GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cys_Met_Meta_PP - CysMet metabolism PLP-dependent enzyme
Pfam: PF01053 (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: CL0061
Length: 386
Sequences: 11108
Seq/Len: 28.78
HH_delta: 0.094 (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
96_H123_T1.673043.932
187_N190_E1.534833.607
134_E168_E1.381023.246
96_H138_R1.378513.240
160_E164_K1.139872.679
163_A174_V1.126582.648
265_E269_E1.115522.622
158_D161_A1.099242.583
143_L175_V1.037012.437
164_K168_E0.970942.282
121_E138_R0.959882.256
148_S181_A0.959212.254
144_V166_A0.951842.237
70_G216_V0.95172.237
96_H141_T0.926022.176
95_D142_K0.922432.168
96_H121_E0.916072.153
167_K194_D0.902982.122
130_L161_A0.901612.119
178_N196_V0.897732.110
132_A135_A0.893712.100
169_H172_I0.890292.092
129_D132_A0.87942.067
134_E165_L0.868562.041
239_S242_D0.849461.996
160_E190_E0.847631.992
123_T138_R0.843621.983
131_E134_E0.8421.979
130_L165_L0.833961.960
279_R308_E0.822791.934
161_A164_K0.814741.915
306_S364_L0.813731.912
278_K310_K0.807211.897
99_A111_L0.803971.889
64_L214_A0.797951.875
326_F337_S0.796621.872
258_E262_E0.781271.836
134_E169_H0.773871.819
69_G187_N0.769491.808
198_H214_A0.76551.799
308_E363_G0.758311.782
131_E135_A0.756351.778
126_D132_A0.751871.767
95_D140_N0.747321.756
270_F382_E0.743571.747
163_A167_K0.737691.734
200_A212_G0.734161.725
125_V136_A0.724561.703
86_A195_I0.722831.699
176_V193_A0.712371.674
58_R62_Q0.705741.659
157_P162_I0.704841.656
367_L381_L0.704291.655
166_A174_V0.698931.643
123_T136_A0.696471.637
101_D126_D0.679841.598
307_F367_L0.674471.585
69_G190_E0.673691.583
167_K174_V0.667951.570
266_A375_D0.66431.561
259_R262_E0.66171.555
60_L246_L0.639731.503
96_H140_N0.637571.498
185_N261_N0.636431.496
83_I106_G0.631721.485
86_A175_V0.626031.471
137_L165_L0.624941.469
166_A172_I0.624811.468
98_V136_A0.624041.467
76_F85_A0.62031.458
270_F378_I0.61431.444
144_V162_I0.612591.440
146_L162_I0.608771.431
270_F274_H0.604851.421
62_Q66_A0.601181.413
374_P377_L0.599421.409
144_V172_I0.593131.394
200_A246_L0.592841.393
137_L172_I0.592781.393
165_L169_H0.585221.375
92_K117_R0.585161.375
91_L120_V0.584241.373
266_A269_E0.583651.372
132_A136_A0.581721.367
68_E198_H0.580851.365
204_L370_G0.577441.357
373_D377_L0.575261.352
267_L378_I0.573281.347
374_P378_I0.571691.344
69_G189_L0.56341.324
82_A197_V0.55911.314
145_F175_V0.557661.311
111_L122_V0.543851.278
163_A192_G0.538591.266
153_T358_A0.53751.263
200_A214_A0.53691.262
60_L75_L0.536871.262
203_Y303_G0.531131.248
137_L144_V0.52981.245
83_I145_F0.529371.244
261_N265_E0.522191.227
323_L339_I0.517661.217
200_A205_S0.515061.210
99_A124_F0.512661.205
175_V197_V0.510461.200
379_A382_E0.509321.197
84_S88_L0.509091.196
47_Y53_G0.508731.196
181_A196_V0.508091.194
133_L162_I0.504341.185
