GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Nuc_H_symport - Nucleoside H symporter
Pfam: PF03825 (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: CL0015
Length: 400
Sequences: 54171
Seq/Len: 135.43
HH_delta: 0.233 (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
89_S93_W2.271633.982
49_A99_L1.779293.119
84_L97_I1.728583.030
77_L104_F1.709532.996
90_S93_W1.517232.659
92_W96_V1.478122.591
81_A97_I1.426152.500
241_S244_T1.406492.465
35_S38_Q1.402192.458
91_F95_F1.359092.382
86_A163_Y1.354012.373
68_K72_A1.342312.353
330_A338_A1.287842.257
57_W107_P1.282172.247
264_G268_K1.259162.207
272_I328_R1.251542.194
331_P334_L1.209862.121
201_L205_K1.178892.066
81_A100_L1.159222.032
271_G274_W1.153662.022
62_D336_A1.142222.002
53_S103_F1.137661.994
282_A314_T1.133591.987
38_Q91_F1.110411.946
126_D129_R1.050791.842
42_L94_L1.048591.838
265_R269_R1.02911.804
217_F350_G1.013911.777
88_S97_I0.997671.749
240_Y244_T0.994921.744
74_L107_P0.993441.741
59_A63_R0.987071.730
45_V95_F0.982261.722
123_R126_D0.980211.718
202_K205_K0.96891.698
49_A53_S0.958481.680
45_V99_L0.957161.678
58_G62_D0.945181.657
163_Y167_I0.943441.654
67_A118_S0.935011.639
88_S93_W0.922211.616
360_W364_A0.916031.606
79_A169_S0.912271.599
266_F270_F0.912271.599
81_A104_F0.90881.593
273_K277_L0.907571.591
69_R73_L0.899191.576
125_K129_R0.888891.558
60_I64_F0.883941.549
98_M102_S0.87171.528
298_P302_A0.871271.527
122_D125_K0.869291.524
85_L97_I0.863081.513
124_G127_Y0.849641.489
262_F265_R0.847371.485
34_F91_F0.841931.476
221_I354_G0.836921.467
93_W97_I0.836421.466
34_F38_Q0.819911.437
69_R72_A0.816811.432
53_S56_F0.816391.431
37_T363_D0.809891.420
274_W277_L0.792821.390
174_G178_F0.79281.390
225_A358_G0.791561.387
84_L87_F0.786651.379
36_G363_D0.78541.377
73_L77_L0.785221.376
53_S106_S0.782691.372
110_P113_D0.781111.369
81_A101_F0.778031.364
202_K334_L0.771581.352
259_F262_F0.765811.342
235_Q242_G0.764921.341
284_A288_L0.763211.338
244_T247_I0.762211.336
115_I119_Y0.760741.333
274_W278_L0.755511.324
64_F70_I0.754091.322
286_R314_T0.750481.315
77_L81_A0.748311.312
70_I73_L0.74261.302
259_F313_L0.739241.296
255_A259_F0.727131.274
162_F165_A0.720421.263
334_L337_T0.718571.259
147_G150_G0.714971.253
296_P299_F0.713711.251
62_D337_T0.711651.247
270_F274_W0.710191.245
56_F59_A0.708941.243
148_L152_Y0.708781.242
163_Y166_A0.705021.236
72_A173_A0.700341.228
92_W95_F0.699431.226
359_G363_D0.698851.225
167_I171_L0.697571.223
80_L84_L0.69731.222
265_R268_K0.696591.221
64_F69_R0.696351.221
86_A166_A0.695821.220
270_F275_L0.694151.217
258_P261_F0.691671.212
261_F265_R0.69071.211
61_A111_L0.689461.208
281_V285_V0.67481.183
83_L166_A0.674561.182
196_L199_D0.672711.179
198_L201_L0.672691.179
85_L94_L0.67171.177
204_L210_L0.663161.162
235_Q245_I0.662491.161
123_R127_Y0.660011.157
197_G200_A0.655821.149
207_P211_V0.652231.143
162_F166_A0.648681.137
76_L173_A0.64811.136
