GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Branch_AA_trans - Branched-chain amino acid transport protein
Pfam: PF05525 (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: CL0062
Length: 427
Sequences: 11109
Seq/Len: 26.02
HH_delta: 0.428 (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
301_Y312_K0.775053.746
219_E223_Y0.595392.878
304_E312_K0.59062.854
356_L360_F0.54752.646
216_D219_E0.517692.502
214_Y220_I0.489062.364
265_Q268_N0.482782.333
255_D269_H0.478152.311
160_I164_F0.468852.266
123_I323_F0.462852.237
223_Y227_A0.455112.200
138_K142_R0.445572.153
306_F311_Y0.436862.111
153_I157_I0.435922.107
265_Q269_H0.425742.058
38_P190_Y0.420132.031
70_S74_P0.419252.026
130_Y319_T0.405631.960
149_P153_I0.399091.929
131_L135_N0.391211.891
301_Y304_E0.385511.863
130_Y134_L0.38521.862
56_I349_I0.381851.845
17_F20_G0.366051.769
117_S120_I0.35811.731
48_V52_L0.357291.727
277_I281_I0.355811.720
236_A240_G0.354281.712
152_L156_A0.353581.709
120_I124_I0.352721.705
78_L82_I0.341341.650
62_G68_L0.336861.628
119_L123_I0.33591.623
13_F16_F0.330731.598
129_T291_A0.328131.586
204_I208_A0.327691.584
70_S77_A0.326971.580
143_I147_L0.319881.546
73_G76_F0.318441.539
156_A160_I0.317731.536
142_R145_K0.314781.521
64_G69_A0.312751.512
273_S278_L0.30941.495
272_G275_G0.308441.491
123_I127_A0.307581.487
330_L334_I0.306481.481
169_P172_A0.305321.476
31_Q34_S0.300031.450
31_Q35_N0.299071.445
316_I320_I0.29841.442
154_L282_I0.296421.433
59_A358_D0.295151.426
30_Q34_S0.293581.419
130_Y314_W0.292491.414
300_E304_E0.292171.412
271_F275_G0.29031.403
216_D220_I0.289571.400
190_Y194_D0.289341.398
161_K165_S0.288991.397
300_E303_S0.288231.393
47_G236_A0.287891.391
241_G245_L0.287321.389
217_K222_K0.282951.368
226_K230_I0.279461.351
79_I83_L0.278321.345
90_P93_A0.27791.343
44_L240_G0.277771.342
129_T295_I0.277351.340
336_I340_I0.27521.330
317_I321_F0.274521.327
305_L308_K0.272631.318
134_L311_Y0.272121.315
134_L316_I0.271881.314
159_I162_G0.271161.311
139_I142_R0.269861.304
306_F309_I0.269691.303
127_A131_L0.269421.302
97_T100_V0.268581.298
220_I223_Y0.268511.298
182_F190_Y0.268331.297
42_G193_M0.265861.285
90_P94_I0.265741.284
159_I241_G0.26481.280
99_A102_F0.263771.275
167_I170_P0.26341.273
259_G265_Q0.260321.258
333_I337_S0.258171.248
170_P173_P0.258011.247
251_G254_P0.257951.247
147_L289_T0.25641.239
133_S292_I0.253831.227
334_I338_V0.253311.224
98_A102_F0.252861.222
216_D223_Y0.249151.204
87_S90_P0.24841.201
295_I299_A0.248161.199
161_K271_F0.2481.199
64_G68_L0.247931.198
130_Y316_I0.247411.196
141_D292_I0.246881.193
323_F327_N0.246791.193
162_G245_L0.246721.192
340_I344_I0.246441.191
108_P111_P0.243911.179
41_I44_L0.243641.178
347_V351_L0.243071.175
106_I109_F0.24271.173
189_G193_M0.242171.170
320_I324_I0.241861.169
41_I190_Y0.240591.163
342_M345_Y0.239921.160
116_I121_F0.239781.159
