GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SHMT - Serine hydroxymethyltransferase
Pfam: PF00464 (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: 399
Sequences: 31178
Seq/Len: 78.14
HH_delta: 0.19 (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
41_G45_T2.5364.155
190_R194_D2.248933.685
162_E195_E2.020683.311
74_R291_K1.907653.126
311_A393_K1.904153.120
311_A389_E1.783742.923
288_V291_K1.737092.846
38_E42_S1.720092.818
158_Y188_R1.713032.807
34_P38_E1.612792.642
315_A318_E1.562692.560
160_E163_K1.552652.544
315_A396_A1.536642.518
304_Q308_N1.517072.486
188_R191_E1.480022.425
300_E303_K1.454992.384
310_K314_E1.453962.382
306_V310_K1.447322.371
112_T145_V1.447052.371
37_R41_G1.399232.293
350_A353_E1.39432.284
191_E195_E1.382892.266
311_A315_A1.375632.254
74_R294_L1.373522.250
148_P160_E1.324332.170
185_D188_R1.323572.169
307_K389_E1.304412.137
112_T143_E1.296622.124
315_A393_K1.294222.121
38_E41_G1.259082.063
228_G241_I1.234452.023
303_K307_K1.214231.989
187_K191_E1.211231.985
73_E77_E1.20311.971
160_E164_L1.197151.961
162_E166_K1.196341.960
117_S148_P1.183561.939
35_A288_V1.180931.935
35_A292_E1.173531.923
77_E294_L1.173521.923
190_R200_L1.164431.908
313_A317_Q1.160171.901
162_E188_R1.150181.885
158_Y192_I1.149031.883
112_T169_K1.134471.859
314_E318_E1.130671.853
193_A198_A1.130061.852
349_K353_E1.127461.847
279_H282_R1.103951.809
112_T166_K1.102781.807
33_S292_E1.094811.794
350_A354_A1.093491.792
39_A288_V1.091761.789
162_E192_I1.091621.789
162_E196_V1.091151.788
35_A295_S1.058271.734
111_D171_K1.052361.724
42_S46_N1.051091.722
389_E393_K1.030661.689
175_C189_F1.021111.673
157_D160_E1.016361.665
150_D153_T1.008471.652
204_I226_V0.996771.633
244_T263_A0.990511.623
159_D163_K0.982581.610
192_I196_V0.981931.609
172_L201_M0.962651.577
102_V225_V0.961731.576
304_Q307_K0.957151.568
343_D346_E0.955081.565
37_R45_T0.938651.538
112_T170_P0.935261.532
315_A319_R0.93161.526
75_A241_I0.924981.516
193_A200_L0.915231.500
351_L358_V0.882511.446
390_E393_K0.878911.440
161_L189_F0.874021.432
117_S146_P0.861961.412
40_L44_L0.860911.411
70_L291_K0.86031.410
322_K336_D0.85881.407
307_K311_A0.856281.403
159_D162_E0.853741.399
390_E394_E0.852821.397
314_E317_Q0.852731.397
309_A313_A0.848631.390
89_N92_P0.846111.386
201_M227_T0.845541.385
74_R77_E0.843311.382
166_K196_V0.840641.377
288_V292_E0.838571.374
102_V201_M0.820361.344
346_E350_A0.813081.332
145_V164_L0.808031.324
308_N311_A0.804441.318
165_A198_A0.794451.302
303_K306_V0.773221.267
245_N261_E0.769431.261
35_A38_E0.768871.260
391_D394_E0.752661.233
311_A314_E0.750041.229
37_R44_L0.749121.227
183_P187_K0.748591.227
223_A226_V0.745751.222
165_A170_P0.741881.216
150_D157_D0.730991.198
173_I193_A0.729571.195
147_Y164_L0.713861.170
159_D188_R0.710681.164
100_L104_M0.707831.160
150_D155_L0.704481.154
174_I201_M0.703671.153
215_L306_V0.702691.151
39_A42_S0.696541.141
163_K167_E0.695781.140
173_I198_A0.688891.129
356_I395_I0.682941.119
302_A306_V0.677711.110
349_K352_E0.67411.104
98_A227_T0.671391.100
166_K195_E0.670841.099
162_E191_E0.670671.099
191_E194_D0.668161.095
260_E264_E0.663511.087
99_N128_S0.660591.082
114_M170_P0.658341.079
278_P281_H0.655941.075
184_I187_K0.650351.066
291_K295_S0.647391.061
165_A192_I0.63651.043
76_K82_E0.629611.032
299_K303_K0.628211.029
225_V244_T0.626331.026
165_A196_V0.624751.024
190_R193_A0.623951.022
194_D222_Y0.623841.022
205_S229_S0.623631.022
92_P240_G0.622761.020
336_D374_G0.622211.019
111_D169_K0.622031.019
34_P45_T0.621951.019
358_V377_L0.621731.019
313_A333_V0.621581.018
34_P37_R0.619951.016
