222.607
66_Q167_L0.794642.586
44_M50_F0.756312.461
167_L171_N0.74162.413
160_T167_L0.736672.397
163_S166_E0.731742.381
52_I223_S0.716332.331
20_A229_A0.705522.296
156_L167_L0.70352.289
32_Y46_P0.657862.141
95_T98_D0.630062.050
54_S57_K0.628442.045
178_M181_T0.626682.039
232_G304_G0.621762.023
154_E158_R0.61792.011
36_A42_K0.604591.968
154_E157_E0.603261.963
168_L173_F0.598031.946
78_P81_K0.597331.944
85_E158_R0.589061.917
22_I229_A0.587311.911
162_K167_L0.585551.906
37_D40_T0.580311.889
35_Y41_G0.570531.857
30_E226_R0.564011.835
58_S231_F0.563241.833
66_Q70_E0.562961.832
233_Q236_L0.56281.832
232_G295_I0.55421.804
63_A168_L0.54191.764
298_D301_N0.536791.747
67_L156_L0.535711.743
59_F221_L0.534761.740
153_G217_G0.532091.732
29_Y33_Y0.530281.726
64_V152_L0.525561.710
48_T194_A0.520231.693
96_I155_I0.520181.693
282_R300_E0.516631.681
64_V100_L0.507681.652
69_D243_S0.501671.633
243_S246_I0.501181.631
170_E174_Q0.500731.630
45_T48_T0.493321.605
55_V228_L0.487591.587
146_N218_A0.486151.582
59_F231_F0.48511.579
173_F178_M0.483871.575
240_L245_S0.482791.571
162_K166_E0.482231.569
98_D139_G0.481891.568
64_V73_L0.481131.566
98_D103_T0.478931.559
20_A306_V0.47171.535
64_V156_L0.468281.524
69_D248_K0.467791.522
22_I304_G0.466671.519
269_G274_I0.464321.511
97_R270_Y0.459511.495
180_H192_R0.458371.492
18_A225_A0.456561.486
57_K144_Y0.455741.483
46_P226_R0.449671.463
166_E170_E0.447911.458
178_M227_D0.446251.452
162_K171_N0.443931.445
20_A225_A0.441681.437
72_K159_V0.429311.397
35_Y40_T0.427961.393
47_D226_R0.422761.376
136_F141_Q0.420081.367
55_V295_I0.418771.363
61_A100_L0.417561.359
104_S148_N0.416011.354
93_K137_P0.414581.349
52_I56_S0.406671.323
68_I75_L0.402911.311
18_A32_Y0.401061.305
54_S144_Y0.398881.298
297_I304_G0.397771.294
18_A50_F0.396341.290
23_H303_L0.396261.290
16_G50_F0.395051.286
242_L246_I0.393771.281
98_D101_T0.392881.279
59_F168_L0.392791.278
18_A44_M0.389711.268
164_F168_L0.384481.251
240_L243_S0.383871.249
67_L160_T0.38281.246
20_A27_I0.381871.243
60_T164_F0.381621.242
155_I159_V0.381151.240
65_M75_L0.379041.234
22_I27_I0.374851.220
21_V305_V0.373031.214
173_F181_T0.372621.213
225_A308_L0.37051.206
183_F221_L0.369881.204
82_Y155_I0.367181.195
69_D246_I0.366861.194
19_V307_I0.366171.192
16_G44_M0.365431.189
178_M231_F0.364541.186
164_F217_G0.362191.179
123_D127_Q0.360911.175
56_S221_L0.35991.171
242_L250_L0.355161.156
178_M223_S0.355071.156
82_Y159_V0.353671.151
44_M48_T0.352941.149
63_A156_L0.352751.148
65_M68_I0.349031.136
68_I73_L0.347771.132
173_F221_L0.345811.125
67_L72_K0.343251.117
145_S148_N0.340681.109
149_Y271_G0.337171.097
61_A271_G0.335181.091
77_D96_I0.334211.088
246_I250_L0.332961.084
73_L159_V0.332291.081
181_T227_D0.332261.081
124_E127_Q0.331191.078
284_Y297_I0.330811.077
136_F140_T0.323981.054
156_L160_T0.323811.054
61_A149_Y0.322881.051
228_L308_L0.322451.049
296_W305_V0.320431.043
194_A197_Y0.320281.042
248_K251_S0.319541.040
36_A48_T0.318611.037
67_L70_E0.315021.025
97_R101_T0.314431.023
59_F228_L0.3121.015
102_H148_N0.311911.015
63_A172_I0.310871.012
232_G297_I0.308821.005
228_L306_V0.308351.003
78_P93_K0.307581.001
281_G301_N0.30690.999
196_G291_Y0.30560.995
79_V99_L0.303730.988
23_H26_K0.303180.987
242_L245_S0.30160.981
177_G230_K0.301380.981
37_D42_K0.300140.977
30_E46_P0.300130.977
284_Y299_P0.298790.972
249_P252_Q0.298520.971
79_V83_L0.297550.968
