GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DcuC - C4-dicarboxylate anaerobic carrier
Pfam: PF03606 (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: CL0182
Length: 465
Sequences: 4832
Seq/Len: 10.39
HH_delta: 0.645 (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
316_K319_G0.339923.377
437_S440_K0.338393.361
397_D403_R0.332063.299
96_H316_K0.28792.860
306_S309_E0.260252.585
96_H309_E0.218572.171
345_D349_H0.202242.009
402_T405_T0.19891.976
106_L110_P0.189791.885
106_L109_K0.189011.878
135_I138_E0.18851.873
380_S383_G0.186281.850
251_K255_L0.177691.765
265_V269_Y0.177271.761
201_Q205_V0.177171.760
330_L334_I0.174991.738
309_E312_K0.17491.737
349_H352_S0.170471.693
338_M343_I0.168961.678
363_A367_M0.166971.659
438_Y442_V0.166911.658
371_Q388_F0.166861.658
396_A406_A0.165351.643
308_N312_K0.164771.637
375_N417_G0.164031.629
102_A253_P0.164011.629
296_I300_R0.158371.573
349_H353_N0.158031.570
241_E245_Q0.157371.563
88_G321_M0.156491.555
342_K345_D0.155951.549
203_P207_F0.154671.536
250_T253_P0.152031.510
331_A334_I0.151531.505
89_G314_F0.151331.503
425_G429_A0.151211.502
254_K258_L0.1511.500
182_V186_Q0.150471.495
210_I214_Y0.150011.490
431_L438_Y0.14981.488
240_E243_E0.149221.482
162_A444_R0.148991.480
213_A217_R0.14861.476
159_T162_A0.147891.469
217_R221_K0.147791.468
315_F319_G0.144661.437
151_I157_P0.144431.435
400_G403_R0.142791.418
373_L377_L0.14161.407
169_G419_S0.14131.404
101_D105_N0.139981.391
312_K319_G0.138481.376
255_L259_L0.138321.374
350_L354_L0.138221.373
240_E244_E0.137971.371
214_Y218_Y0.137461.365
97_T300_R0.136871.360
258_L299_I0.136831.359
236_E240_E0.136321.354
164_V168_A0.136311.354
130_G134_G0.134961.341
221_K225_D0.133981.331
223_K226_P0.132771.319
232_Y238_E0.131951.311
369_L373_L0.131641.308
367_M392_M0.13151.306
235_D239_E0.131131.303
258_L262_L0.129591.287
120_P216_H0.12951.286
88_G317_G0.129221.284
135_I139_A0.128711.279
207_F211_A0.127741.269
105_N109_K0.127611.268
409_A413_G0.12661.258
263_P292_I0.126591.258
346_T349_H0.125971.251
335_S338_M0.125851.250
96_H313_A0.125541.247
170_A173_A0.125041.242
440_K443_K0.124591.238
130_G133_I0.124481.237
84_I321_M0.124461.236
236_E239_E0.124051.232
162_A167_G0.123621.228
212_I216_H0.122891.221
362_I365_I0.122781.220
222_V225_D0.122491.217
243_E246_E0.122171.214
326_L329_G0.122081.213
209_L213_A0.121941.211
395_L398_L0.121791.210
253_P256_Y0.121551.207
342_K346_T0.121411.206
132_T135_I0.12091.201
92_G313_A0.120421.196
295_I299_I0.120421.196
417_G424_S0.120281.195
159_T163_A0.120051.193
217_R220_Q0.119841.190
233_E236_E0.118891.181
195_S404_Q0.118871.181
197_F201_Q0.118871.181
204_F208_T0.118521.177
375_N381_G0.118391.176
376_F421_S0.11791.171
375_N414_D0.117831.170
381_G414_D0.117761.170
128_G132_T0.117541.168
183_G187_K0.116891.161
242_E246_E0.116491.157
216_H220_Q0.116291.155
242_E247_E0.115951.152
243_E247_E0.115811.150
375_N418_N0.115521.148
342_K347_I0.115371.146
192_P195_S0.115361.146
330_L335_S0.115351.146
337_F341_G0.115051.143
295_I298_L0.114291.135
96_H305_K0.113841.131
346_T350_L0.113661.129
297_G310_I0.113051.123
408_L412_F0.113031.123
328_V338_M0.11271.120
262_L266_L0.112371.116
222_V226_P0.111591.109
210_I451_I0.111361.106