318_R322_A0.50211.180
73_A216_V0.501061.178
112_E116_P0.49971.174
149_P301_G0.499611.174
217_V224_Y0.496181.166
121_E140_N0.496151.166
278_K363_G0.495221.164
266_A374_P0.494041.161
263_N266_A0.493521.160
262_E266_A0.491831.156
146_L174_V0.488851.149
219_G222_E0.487061.145
173_L223_L0.486871.144
373_D376_D0.485071.140
330_P365_I0.483061.135
62_Q65_A0.481751.132
264_A268_A0.476391.120
221_S225_D0.476131.119
180_F332_L0.475321.117
308_E361_S0.475051.116
83_I175_V0.473251.112
130_L134_E0.472291.110
257_M260_Q0.471621.108
269_E273_E0.4651.093
326_F381_L0.464851.092
138_R141_T0.464741.092
278_K308_E0.462841.088
92_K95_D0.460041.081
98_V125_V0.459041.079
71_E219_G0.459031.079
174_V193_A0.458721.078
263_N374_P0.458151.077
137_L169_H0.455211.070
193_A196_V0.454521.068
160_E191_L0.451491.061
90_L173_L0.450991.060
312_G315_A0.450381.058
313_E317_R0.446621.050
267_L369_V0.445621.047
99_A103_L0.444471.045
260_Q303_G0.444251.044
57_V243_A0.443161.041
154_L283_P0.442111.039
134_E161_A0.439191.032
254_P258_E0.439111.032
60_L214_A0.438871.031
164_K167_K0.436741.026
72_D221_S0.436641.026
70_G189_L0.436181.025
267_L377_L0.435851.024
309_L319_F0.43441.021
137_L141_T0.431791.015
125_V133_L0.430931.013
146_L159_L0.4250.999
212_G246_L0.423980.996
380_D383_Q0.421990.992
102_D155_E0.421670.991
182_T186_Q0.421390.990
146_L176_V0.420260.988
159_L176_V0.42020.988
72_D219_G0.418210.983
304_L368_S0.417330.981
58_R61_E0.416750.979
87_L143_L0.416620.979
102_D157_P0.416180.978
100_S146_L0.415920.977
85_A236_A0.414390.974
375_D379_A0.41320.971
65_A73_A0.41190.968
154_L305_L0.410840.966
267_L381_L0.410760.965
222_E225_D0.408850.961
91_L97_I0.408250.959
259_R263_N0.405450.953
163_A193_A0.40540.953
223_L227_L0.403510.948
149_P302_G0.40140.943
266_A378_I0.399890.940
73_A214_A0.399210.938
378_I382_E0.394330.927
83_I197_V0.39310.924
99_A122_V0.392160.922
335_V371_L0.391420.920
86_A215_V0.391070.919
59_A63_R0.39020.917
63_R247_L0.389150.915
217_V223_L0.388070.912
47_Y58_R0.387050.910
194_D218_N0.385950.907
260_Q263_N0.383880.902
238_L243_A0.382810.900
326_F377_L0.382060.898
166_A170_G0.381970.898
133_L144_V0.379580.892
274_H382_E0.379440.892
269_E272_E0.377930.888
313_E362_D0.376920.886
133_L137_L0.376210.884
266_A270_F0.372720.876
339_I365_I0.37190.874
98_V141_T0.371290.873
165_L168_E0.370290.870
57_V238_L0.36930.868
159_L163_A0.365750.860
146_L157_P0.364970.858
91_L95_D0.363840.855
87_L111_L0.363340.854
63_R66_A0.362710.852
68_E188_P0.362610.852
272_E285_L0.361880.850
130_L133_L0.360890.848
319_F339_I0.360850.848
76_F215_V0.360740.848
376_D380_D0.359190.844
63_R251_R0.358870.843
317_R321_D0.356050.837
87_L91_L0.355910.836
217_V221_S0.355570.836
49_Y329_A0.353840.832
377_L380_D0.352590.829
182_T198_H0.352540.829
238_L246_L0.351870.827
94_G142_K0.350510.824
156_V290_Q0.349210.821