249_P253_W0.296110.964
53_G291_Y0.295780.963
180_H227_D0.294920.960
55_V293_S0.294660.959
247_L250_L0.292580.952
59_F178_M0.29220.951
37_D41_G0.292070.950
178_M230_K0.288820.940
273_W286_H0.281880.917
149_Y152_L0.28090.914
83_L158_R0.280510.913
268_Y273_W0.28010.912
96_I152_L0.278510.906
233_Q237_N0.277720.904
62_T235_L0.277420.903
137_P140_T0.276230.899
66_Q172_I0.275250.896
136_F143_A0.274740.894
250_L253_W0.274250.892
63_A160_T0.273750.891
126_L154_E0.272860.888
238_G253_W0.27250.887
180_H224_T0.270290.880
35_Y42_K0.269980.879
22_I233_Q0.26820.873
73_L96_I0.267340.870
235_L272_W0.267010.869
23_H28_V0.266930.869
287_S294_F0.266510.867
79_V155_I0.266330.867
157_E160_T0.265860.865
32_Y44_M0.265690.865
15_P38_K0.265420.864
236_L239_G0.265350.864
97_R254_M0.262890.856
49_V222_F0.26280.855
25_G233_Q0.261810.852
75_L270_Y0.261040.850
229_A306_V0.260310.847
27_I30_E0.260160.847
142_F273_W0.259870.846
239_G247_L0.259670.845
9_M33_Y0.258450.841
103_T139_G0.257710.839
160_T163_S0.257590.838
80_S92_E0.257250.837
157_E163_S0.257140.837
35_Y43_P0.256740.836
68_I74_D0.254770.829
100_L149_Y0.254220.827
49_V180_H0.2540.827
272_W297_I0.253240.824
99_L104_S0.2530.823
57_K288_G0.252080.820
168_L172_I0.251260.818
19_V29_Y0.250590.815
225_A229_A0.250140.814
96_I159_V0.248010.807
156_L164_F0.247060.804
52_I228_L0.246820.803
74_D82_Y0.246640.803
51_R222_F0.245980.800
164_F183_F0.243930.794
60_T217_G0.243840.794
283_I298_D0.24350.792
66_Q69_D0.243240.792
54_S288_G0.242860.790
245_S249_P0.242590.789
169_Q173_F0.241880.787
150_Q218_A0.241160.785
186_P189_W0.240270.782
142_F268_Y0.240180.782
38_K197_Y0.239580.780
281_G300_E0.238710.777
242_L247_L0.238610.777
153_G164_F0.238040.775
165_E169_Q0.237980.774
94_I104_S0.236130.768
88_D92_E0.235850.768
168_L221_L0.235440.766
229_A304_G0.234920.765
166_E169_Q0.234590.763
102_H286_H0.234210.762
168_L183_F0.232210.756
74_D97_R0.231690.754
83_L155_I0.231610.754
20_A304_G0.231050.752
176_L234_L0.23040.750
108_D218_A0.230090.749
246_I249_P0.228530.744
55_V58_S0.228350.743
127_Q131_N0.227210.739
135_N143_A0.226070.736
100_L152_L0.22530.733
50_F308_L0.223770.728
52_I308_L0.223650.728
19_V31_Q0.223390.727
17_A309_S0.22320.726
90_G137_P0.223090.726
73_L155_I0.222930.725
34_G43_P0.222350.724
228_L232_G0.222320.723
295_I306_V0.221970.722
247_L252_Q0.221670.721
244_P248_K0.221560.721
83_L154_E0.221310.720
172_I176_L0.220830.719
274_I282_R0.220020.716
101_T270_Y0.219460.714
73_L82_Y0.219330.714
18_A308_L0.218080.710
242_L252_Q0.217510.708
30_E225_A0.217340.707
72_K160_T0.215840.702
49_V192_R0.215770.702
62_T66_Q0.215720.702
94_I98_D0.215390.701
53_G293_S0.214350.698
47_D180_H0.214190.697
228_L295_I0.213350.694
292_G311_R0.212390.691
35_Y39_Q0.212240.691
234_L246_I0.212030.690
59_F173_F0.211910.690
58_S61_A0.21150.688
63_A171_N0.211380.688
74_D96_I0.210410.685
80_S91_K0.210390.685
252_Q255_M0.210090.684
103_T142_F0.209750.683
67_L167_L0.20960.682
60_T153_G0.209050.680
283_I296_W0.20790.677
227_D230_K0.207060.674
16_G34_G0.207030.674
94_I106_L0.20680.673
226_R230_K0.206590.672
232_G306_V0.206560.672
181_T224_T0.206380.672
58_S295_I0.206260.671
98_D138_P0.205860.670
106_L151_L0.205290.668
9_M17_A0.204550.666
15_P311_R0.203150.661
234_L239_G0.20280.660
274_I277_S0.201310.655
79_V82_Y0.201040.654
272_W295_I0.2010.654
108_D147_T0.19910.648
58_S272_W0.198990.648
172_I175_P0.198350.645
78_P82_Y0.197980.644
