GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Transpeptidase - Penicillin binding protein transpeptidase domain
Pfam: PF00905 (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: 304
Sequences: 8113
Seq/Len: 26.69
HH_delta: 0.089 (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
5_V279_V1.379833.158
267_V280_A1.264442.894
12_E186_H1.245522.851
3_V302_I1.214172.779
170_A280_A1.208872.767
220_T269_F1.173892.687
95_R225_E1.149252.631
193_D197_K1.141942.614
12_E189_K1.130472.588
243_G266_F1.061842.431
67_T91_N1.024172.344
7_D12_E1.014022.321
58_E215_T0.986272.258
59_S117_K0.98322.251
92_V102_S0.967462.214
8_P278_A0.958172.193
224_R240_P0.945062.163
95_R221_E0.934642.139
5_V302_I0.933612.137
84_W290_Y0.915372.095
120_D124_K0.913792.092
97_A105_Y0.897612.055
181_V209_Q0.885222.026
7_D10_T0.865131.980
96_D100_R0.861921.973
171_S182_Y0.860961.971
54_A215_T0.838141.918
6_M170_A0.833511.908
51_F172_A0.831731.904
63_S66_T0.808451.851
14_L277_Y0.802631.837
99_A225_E0.79051.809
5_V277_Y0.789931.808
300_K304_E0.782211.790
55_A121_Y0.771771.767
96_D99_A0.768211.758
66_T112_D0.765941.753
7_D276_Q0.75951.738
179_G217_Y0.745791.707
110_A156_A0.738741.691
50_P176_I0.738011.689
9_K276_Q0.728161.667
225_E229_E0.72161.652
48_F122_A0.717111.641
299_F303_M0.706361.617
89_H102_S0.705731.615
174_A278_A0.705581.615
93_T96_D0.692561.585
58_E212_S0.685171.568
166_P280_A0.682171.561
268_G299_F0.675361.546
173_Y267_V0.67021.534
213_P217_Y0.665091.522
224_R228_T0.663831.519
175_T182_Y0.663811.519
70_D102_S0.662911.517
173_Y223_L0.661521.514
3_V281_V0.656341.502
268_G303_M0.655951.501
108_K112_D0.649031.486
9_K274_T0.648171.484
54_A211_I0.646281.479
211_I216_A0.634551.452
92_V96_D0.630331.443
69_D91_N0.626831.435
117_K120_D0.625081.431
171_S185_P0.624781.430
212_S215_T0.624641.430
56_A109_L0.623841.428
83_N102_S0.619211.417
75_P80_T0.617871.414
7_D14_L0.615831.410
6_M185_P0.612441.402
54_A125_F0.603581.382
179_G213_P0.590891.353
281_V299_F0.583961.337
97_A106_F0.576111.319
110_A118_F0.575081.316
58_E124_K0.574261.314
64_P222_M0.573851.314
242_A269_F0.572081.309
62_I94_L0.571071.307
221_E224_R0.561731.286
179_G220_T0.561491.285
99_A229_E0.558631.279
98_L222_M0.558041.277
283_V298_I0.553341.267
34_F40_S0.545211.248
13_I187_L0.544431.246
176_I219_L0.544221.246
70_D83_N0.5431.243
220_T242_A0.542041.241
53_A106_F0.540881.238
44_P164_V0.538131.232
119_R123_K0.537251.230
47_T169_M0.535631.226
127_F164_V0.532791.220
4_V167_L0.525981.204
169_M265_W0.518031.186
236_I300_K0.517171.184
263_D282_W0.516741.183
121_Y124_K0.513551.176
182_Y208_K0.51081.169
116_E120_D0.506291.159
279_V302_I0.50561.157
3_V279_V0.50461.155
169_M267_V0.496331.136
6_M174_A0.495171.133
62_I66_T0.492321.127
209_Q213_P0.491951.126
227_V241_V0.490661.123
50_P173_Y0.490611.123
8_P174_A0.489351.120
227_V243_G0.488241.118
125_F211_I0.487851.117
177_A269_F0.485541.111
75_P78_G0.484341.109
59_S121_Y0.482621.105
71_S108_K0.479261.097
6_M278_A0.475671.089
228_T235_K0.475491.088
4_V166_P0.475021.087
178_N183_V0.474721.087
301_K304_E0.472231.081
16_M37_A0.4721.080