161_A424_S0.111081.103
84_I136_P0.11081.101
369_L450_L0.110731.100
147_I157_P0.110591.099
414_D418_N0.110361.096
345_D353_N0.11021.095
431_L441_W0.109991.093
330_L337_F0.109981.093
103_L106_L0.109921.092
150_L160_A0.109921.092
192_P354_L0.109661.089
259_L262_L0.109571.088
170_A174_G0.109441.087
98_G101_D0.108921.082
393_P397_D0.107451.067
198_W202_I0.107121.064
158_I162_A0.107061.064
293_G297_G0.107061.064
309_E313_A0.106911.062
83_F138_E0.10671.060
232_Y239_E0.106441.057
352_S355_L0.106351.056
412_F415_G0.106111.054
445_T449_M0.105421.047
256_Y259_L0.105061.044
127_S130_G0.104951.043
345_D394_P0.104491.038
91_F140_I0.104361.037
418_N424_S0.104281.036
167_G171_G0.104231.035
389_M407_V0.104021.033
389_M410_F0.103941.033
127_S209_L0.103821.031
257_L260_P0.103821.031
392_M396_A0.103781.031
281_Y284_E0.103661.030
375_N384_Q0.103341.027
185_A407_V0.103131.024
150_L155_Y0.103071.024
95_N101_D0.103061.024
159_T215_V0.102411.017
307_P311_V0.102361.017
342_K349_H0.102331.017
312_K316_K0.102141.015
139_A168_A0.101961.013
99_A102_A0.10191.012
99_A257_L0.101251.006
205_V209_L0.101221.005
345_D348_V0.101111.004
183_G186_Q0.100651.000
92_G96_H0.100580.999
202_I209_L0.10040.997
214_Y217_R0.099910.992
334_I337_F0.09960.989
401_I405_T0.099470.988
133_I139_A0.099390.987
240_E245_Q0.09930.986
331_A383_G0.099180.985
359_P362_I0.099150.985
186_Q192_P0.099020.984
252_R255_L0.098950.983
263_P266_L0.098870.982
208_T212_I0.098590.979
390_P394_P0.098530.979
446_W450_L0.098390.977
187_K190_G0.098180.975
105_N152_A0.09790.973
133_I136_P0.097530.969
206_I210_I0.097440.968
347_I350_L0.097430.968
92_G317_G0.097120.965
93_V293_G0.097040.964
331_A338_M0.097030.964
96_H312_K0.096960.963
444_R447_P0.096660.960
321_M324_F0.096620.960
89_G293_G0.096380.957
99_A253_P0.096360.957
365_I369_L0.096260.956
77_A332_R0.096190.956
109_K242_E0.096190.956
293_G300_R0.096170.955
429_A433_I0.096090.955
332_R335_S0.096040.954
163_A167_G0.095940.953
379_G418_N0.095910.953
439_G442_V0.095860.952
342_K348_V0.09580.952
415_G423_T0.095710.951
384_Q388_F0.095680.950
134_G137_E0.095650.950
232_Y235_D0.095650.950
244_E247_E0.095440.948
102_A106_L0.095340.947
161_A434_A0.094910.943
255_L258_L0.093950.933
239_E242_E0.093870.932
260_P379_G0.093780.932
187_K192_P0.093770.931
439_G443_K0.093750.931
89_G93_V0.093580.930
145_I414_D0.093560.929
109_K244_E0.093470.929
166_L449_M0.093470.929
193_L196_G0.093410.928
128_G142_F0.093320.927
295_I373_L0.093280.927
385_A410_F0.093080.925
335_S339_E0.092960.923
326_L330_L0.09290.923
92_G95_N0.092620.920
394_P397_D0.09260.920
305_K310_I0.092520.919
156_D440_K0.092480.919
358_L399_L0.092420.918
297_G300_R0.09220.916
347_I351_L0.09210.915
288_L292_I0.092090.915
239_E247_E0.091930.913
215_V219_A0.091880.913
121_I212_I0.091870.913
282_F285_I0.091740.911
305_K309_E0.091690.911
341_G345_D0.091670.911
339_E390_P0.091660.911
165_I168_A0.091440.908
80_I332_R0.091350.907
109_K239_E0.091250.906
234_D239_E0.091230.906
353_N356_S0.09110.905
234_D238_E0.091090.905
242_E245_Q0.090960.904
138_E379_G0.090830.902
354_L357_G0.090830.902
331_A337_F0.090740.901
138_E381_G0.090640.900
244_E248_K0.090580.900
381_G419_S0.090570.900
103_L260_P0.090320.897
286_A290_L0.090260.897