307_K310_K0.619251.015
317_Q323_V0.618711.014
106_L199_Y0.61841.013
103_Y174_I0.61771.012
239_G285_A0.614641.007
42_S45_T0.614331.007
345_K349_K0.608420.997
107_L142_F0.607480.995
108_K111_D0.606160.993
356_I394_E0.606110.993
312_L315_A0.601520.986
73_E76_K0.599740.983
377_L395_I0.592020.970
300_E304_Q0.590960.968
308_N389_E0.585620.960
99_N227_T0.584540.958
114_M164_L0.584020.957
127_G131_N0.580930.952
38_E45_T0.578110.947
99_N201_M0.576360.944
70_L73_E0.574930.942
166_K169_K0.574920.942
301_Y305_V0.573830.940
346_E349_K0.569370.933
40_L285_A0.56750.930
107_L113_I0.567160.929
230_T286_L0.562980.922
79_F243_L0.556650.912
72_I76_K0.555230.910
192_I195_E0.554660.909
158_Y162_E0.553330.907
189_F200_L0.549520.900
308_N392_M0.549420.900
113_I172_L0.548770.899
336_D373_S0.545080.893
312_L377_L0.543760.891
175_C186_F0.542480.889
192_I198_A0.534310.875
74_R78_L0.534040.875
106_L225_V0.53380.875
194_D224_D0.532880.873
358_V375_L0.530810.870
78_L294_L0.528450.866
93_H97_Q0.523860.858
115_G146_P0.523120.857
81_A243_L0.522780.857
41_G44_L0.52170.855
351_L356_I0.521590.855
224_D245_N0.517440.848
193_A196_V0.516050.846
393_K396_A0.515710.845
219_P222_Y0.514440.843
335_V377_L0.513250.841
32_M37_R0.512430.840
193_A197_G0.510130.836
322_K338_R0.509190.834
66_E70_L0.506840.830
312_L333_V0.505310.828
164_L167_E0.504240.826
173_I189_F0.504010.826
299_K302_A0.501430.822
301_Y304_Q0.499630.819
158_Y185_D0.498190.816
284_A288_V0.49710.814
95_G227_T0.496860.814
343_D372_P0.496780.814
63_Y66_E0.496360.813
115_G144_S0.492690.807
348_E352_E0.492520.807
39_A43_D0.491090.805
128_S131_N0.491010.804
347_A375_L0.490280.803
348_E360_K0.490090.803
70_L74_R0.48830.800
128_S132_F0.487040.798
230_T236_G0.484450.794
155_L185_D0.483740.793
310_K313_A0.483340.792
187_K222_Y0.482890.791
313_A323_V0.476840.781
150_D160_E0.476140.780
391_D396_A0.474370.777
68_E72_I0.473920.776
166_K170_P0.4730.775
163_K166_K0.472990.775
89_N243_L0.472660.774
41_G46_N0.469240.769
265_K268_S0.467590.766
312_L392_M0.462890.758
106_L172_L0.461360.756
292_E295_S0.460230.754
234_L239_G0.459520.753
161_L192_I0.456330.748
184_I188_R0.456190.747
230_T241_I0.454970.745
42_S288_V0.454950.745
208_A228_G0.452840.742
199_Y225_V0.452060.741
352_E357_I0.451010.739
89_N93_H0.448010.734
103_Y113_I0.44710.733
305_V308_N0.44640.731
40_L284_A0.444510.728
158_Y161_L0.443770.727
99_N174_I0.443640.727
35_A39_A0.442960.726
148_P157_D0.442590.725
312_L316_L0.441840.724
115_G174_I0.440.721
93_H98_A0.439540.720
71_A74_R0.439510.720
139_G142_F0.439050.719
348_E358_V0.43810.718
129_S132_F0.437790.717
347_A350_A0.437620.717
315_A392_M0.437610.717
391_D395_I0.436810.716
72_I91_Q0.435940.714
225_V242_I0.434740.712
245_N260_E0.433870.711
74_R290_L0.433560.710
99_N229_S0.433350.710
220_F226_V0.432030.708
190_R222_Y0.432020.708
188_R192_I0.431880.708
175_C200_L0.428720.702
218_N221_P0.427350.700
161_L165_A0.427240.700
145_V166_K0.426970.700
263_A267_D0.426830.699
40_L237_P0.426220.698
347_A351_L0.425280.697
116_L185_D0.425040.696
289_A293_A0.422980.693
32_M36_V0.42280.693
302_A305_V0.422770.693
312_L379_T0.420070.688
177_A186_F0.418480.686
274_L277_G0.417390.684
106_L201_M0.415980.682
92_P98_A0.415640.681
74_R286_L0.411870.675
161_L173_I0.408750.670
118_L184_I0.407890.668
70_L286_L0.406760.666
319_R396_A0.402660.660
173_I176_G0.400810.657
102_V227_T0.399820.655
279_H283_I0.399690.655
286_L291_K0.399360.654
208_A234_L0.399260.654
261_E264_E0.39920.654
112_T171_K0.399070.654
116_L175_C0.398180.652
36_V288_V0.396530.650
273_G276_G0.395020.647
324_V338_R0.394980.647