68_F112_D0.466821.069
54_A219_L0.464681.064
58_E121_Y0.463171.060
102_S105_Y0.460771.055
177_A242_A0.45921.051
4_V170_A0.455461.043
264_A291_G0.449511.029
192_E198_V0.449271.028
41_Q163_S0.445671.020
57_L222_M0.445161.019
225_E228_T0.44361.015
62_I112_D0.443081.014
68_F105_Y0.439661.006
216_A220_T0.437461.001
154_S160_G0.436460.999
164_V169_M0.436090.998
279_V299_F0.433730.993
8_P277_Y0.433410.992
64_P218_I0.432420.990
226_V232_G0.429390.983
16_M35_N0.429320.983
183_V207_K0.42870.981
121_Y125_F0.420120.962
50_P98_L0.418820.959
92_V100_R0.418010.957
82_K86_N0.417910.957
114_G117_K0.416530.953
290_Y293_A0.414740.949
220_T223_L0.413330.946
190_K198_V0.412730.945
265_W282_W0.412450.944
227_V266_F0.412140.943
43_Q263_D0.411040.941
85_N89_H0.410660.940
128_G168_Q0.407370.932
292_S296_A0.4060.929
279_V303_M0.405970.929
215_T218_I0.405250.928
94_L105_Y0.404850.927
59_S113_L0.401770.920
74_Y111_Q0.401640.919
67_T93_T0.401250.918
123_K129_S0.40090.918
264_A295_A0.397690.910
281_V298_I0.393950.902
54_A121_Y0.392550.899
170_A278_A0.391540.896
159_Q249_E0.390220.893
214_E218_I0.389630.892
54_A216_A0.389450.891
16_M38_T0.387580.887
117_K121_Y0.384990.881
184_K205_P0.382730.876
53_A94_L0.381830.874
51_F122_A0.381640.874
4_V16_M0.379510.869
89_H100_R0.379390.868
124_K208_K0.378980.867
57_L218_I0.3780.865
217_Y220_T0.377270.864
154_S159_Q0.373810.856
16_M187_L0.372880.854
120_D123_K0.371250.850
57_L215_T0.368410.843
177_A278_A0.368140.843
264_A289_G0.36320.831
46_S49_K0.362880.831
264_A294_I0.360460.825
291_G296_A0.355890.815
169_M172_A0.355120.813
113_L117_K0.354570.812
104_T108_K0.351410.804
62_I109_L0.350990.803
263_D284_G0.350330.802
59_S62_I0.348890.799
8_P177_A0.34860.798
283_V295_A0.348040.797
95_R222_M0.347360.795
215_T219_L0.347310.795
2_A37_A0.345540.791
114_G152_L0.345180.790
52_T118_F0.342990.785
92_V105_Y0.342880.785
165_T168_Q0.340770.780
10_T186_H0.340440.779
51_F125_F0.337950.774
50_P223_L0.335520.768
123_K128_G0.334070.765
73_K80_T0.333370.763
36_R284_G0.333240.763
232_G245_T0.331080.758
83_N89_H0.330090.756
42_R263_D0.330060.756
89_H92_V0.330020.755
171_S184_K0.329510.754
34_F39_Q0.329080.753
221_E225_E0.32850.752
220_T224_R0.328130.751
196_G199_I0.327570.750
70_D90_G0.327120.749
294_I297_P0.326720.748
111_Q153_A0.323850.741
81_F107_V0.323160.740
218_I221_E0.322680.739
2_A166_P0.322110.737
70_D89_H0.321720.736
62_I68_F0.321210.735
163_S166_P0.320160.733
94_L109_L0.31920.731
266_F296_A0.317390.726
35_N38_T0.31630.724
42_R282_W0.316210.724
56_A62_I0.315290.722
214_E217_Y0.311920.714
224_R227_V0.311290.713
110_A115_P0.310990.712
53_A222_M0.310930.712
69_D108_K0.310810.711
6_M171_S0.308690.707
54_A176_I0.30720.703
179_G216_A0.307130.703
243_G296_A0.306550.702
236_I304_E0.306250.701
10_T183_V0.305730.700
108_K111_Q0.303690.695
216_A219_L0.302990.694
106_F109_L0.301920.691
283_V294_I0.301020.689
83_N104_T0.300250.687
127_F172_A0.299570.686
72_P88_Y0.298880.684
118_F122_A0.298790.684
169_M280_A0.297290.680
262_Y289_G0.297150.680
178_N181_V0.294280.674
121_Y211_I0.293850.673
170_A267_V0.293820.673
219_L222_M0.293070.671