206_I255_L0.090170.896
381_G418_N0.090080.895
290_L293_G0.089970.894
262_L295_I0.089770.892
380_S425_G0.089650.891
293_G296_I0.089470.889
312_K315_F0.089420.888
337_F340_G0.089340.887
264_F267_L0.089290.887
195_S298_L0.089120.885
168_A171_G0.088610.880
331_A335_S0.088410.878
447_P451_I0.088380.878
341_G348_V0.088270.877
110_P258_L0.088180.876
160_A183_G0.087930.873
170_A211_A0.087880.873
335_S426_V0.087690.871
171_G178_N0.087520.869
428_M433_I0.087490.869
133_I177_S0.087460.869
137_E171_G0.087420.868
167_G423_T0.087410.868
265_V444_R0.087160.866
213_A221_K0.087010.864
169_G174_G0.086980.864
380_S427_L0.086930.864
175_P183_G0.08670.861
413_G417_G0.086670.861
257_L261_V0.086660.861
236_E246_E0.086630.861
103_L257_L0.086610.860
298_L312_K0.086590.860
247_E309_E0.086570.860
165_I419_S0.08650.859
241_E247_E0.086450.859
109_K243_E0.086320.857
126_F209_L0.086260.857
192_P341_G0.086120.855
235_D243_E0.086110.855
350_L353_N0.086070.855
424_S428_M0.086060.855
299_I309_E0.086050.855
246_E295_I0.085850.853
127_S208_T0.085760.852
327_V381_G0.085620.851
444_R449_M0.085570.850
109_K190_G0.085530.850
385_A414_D0.085440.849
168_A429_A0.08530.847
105_N246_E0.085240.847
260_P264_F0.085230.847
117_P120_P0.085220.847
83_F87_I0.085110.845
201_Q207_F0.085060.845
246_E253_P0.085050.845
441_W444_R0.084990.844
396_A409_A0.08490.843
86_I250_T0.084880.843
113_G238_E0.084850.843
161_A436_V0.084750.842
196_G200_R0.084690.841
306_S310_I0.084630.841
254_K260_P0.084620.841
120_P267_L0.084560.840
351_L370_I0.084260.837
221_K233_E0.084220.837
87_I168_A0.084160.836
202_I205_V0.084020.835
174_G202_I0.083970.834
89_G318_M0.083960.834
101_D104_V0.083830.833
149_I153_L0.083750.832
244_E306_S0.083740.832
176_P197_F0.083720.832
339_E342_K0.083710.832
307_P310_I0.083640.831
371_Q384_Q0.083640.831
193_L200_R0.083630.831
105_N247_E0.083580.830
141_A144_P0.083460.829
311_V367_M0.083270.827
122_L146_L0.08320.826
392_M410_F0.08320.826
376_F417_G0.083050.825
82_F86_I0.083030.825
235_D238_E0.082970.824
183_G388_F0.082880.823
87_I91_F0.082850.823
240_E246_E0.08270.822
173_A381_G0.082640.821
176_P201_Q0.082610.821
193_L197_F0.082610.821
156_D159_T0.082570.820
262_L265_V0.082570.820
206_I265_V0.082540.820
368_F409_A0.08250.820
156_D219_A0.082220.817
306_S312_K0.08220.817
395_L399_L0.082160.816
128_G149_I0.082060.815
259_L300_R0.082050.815
102_A105_N0.081920.814
87_I140_I0.081890.813
313_A316_K0.081860.813
310_I313_A0.081840.813
368_F413_G0.081780.812
93_V294_I0.081730.812
314_F317_G0.08160.811
334_I338_M0.081540.810
146_L149_I0.081530.810
211_A215_V0.081450.809
259_L263_P0.081430.809
151_I154_G0.081360.808
341_G347_I0.081340.808
172_F415_G0.081320.808
363_A366_G0.081260.807
119_I167_G0.081050.805
191_L404_Q0.081010.805
324_F330_L0.080960.804
108_I266_L0.080920.804
112_K116_N0.080870.803
245_Q251_K0.080840.803
384_Q417_G0.080810.803
245_Q248_K0.08070.802
374_I424_S0.080690.802
217_R223_K0.080660.801
371_Q413_G0.080660.801
76_Q333_A0.080560.800
259_L295_I0.080490.800
316_K320_D0.080420.799
418_N426_V0.080340.798
367_M371_Q0.080310.798
196_G407_V0.080250.797
378_I387_A0.08020.797
189_A397_D0.080020.795
441_W445_T0.079910.794
91_F135_I0.079840.793
130_G136_P0.079790.793
171_G175_P0.079770.792