112_E124_F0.347490.817
50_S57_V0.346980.815
162_I174_V0.346830.815
148_S159_L0.34660.815
64_L204_L0.345460.812
197_V215_V0.345050.811
149_P186_Q0.344820.810
270_F273_E0.344610.810
212_G238_L0.343960.808
184_Y258_E0.343850.808
186_Q191_L0.343680.808
108_Y112_E0.343080.806
101_D155_E0.342950.806
219_G223_L0.340110.799
324_K383_Q0.337970.794
204_L250_L0.335250.788
125_V132_A0.334550.786
267_L374_P0.333520.784
255_L371_L0.333440.784
81_A236_A0.332920.782
279_R363_G0.331550.779
127_P157_P0.330750.777
248_R251_R0.330660.777
128_T290_Q0.329710.775
195_I215_V0.329640.775
224_Y228_R0.329560.775
88_L228_R0.327860.771
88_L118_F0.326740.768
166_A169_H0.326450.767
111_L145_F0.326380.767
48_I52_Y0.325530.765
159_L191_L0.32550.765
97_I111_L0.325150.764
252_T255_L0.324880.764
270_F375_D0.324830.763
218_N221_S0.324180.762
71_E221_S0.32410.762
82_A215_V0.322980.759
241_F245_L0.322880.759
225_D228_R0.322690.758
52_Y232_R0.322370.758
98_V123_T0.322170.757
109_R112_E0.321890.756
218_N223_L0.32140.755
149_P181_A0.321180.755
84_S110_L0.320360.753
67_L182_T0.320260.753
167_K170_G0.319850.752
267_L367_L0.319350.751
167_K172_I0.319350.751
147_E151_N0.315580.742
101_D124_F0.31510.741
148_S178_N0.314630.739
80_M83_I0.314440.739
268_A272_E0.31360.737
144_V167_K0.313480.737
178_N181_A0.312420.734
101_D357_E0.312180.734
180_F304_L0.31150.732
263_N267_L0.310160.729
261_N300_G0.308420.725
200_A204_L0.307160.722
148_S186_Q0.304460.716
238_L242_D0.304190.715
204_L371_L0.303380.713
126_D129_D0.303160.712
159_L193_A0.302430.711
379_A383_Q0.302170.710
68_E216_V0.30190.710
161_A165_L0.301490.709
79_G179_T0.300680.707
223_L226_R0.300510.706
145_F197_V0.300270.706
192_G218_N0.300230.706
129_D135_A0.300130.705
188_P192_G0.299280.703
139_P142_K0.299090.703
221_S227_L0.297340.699
316_A365_I0.296410.697
123_T140_N0.295980.696
222_E226_R0.295090.694
267_L270_F0.29450.692
115_L120_V0.294330.692
183_P198_H0.294320.692
276_K310_K0.294140.691
281_Y308_E0.294090.691
90_L175_V0.294010.691
262_E374_P0.293870.691
195_I217_V0.293740.690
217_V227_L0.293340.689
92_K118_F0.293310.689
80_M84_S0.291760.686
255_L259_R0.291670.685
61_E75_L0.291520.685
150_S153_T0.291460.685
75_L214_A0.291330.685
208_S334_G0.290960.684
143_L173_L0.290470.683
90_L195_I0.29030.682
251_R336_E0.289720.681
148_S196_V0.288480.678
377_L381_L0.288460.678
159_L186_Q0.28640.673
64_L216_V0.28620.673
200_A238_L0.285480.671
54_N58_R0.285290.670
98_V144_V0.285290.670
163_A191_L0.284810.669
318_R321_D0.284310.668
88_L230_F0.28420.668
189_L196_V0.283510.666
311_G315_A0.283250.666
139_P169_H0.282160.663
108_Y124_F0.281820.662
221_S224_Y0.279630.657
188_P196_V0.279420.657
97_I143_L0.279260.656
84_S234_L0.278190.654
57_V75_L0.278020.653
265_E272_E0.277970.653
182_T203_Y0.27790.653
224_Y227_L0.277570.652
343_A362_D0.276260.649