278_L282_A0.642131.125
324_R328_R0.641171.124
138_F141_A0.64071.123
207_P210_L0.638481.119
263_S317_L0.637581.118
289_L292_Y0.636961.116
199_D202_K0.635151.113
46_G50_R0.634591.112
302_A305_L0.629241.103
98_M101_F0.628711.102
37_T41_I0.628241.101
210_L214_L0.627861.100
48_L352_A0.627551.100
127_Y131_R0.626761.099
160_L163_Y0.622431.091
233_Y238_G0.62221.091
271_G275_L0.619771.086
72_A76_L0.619021.085
153_L157_G0.617711.083
332_P335_R0.615171.078
243_S247_I0.615121.078
65_G69_R0.614181.076
361_L365_F0.613271.075
118_S335_R0.610891.071
209_F213_L0.610841.071
258_P262_F0.610821.071
58_G336_A0.610551.070
55_P59_A0.609521.068
83_L87_F0.607941.066
115_I118_S0.607261.064
44_A356_L0.606691.063
41_I45_V0.606071.062
360_W363_D0.606021.062
76_L80_L0.604441.059
72_A176_A0.60421.059
96_V100_L0.604061.059
350_G354_G0.602821.057
129_R133_W0.600851.053
137_G141_A0.598671.049
288_L292_Y0.598371.049
60_I70_I0.596911.046
131_R134_G0.596111.045
127_Y130_I0.594181.041
213_L345_L0.591751.037
288_L291_A0.590571.035
128_G132_L0.590091.034
262_F266_F0.586071.027
224_A351_G0.585431.026
40_G44_A0.585361.026
282_A286_R0.584741.025
234_L240_Y0.584621.025
124_G129_R0.582611.021
233_Y237_L0.580521.017
141_A144_A0.579291.015
96_V99_L0.578621.014
164_I167_I0.578151.013
41_I356_L0.578131.013
112_S115_I0.575711.009
279_A318_F0.574811.007
73_L76_L0.572631.004
35_S363_D0.571981.003
320_A324_R0.568910.997
188_A191_S0.564340.989
44_A352_A0.564280.989
82_L98_M0.561720.985
151_G154_G0.560110.982
356_L360_W0.555420.974
125_K128_G0.554830.972
247_I251_L0.55480.972
216_A342_Y0.554710.972
93_W96_V0.553910.971
116_A120_L0.543990.953
114_S118_S0.543230.952
176_A180_P0.543220.952
107_P110_P0.542490.951
264_G267_L0.540620.948
279_A317_L0.540270.947
117_L120_L0.540040.947
81_A84_L0.538390.944
278_L281_V0.537810.943
45_V49_A0.535770.939
38_Q95_F0.533070.934
89_S92_W0.530750.930
42_L95_F0.529480.928
46_G98_M0.529370.928
355_S359_G0.528110.926
187_S190_E0.527630.925
124_G128_G0.52670.923
107_P111_L0.525860.922
123_R129_R0.525860.922
197_G201_L0.524360.919
130_I133_W0.523670.918
208_R211_V0.523090.917
323_V327_D0.522390.916
277_L281_V0.52220.915
38_Q41_I0.520220.912
129_R132_L0.520020.911
214_L217_F0.519010.910
74_L104_F0.517330.907
79_A166_A0.516610.905
289_L303_L0.515670.904
151_G243_S0.515090.903
277_L280_L0.513720.900
166_A170_L0.513010.899
54_P343_S0.511470.896
275_L278_L0.51130.896
43_L228_T0.511150.896
254_V258_P0.510690.895
285_V289_L0.51050.895
327_D339_Q0.510460.895
252_G256_E0.510180.894
132_L135_S0.508370.891
286_R311_H0.506020.887
61_A67_A0.503020.882
206_N210_L0.502330.880
110_P114_S0.501190.878
157_G160_L0.50020.877
234_L237_L0.499940.876
357_I360_W0.495310.868
122_D126_D0.49480.867
139_I142_A0.493210.864
139_I143_L0.491850.862
174_G177_L0.491680.862
124_G268_K0.491030.861
189_K192_V0.490730.860
232_I236_E0.490070.859
210_L213_L0.490050.859
49_A102_S0.487690.855
232_I235_Q0.486810.853