245_S250_L0.197260.642
76_D95_T0.196980.641
164_F173_F0.196950.641
68_I96_I0.196850.641
58_S232_G0.196740.640
35_Y38_K0.19650.639
60_T168_L0.195220.635
36_A39_Q0.194830.634
223_S228_L0.194730.634
37_D195_I0.194290.632
90_G94_I0.19420.632
27_I233_Q0.194130.632
17_A307_I0.192980.628
16_G310_N0.192840.628
251_S255_M0.190970.621
53_G219_G0.190430.620
56_S220_G0.190340.619
245_S252_Q0.190250.619
86_F89_P0.189830.618
62_T172_I0.188470.613
17_A20_A0.188290.613
9_M14_I0.188190.612
108_D145_S0.18790.611
149_Y268_Y0.187590.610
121_F124_E0.187520.610
19_V33_Y0.187160.609
254_M257_S0.186690.608
36_A44_M0.186640.607
236_L304_G0.186530.607
272_W285_G0.186010.605
102_H149_Y0.185860.605
298_D303_L0.185450.604
51_R220_G0.185170.603
80_S93_K0.185070.602
67_L159_V0.184180.599
233_Q304_G0.183390.597
53_G290_G0.182890.595
235_L255_M0.182580.594
64_V155_I0.182240.593
299_P303_L0.182070.593
209_G214_P0.181960.592
52_I55_V0.181650.591
127_Q130_A0.181520.591
58_S286_H0.181270.590
75_L78_P0.18110.589
211_N214_P0.180940.589
144_Y288_G0.180780.588
65_M100_L0.180650.588
253_W257_S0.180140.586
49_V182_G0.179680.585
176_L230_K0.179350.584
75_L97_R0.178660.581
27_I229_A0.178650.581
66_Q246_I0.178610.581
209_G213_N0.176250.574
56_S60_T0.176120.573
244_P247_L0.17560.571
34_G310_N0.175470.571
107_P135_N0.175440.571
39_Q42_K0.175220.570
56_S183_F0.17510.570
246_I252_Q0.174350.567
245_S248_K0.172760.562
182_G185_P0.172750.562
210_Y213_N0.172440.561
224_T227_D0.171970.560
268_Y286_H0.170980.556
136_F139_G0.170680.555
190_P193_D0.170540.555
65_M246_I0.170210.554
241_I246_I0.170190.554
89_P92_E0.170090.554
168_L181_T0.16960.552
53_G218_A0.169480.552
273_W285_G0.169410.551
123_D158_R0.169330.551
155_I158_R0.169140.550
102_H268_Y0.169110.550
285_G296_W0.168960.550
208_P213_N0.168930.550
153_G157_E0.16870.549
237_N241_I0.168590.549
275_N285_G0.168580.549
225_A306_V0.168320.548
182_G222_F0.167940.547
237_N240_L0.167930.546
32_Y225_A0.166980.543
63_A67_L0.166960.543
23_H302_G0.166850.543
24_N27_I0.166490.542
171_N175_P0.166010.540
157_E164_F0.165960.540
14_I309_S0.16580.540
58_S268_Y0.165670.539
179_K227_D0.165320.538
19_V305_V0.164810.536
49_V224_T0.164120.534
65_M272_W0.1640.534
52_I293_S0.163990.534
129_L147_T0.163930.533
239_G243_S0.163150.531
25_G28_V0.162910.530
27_I226_R0.162310.528
21_V303_L0.161040.524
250_L254_M0.1610.524
241_I245_S0.160990.524
63_A66_Q0.160630.523
20_A30_E0.160460.522
243_S252_Q0.160440.522
51_R218_A0.160280.522
57_K286_H0.15990.520
253_W256_P0.159310.518
52_I221_L0.159170.518
160_T171_N0.158930.517
99_L152_L0.158850.517
234_L247_L0.158680.516
65_M69_D0.158430.516
70_E167_L0.158350.515
14_I17_A0.158250.515
243_S250_L0.158190.515
212_P215_Y0.15810.515
15_P310_N0.157730.513
57_K146_N0.157720.513
182_G186_P0.157330.512
238_G249_P0.156390.509
200_N203_Q0.155470.506
274_I284_Y0.155270.505
235_L284_Y0.155150.505
18_A21_V0.155090.505
53_G57_K0.154670.503
234_L238_G0.15430.502
62_T247_L0.154110.502
223_S227_D0.154110.502
53_G144_Y0.153930.501
74_D81_K0.153920.501
68_I77_D0.15380.501
272_W286_H0.153430.499
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
4gdnA0.97571000.092
2qmiA0.98481000.11
4ivkA0.98481000.121
3tg9A0.96351000.122
3rjuA0.97261000.128
1ci9A0.98481000.13
4e6wA0.96961000.133
3o3vA0.96961000.133
2drwA0.97571000.137
1zkjA0.95441000.137

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