175_V195_I0.275950.649
189_L218_N0.275710.648
325_L377_L0.275120.647
326_F339_I0.270360.635
263_N371_L0.270180.635
114_L118_F0.269850.634
74_L224_Y0.269460.633
63_R250_L0.26910.632
127_P133_L0.268410.631
135_A139_P0.268220.630
74_L215_V0.267410.628
223_L228_R0.267280.628
218_N222_E0.266550.626
86_A197_V0.265970.625
375_D378_I0.265110.623
92_K142_K0.2650.623
68_E196_V0.264320.621
97_I122_V0.264070.621
205_S246_L0.263830.620
103_L107_T0.263650.620
77_S81_A0.263430.619
268_A285_L0.263410.619
78_S81_A0.26340.619
123_T141_T0.263340.619
159_L174_V0.263310.619
251_R255_L0.263280.619
320_L339_I0.262620.617
308_E364_L0.262070.616
173_L194_D0.26110.614
105_G109_R0.260660.613
225_D229_E0.260520.612
376_D379_A0.259970.611
72_D224_Y0.25940.610
59_A62_Q0.25890.608
65_A70_G0.258650.608
83_I86_A0.257260.605
185_N257_M0.25710.604
326_F367_L0.256940.604
319_F323_L0.256760.603
179_T199_S0.256180.602
113_E229_E0.255370.600
134_E164_K0.2550.599
185_N300_G0.254730.599
322_A325_L0.254540.598
151_N202_K0.253950.597
315_A318_R0.253280.595
85_A230_F0.253050.595
254_P259_R0.253020.595
236_A239_S0.251620.591
322_A384_A0.250620.589
241_F244_W0.250120.588
206_G212_G0.249460.586
281_Y288_H0.249350.586
242_D245_L0.248950.585
74_L228_R0.248890.585
144_V165_L0.247710.582
269_E285_L0.247370.581
96_H142_K0.24720.581
284_G301_G0.247060.581
315_A363_G0.246540.579
258_E261_N0.246150.578
240_P243_A0.245380.577
148_S156_V0.244710.575
60_L64_L0.244690.575
105_G342_P0.244310.574
76_F82_A0.243410.572
56_T244_W0.243380.572
105_G347_H0.242950.571
356_A361_S0.242460.570
148_S191_L0.242190.569
47_Y50_S0.241170.567
111_L124_F0.241080.567
86_A143_L0.240330.565
60_L247_L0.239910.564
238_L241_F0.239810.564
202_K366_R0.239120.562
95_D120_V0.239020.562
380_D384_A0.238870.561
115_L118_F0.238720.561
147_E157_P0.238660.561
372_E377_L0.238610.561
134_E137_L0.237390.558
374_P382_E0.23730.558
128_T155_E0.236220.555
55_P59_A0.235860.554
102_D153_T0.235450.553
320_L330_P0.234970.552
282_Y305_L0.234840.552
221_S228_R0.234760.552
268_A280_V0.234660.551
317_R332_L0.234440.551
76_F231_R0.234130.550
75_L238_L0.234020.550
64_L75_L0.233410.549
102_D150_S0.232830.547
181_A184_Y0.232260.546
88_L234_L0.231880.545
331_S334_G0.231780.545
377_L382_E0.231410.544
71_E217_V0.230930.543
56_T59_A0.230420.542
316_A363_G0.230040.541
91_L143_L0.229640.540
219_G225_D0.229570.540
274_H378_I0.229340.539
64_L200_A0.22910.538
195_I223_L0.228820.538
76_F236_A0.228230.536
123_T139_P0.228190.536
319_F381_L0.227570.535
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
4kamA0.99481000.094
3ri6A0.98961000.118
2fq6A0.97931000.139
1qgnA0.98961000.14
3ndnA0.9871000.142
3nmyA0.97151000.148
3qhxA0.96891000.182
3aczA0.98451000.217
2ctzA0.99481000.217
3cogA0.97411000.219

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