61_A336_A0.486730.853
281_V284_A0.486610.853
326_I342_Y0.484850.850
62_D67_A0.484190.849
47_P51_I0.483680.848
130_I134_G0.481810.844
234_L238_G0.479440.840
267_L271_G0.479190.840
224_A227_Y0.477590.837
78_S82_L0.476670.835
138_F142_A0.476340.835
46_G102_S0.476060.834
279_A314_T0.475630.834
216_A220_G0.475230.833
85_L101_F0.473420.830
69_R181_K0.472870.829
36_G236_E0.472820.829
128_G131_R0.472620.828
97_I101_F0.470590.825
31_S156_S0.470430.825
261_F264_G0.469760.823
256_E260_F0.469470.823
133_W137_G0.46920.822
79_A83_L0.468370.821
267_L321_A0.467090.819
59_A337_T0.466810.818
160_L164_I0.464670.814
104_F107_P0.463760.813
251_L255_A0.462670.811
57_W60_I0.462170.810
102_S106_S0.461820.809
250_A253_V0.461590.809
51_I352_A0.461270.808
154_G157_G0.460420.807
113_D116_A0.460.806
34_F39_I0.459350.805
162_F167_I0.458350.803
219_I318_F0.456240.800
126_D130_I0.452340.793
255_A258_P0.45190.792
317_L321_A0.449870.789
46_G105_F0.449770.788
76_L79_A0.449170.787
213_L217_F0.44860.786
252_G312_G0.448420.786
324_R327_D0.448390.786
266_F275_L0.448360.786
310_L314_T0.448170.786
190_E194_K0.446930.783
172_L175_F0.446770.783
194_K197_G0.446660.783
111_L116_A0.445670.781
81_A85_L0.445560.781
68_K181_K0.445170.780
37_T360_W0.444930.780
226_Y230_F0.444870.780
149_L152_Y0.443090.777
48_L51_I0.443060.777
83_L163_Y0.442960.776
265_R270_F0.442660.776
218_L222_S0.442280.775
289_L293_F0.441790.774
84_L93_W0.441680.774
177_L180_P0.440620.772
170_L174_G0.440570.772
283_Y286_R0.439240.770
41_I44_A0.43920.770
259_F263_S0.438970.769
165_A168_L0.436690.765
41_I95_F0.435880.764
214_L218_L0.435530.763
51_I344_A0.435380.763
260_F264_G0.432490.758
299_F302_A0.432260.758
297_W301_V0.431360.756
67_A181_K0.43040.754
117_L335_R0.430290.754
353_I356_L0.430030.754
65_G70_I0.42910.752
152_Y155_I0.428770.752
135_S138_F0.427950.750
339_Q343_S0.425010.745
116_A119_Y0.424950.745
335_R339_Q0.424160.743
113_D117_L0.423940.743
246_G250_A0.423430.742
319_H323_V0.422760.741
150_G153_L0.422680.741
157_G162_F0.421940.740
195_L199_D0.421830.739
263_S266_F0.421780.739
120_L126_D0.421690.739
126_D133_W0.421550.739
54_P340_G0.420730.737
52_V55_P0.420710.737
206_N329_I0.419660.736
38_Q42_L0.419240.735
71_L112_S0.418210.733
79_A173_A0.41770.732
202_K333_E0.417050.731
140_V144_A0.416080.729
115_I179_L0.414230.726
270_F278_L0.414130.726
196_L201_L0.413630.725
40_G229_F0.413480.725
134_G138_F0.41230.723
149_L153_L0.41180.722
140_V143_L0.411220.721
220_G224_A0.411140.721
349_L353_I0.410470.719
253_V257_I0.410230.719
336_A340_G0.410120.719
203_L338_A0.409270.717
80_L83_L0.408380.716
79_A170_L0.408120.715
40_G359_G0.40810.715
287_W291_A0.407720.715
175_F178_F0.406720.713
254_V257_I0.406420.712
180_P183_P0.40570.711
67_A114_S0.403980.708
352_A356_L0.402470.705
87_F163_Y0.402050.705
325_Y329_I0.401350.703
202_K206_N0.401040.703
47_P355_S0.400510.702
53_S57_W0.399810.701
106_S110_P0.399620.700