5_V8_P0.292360.669
166_P170_A0.292330.669
13_I167_L0.290970.666
47_T267_V0.290710.665
2_A282_W0.289950.664
3_V298_I0.289040.662
155_T158_G0.288990.661
173_Y278_A0.288440.660
57_L94_L0.288410.660
4_V280_A0.286020.655
167_L185_P0.285560.654
51_F169_M0.284370.651
291_G294_I0.283780.650
176_I220_T0.283780.650
55_A59_S0.282880.648
98_L223_L0.282450.647
53_A98_L0.282220.646
160_G163_S0.281450.644
264_A292_S0.281310.644
164_V168_Q0.281180.644
190_K201_F0.280130.641
166_P265_W0.279430.640
81_F157_I0.279220.639
210_V216_A0.277430.635
171_S175_T0.276610.633
43_Q248_A0.275980.632
155_T162_V0.275720.631
45_G248_A0.275190.630
93_T105_Y0.274650.629
157_I160_G0.274420.628
94_L222_M0.272210.623
154_S157_I0.270350.619
2_A18_G0.270170.618
99_A226_V0.26950.617
198_V201_F0.267680.613
241_V299_F0.267580.612
154_S158_G0.267190.612
198_V202_T0.266990.611
38_T167_L0.266290.610
193_D196_G0.266170.609
151_N154_S0.265580.608
68_F108_K0.265320.607
159_Q248_A0.264430.605
129_S168_Q0.263160.602
42_R284_G0.261020.597
107_V157_I0.260810.597
186_H202_T0.260140.595
103_N107_V0.259460.594
115_P152_L0.259410.594
188_I191_I0.258950.593
6_M13_I0.258910.593
107_V111_Q0.258110.591
171_S183_V0.257520.589
184_K206_K0.257460.589
186_H189_K0.257290.589
239_Y276_Q0.255810.586
68_F109_L0.255290.584
192_E196_G0.254930.584
104_T107_V0.254910.583
266_F299_F0.254340.582
18_G37_A0.254220.582
211_I215_T0.253790.581
234_A238_G0.253320.580
191_I196_G0.252380.578
239_Y304_E0.252030.577
8_P275_P0.25140.575
179_G182_Y0.25040.573
92_V97_A0.249840.572
127_F169_M0.249680.572
244_K247_T0.248950.570
76_I153_A0.247020.565
53_A109_L0.246960.565
85_N88_Y0.246240.564
155_T159_Q0.246080.563
44_P169_M0.245970.563
20_P23_D0.245180.561
269_F278_A0.243280.557
237_P300_K0.242570.555
243_G268_G0.242320.555
113_L118_F0.241470.553
43_Q265_W0.241060.552
218_I222_M0.240510.551
281_V295_A0.239940.549
181_V207_K0.239710.549
9_K178_N0.238730.546
3_V17_V0.238670.546
95_R99_A0.238620.546
81_F154_S0.238380.546
4_V278_A0.238380.546
6_M167_L0.238370.546
292_S295_A0.237880.545
171_S174_A0.237560.544
52_T156_A0.237440.543
106_F222_M0.236720.542
34_F37_A0.236210.541
4_V37_A0.235870.540
88_Y104_T0.235650.539
241_V266_F0.235220.538
173_Y176_I0.234930.538
183_V204_K0.233750.535
71_S104_T0.232940.533
174_A183_V0.232440.532
6_M280_A0.231030.529
189_K192_E0.230530.528
175_T210_V0.230460.528
233_R293_A0.229170.525
170_A174_A0.228840.524
48_F162_V0.228120.522
296_A300_K0.227020.520
41_Q168_Q0.227010.520
64_P95_R0.226510.518
289_G294_I0.226220.518
49_K245_T0.225250.516
223_L269_F0.225090.515
127_F168_Q0.224430.514
85_N102_S0.22440.514
13_I16_M0.224210.513
55_A113_L0.224010.513
49_K244_K0.223960.513
47_T265_W0.223960.513
122_A127_F0.223770.512
226_V231_T0.223710.512
57_L219_L0.223470.512
176_I269_F0.223390.511
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
3un7A0.9771000.089
3ue3A0.95071000.097
4jbfA0.97371000.104
1qmeA0.99011000.106
3equA0.94741000.107
3pbtA0.95391000.107
2wadA0.97371000.117
3vskA0.97371000.127
3udfA0.86181000.147
1vqqA0.95071000.15

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