315_A389_E0.393870.645
305_V309_A0.392110.642
202_A223_A0.391430.641
234_L286_L0.388850.637
280_M283_I0.388510.637
44_L281_H0.38680.634
40_L280_M0.386360.633
36_V289_A0.385710.632
147_Y160_E0.383310.628
127_G132_F0.383290.628
71_A285_A0.382620.627
215_L221_P0.382260.626
167_E170_P0.380250.623
308_N312_L0.380030.623
101_A242_I0.379510.622
82_E245_N0.378370.620
291_K294_L0.378260.620
392_M396_A0.377980.619
145_V170_P0.377040.618
206_H376_R0.376260.616
292_E299_K0.376240.616
293_A302_A0.375670.616
191_E222_Y0.375480.615
98_A242_I0.373460.612
264_E268_S0.373330.612
270_V274_L0.372360.610
162_E165_A0.372280.610
313_A325_T0.372150.610
89_N94_S0.370880.608
77_E291_K0.37050.607
103_Y107_L0.369460.605
311_A392_M0.369240.605
76_K89_N0.366760.601
99_N103_Y0.366380.600
82_E260_E0.366110.600
201_M225_V0.363940.596
199_Y262_L0.363620.596
354_A394_E0.363580.596
95_G205_S0.362280.594
77_E80_G0.361630.593
76_K81_A0.360760.591
194_D200_L0.358290.587
64_I68_E0.358030.587
150_D185_D0.35480.581
262_L265_K0.35440.581
156_I161_L0.354270.580
238_R280_M0.354170.580
102_V242_I0.353250.579
39_A291_K0.353220.579
114_M145_V0.353170.579
170_P198_A0.35240.577
186_F202_A0.350990.575
235_R380_P0.350290.574
92_P95_G0.349960.573
105_A269_A0.349590.573
89_N95_G0.349290.572
107_L111_D0.34880.571
148_P164_L0.348440.571
242_I266_I0.348250.571
290_L294_L0.347730.570
187_K190_R0.347150.569
342_I346_E0.34710.569
289_A292_E0.346230.567
114_M147_Y0.344940.565
65_D68_E0.344740.565
154_G322_K0.343620.563
312_L395_I0.342980.562
78_L290_L0.342960.562
67_I71_A0.340070.557
97_Q274_L0.338960.555
211_I302_A0.33740.553
311_A396_A0.337310.553
264_E267_D0.336990.552
35_A291_K0.336040.551
244_T262_L0.335520.550
194_D197_G0.335220.549
283_I286_L0.334720.548
206_H231_H0.33390.547
317_Q322_K0.333760.547
176_G179_S0.332150.544
345_K360_K0.330060.541
119_P176_G0.327750.537
298_F301_Y0.326560.535
61_C64_I0.326310.535
94_S97_Q0.326160.534
114_M161_L0.325590.533
239_G282_R0.324920.532
40_L43_D0.324520.532
114_M173_I0.324420.532
306_V309_A0.324050.531
115_G119_P0.322660.529
312_L396_A0.321530.527
314_E389_E0.321270.526
344_G360_K0.320940.526
336_D339_S0.320470.525
210_L293_A0.320060.524
77_E295_S0.319270.523
71_A75_A0.319230.523
304_Q389_E0.318890.522
105_A266_I0.317830.521
33_S36_V0.317470.520
90_V93_H0.3160.518
40_L281_H0.315440.517
344_G373_S0.315160.516
157_D163_K0.314850.516
215_L222_Y0.314520.515
286_L290_L0.314390.515
205_S231_H0.314050.515
47_K63_Y0.313770.514
62_E68_E0.313410.514
316_L335_V0.312660.512
79_F208_A0.312050.511
36_V40_L0.311910.511
295_S299_K0.311870.511
116_L189_F0.311160.510
75_A228_G0.310680.509
76_K243_L0.310680.509
314_E393_K0.309940.508
272_P275_Q0.309290.507
97_Q101_A0.308670.506
75_A290_L0.307390.504
347_A358_V0.307080.503
40_L282_R0.30580.501
310_K317_Q0.305590.501
337_L375_L0.304570.499
325_T338_R0.30410.498
316_L319_R0.304060.498
149_V157_D0.303960.498
116_L120_H0.303560.497
202_A220_F0.302770.496
92_P242_I0.302150.495
103_Y172_L0.301880.495
343_D373_S0.300560.492
263_A266_I0.299040.490
72_I90_V0.29880.490
156_I185_D0.298050.488
237_P285_A0.297850.488
79_F241_I0.297710.488
266_I270_V0.297640.488
34_P41_G0.297550.488
232_K376_R0.297510.487
322_K340_F0.29620.485
37_R40_L0.295760.485
76_K79_F0.295290.484
345_K348_E0.294310.482
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
2a7vA11000.19
3ou5A11000.215
4j5uA0.94491000.231
1rv3A11000.24
3h7fA0.94241000.285
3n0lA0.94241000.292
3ecdA0.94491000.297
3gbxA0.94741000.302
2vi8A0.94241000.318
2dkjA0.94491000.325

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