193_K196_L0.39870.699
147_G151_G0.397610.697
42_L91_F0.39730.696
82_L101_F0.397050.696
124_G130_I0.396580.695
118_S121_G0.396160.694
243_S246_G0.396080.694
127_Y134_G0.395580.693
52_V56_F0.395550.693
263_S267_L0.395350.693
172_L176_A0.394230.691
229_F232_I0.393150.689
326_I329_I0.392790.688
312_G316_G0.392140.687
87_F93_W0.391780.687
72_A177_L0.391520.686
36_G362_Y0.391420.686
316_G320_A0.389740.683
242_G246_G0.389630.683
300_I304_Q0.388570.681
247_I250_A0.388040.680
168_L171_L0.387280.679
138_F143_L0.386490.677
268_K272_I0.385880.676
47_P50_R0.385750.676
286_R290_Y0.385560.676
220_G223_H0.385490.676
229_F358_G0.385440.676
133_W136_I0.385290.675
135_S139_I0.385160.675
266_F269_R0.38480.674
97_I100_L0.38450.674
198_L202_K0.384410.674
78_S105_F0.383970.673
327_D335_R0.383680.672
116_A121_G0.383310.672
135_S142_A0.38230.670
44_A47_P0.382120.670
256_E316_G0.381240.668
211_V214_L0.381210.668
131_R135_S0.380570.667
353_I357_I0.379620.665
206_N334_L0.375890.659
268_K271_G0.375450.658
252_G259_F0.374250.656
54_P344_A0.373580.655
111_L114_S0.373120.654
187_S191_S0.37290.654
58_G61_A0.372720.653
209_F338_A0.371930.652
49_A52_V0.371160.651
82_L165_A0.370460.649
193_K199_D0.370280.649
211_V215_A0.370280.649
75_S173_A0.370150.649
99_L103_F0.369760.648
208_R329_I0.36930.647
173_A177_L0.368680.646
179_L182_T0.367790.645
282_A310_L0.366090.642
37_T40_G0.365880.641
85_L88_S0.365660.641
286_R289_L0.365640.641
296_P300_I0.365380.640
298_P301_V0.364390.639
295_D298_P0.364220.638
42_L98_M0.364210.638
169_S173_A0.364020.638
164_I168_L0.362450.635
124_G132_L0.362330.635
219_I222_S0.362170.635
244_T248_L0.361430.633
165_A169_S0.361130.633
280_L284_A0.361040.633
250_A254_V0.360510.632
41_I91_F0.36050.632
213_L342_Y0.359620.630
77_L100_L0.35860.629
126_D131_R0.358360.628
184_P187_S0.358080.628
191_S194_K0.358030.628
320_A323_V0.358020.628
57_W70_I0.357420.626
156_S160_L0.357330.626
219_I223_H0.357240.626
238_G241_S0.3570.626
231_S235_Q0.356880.626
99_L102_S0.35670.625
223_H227_Y0.355610.623
137_G142_A0.354890.622
123_R128_G0.354810.622
326_I330_A0.353880.620
127_Y133_W0.353760.620
194_K199_D0.353170.619
175_F179_L0.352720.618
351_G355_S0.352540.618
30_E33_G0.352340.618
301_V305_L0.352260.617
39_I232_I0.351970.617
319_H322_S0.351860.617
195_L198_L0.351830.617
88_S92_W0.351810.617
318_F321_A0.351780.617
221_I224_A0.351610.616
41_I360_W0.351370.616
61_A70_I0.351110.615
153_L160_L0.350660.615
325_Y328_R0.350620.615
316_G319_H0.350210.614
67_A70_I0.349530.613
252_G260_F0.348040.610
201_L204_L0.347230.609
50_R54_P0.347070.608
108_T112_S0.347030.608
276_L322_S0.347020.608
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
1pw4A0.961000.233
3o7qA0.9551000.236
4j05A0.9651000.239
2gfpA0.921000.286
2cfqA0.9551000.292
4apsA0.95751000.324
4gc0A0.98751000.339
4jr9A0.9351000.34
4iu9B0.93251000.342
2xutA0.97251000.393

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