265_V361_V0.079750.792
226_P399_L0.079680.792
77_A329_G0.079660.791
172_F381_G0.079650.791
421_S424_S0.079590.791
153_L324_F0.079510.790
167_G196_G0.079510.790
280_W285_I0.079510.790
277_K321_M0.079470.789
114_K117_P0.079460.789
132_T138_E0.079370.788
136_P139_A0.079360.788
247_E250_T0.079310.788
298_L358_L0.079220.787
162_A441_W0.079070.785
143_M382_S0.078780.783
382_S385_A0.078620.781
298_L307_P0.078550.780
245_Q255_L0.078420.779
380_S384_Q0.078380.779
161_A165_I0.078310.778
85_M321_M0.078280.778
238_E283_P0.078280.778
309_E394_P0.078260.777
379_G424_S0.078240.777
170_A212_I0.078170.777
348_V351_L0.078130.776
161_A378_I0.078090.776
372_F417_G0.078080.776
84_I87_I0.078010.775
287_A293_G0.077970.775
101_D241_E0.077930.774
84_I296_I0.077770.773
140_I364_A0.077680.772
172_F176_P0.077670.772
393_P407_V0.077670.772
424_S427_L0.077640.771
372_F416_L0.07760.771
421_S425_G0.077550.770
446_W449_M0.077540.770
83_F165_I0.077530.770
388_F428_M0.077520.770
111_L117_P0.077430.769
391_I395_L0.077410.769
217_R222_V0.077370.769
90_F304_G0.077330.768
136_P178_N0.077330.768
250_T255_L0.077330.768
234_D243_E0.077270.768
304_G307_P0.077250.767
384_Q414_D0.077250.767
105_N241_E0.07720.767
345_D350_L0.077110.766
141_A175_P0.077040.765
221_K224_K0.076950.764
183_G386_A0.076890.764
239_E243_E0.07670.762
238_E241_E0.076610.761
255_L316_K0.076480.760
438_Y441_W0.07640.759
204_F207_F0.076390.759
91_F428_M0.076310.758
97_T145_I0.07630.758
371_Q417_G0.076240.757
210_I213_A0.07620.757
88_G140_I0.076140.756
159_T219_A0.076070.756
375_N428_M0.076050.755
84_I332_R0.075930.754
174_G181_T0.075920.754
410_F426_V0.075850.753
137_E178_N0.07580.753
379_G423_T0.075770.753
84_I380_S0.075720.752
92_G320_D0.075630.751
329_G334_I0.075460.750
411_Q415_G0.075390.749
132_T266_L0.075320.748
359_P366_G0.075150.747
147_I164_V0.075130.746
295_I345_D0.075120.746
89_G142_F0.075040.745
417_G425_G0.075020.745
158_I444_R0.074950.745
310_I318_M0.074940.744
378_I424_S0.074940.744
383_G425_G0.074940.744
174_G178_N0.074880.744
211_A452_W0.074730.742
414_D417_G0.074720.742
131_L136_P0.074650.742
343_I346_T0.074620.741
148_P375_N0.074610.741
166_L211_A0.074520.740
171_G176_P0.074520.740
183_G194_F0.074520.740
214_Y451_I0.074510.740
219_A223_K0.074450.740
103_L220_Q0.074440.739
419_S430_V0.07430.738
397_D402_T0.074240.737
105_N242_E0.074220.737
203_P388_F0.074160.737
246_E258_L0.074090.736
109_K221_K0.074080.736
153_L308_N0.073960.735
108_I145_I0.073890.734
132_T136_P0.073870.734
239_E262_L0.073870.734
194_F370_I0.073860.734
253_P257_L0.073750.733
424_S430_V0.073720.732
183_G327_V0.07370.732
113_G153_L0.073680.732
330_L381_G0.073660.732
213_A298_L0.073620.731
173_A414_D0.073590.731
341_G346_T0.073570.731
202_I207_F0.073540.731
186_Q407_V0.073510.730
113_G116_N0.073490.730
330_L333_A0.073430.729
87_I368_F0.07340.729
117_P155_Y0.073360.729
199_F203_P0.073320.728
167_G415_G0.073270.728
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
4f35D0.879699.90.645
4f35D0.477498.50.871
2a65A0.602223.50.964
2gfpA0.18714.80.973
4eneA0.21294.30.973
2l2tA0.09463.90.974
2kncA0.11613.40.975
3rkoJ0.35912.60.976
2rddB0.07962.50.976
3qnqA0.48391.90.977
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