15_M18_G0.239681.158
157_I161_K0.239041.155
310_S313_V0.237251.147
337_S345_Y0.236141.141
319_T322_S0.236141.141
40_M244_Y0.235811.140
32_A35_N0.234691.134
144_G289_T0.234691.134
142_R146_F0.233741.130
75_K79_I0.233061.126
69_A80_F0.232291.123
215_K220_I0.23111.117
348_A351_L0.230921.116
109_F280_G0.230791.115
219_E222_K0.230731.115
237_L241_G0.228431.104
261_E265_Q0.227611.100
324_I327_N0.227591.100
119_L122_S0.226021.092
66_E81_T0.225721.091
331_D335_K0.224491.085
211_Q221_K0.224131.083
345_Y348_A0.22371.081
13_F18_G0.223371.080
279_L282_I0.222891.077
13_F231_A0.222541.076
357_F361_I0.219771.062
85_Y91_L0.21831.055
84_I88_I0.21821.055
286_A289_T0.217561.051
107_A110_F0.217551.051
188_E191_Q0.216811.048
116_I120_I0.216311.045
54_G225_I0.215991.044
251_G255_D0.215721.043
244_Y248_T0.21571.042
67_D71_R0.214821.038
151_L286_A0.214381.036
61_S68_L0.213821.033
325_I328_L0.213461.032
88_I294_L0.213121.030
62_G212_K0.212261.026
97_T101_S0.212141.025
217_K220_I0.210781.019
135_N139_I0.210171.016
159_I163_I0.20921.011
133_S295_I0.208891.010
131_L134_L0.208441.007
65_I68_L0.208121.006
144_G292_I0.207991.005
54_G229_L0.207631.003
159_I242_L0.207171.001
66_E70_S0.207021.001
189_G192_T0.206750.999
330_L345_Y0.206610.999
332_Q336_I0.206510.998
30_Q35_N0.206480.998
103_E121_F0.206170.996
54_G57_A0.205990.996
330_L335_K0.205690.994
58_V61_S0.205110.991
123_I327_N0.204850.990
230_I237_L0.203450.983
128_I288_L0.203450.983
345_Y349_I0.203410.983
203_I207_N0.203330.983
63_G67_D0.202380.978
88_I91_L0.202310.978
41_I45_L0.202140.977
227_A230_I0.202060.977
38_P182_F0.20180.975
60_K224_T0.201070.972
107_A111_P0.200850.971
137_S296_S0.200070.967
62_G67_D0.199270.963
43_F263_L0.199060.962
73_G77_A0.198930.961
156_A159_I0.198790.961
127_A319_T0.198360.959
124_I128_I0.198320.958
44_L48_V0.198280.958
178_A181_P0.19790.956
186_F191_Q0.197620.955
69_A76_F0.196620.950
125_F291_A0.196520.950
245_L249_S0.19590.947
120_I123_I0.195840.947
39_A244_Y0.195560.945
179_S182_F0.195520.945
197_A201_F0.194820.942
319_T323_F0.194690.941
192_T196_L0.194090.938
89_G92_F0.19370.936
264_S280_G0.193670.936
132_L136_P0.193660.936
205_I297_A0.193570.936
164_F167_I0.193510.935
334_I342_M0.193460.935
151_L289_T0.193010.933
100_V104_M0.192580.931
122_S326_A0.192440.930
318_F321_F0.191120.924
97_T102_F0.191070.923
334_I349_I0.190020.918
228_G231_A0.189950.918
209_I296_S0.189450.916
333_I345_Y0.188690.912
194_D198_A0.188240.910
332_Q335_K0.188190.910
303_S312_K0.187790.908
349_I352_I0.186990.904
190_Y193_M0.18690.903
91_L94_I0.186840.903
246_G251_G0.186740.903
73_G78_L0.186460.901
47_G232_G0.186380.901
78_L81_T0.186330.901
204_I207_N0.184920.894
338_V341_L0.184790.893
220_I224_T0.18450.892
136_P139_I0.184060.890
87_S91_L0.184040.889
271_F274_A0.183630.887
55_V226_K0.183620.887
47_G201_F0.183410.886
318_F323_F0.183320.886
356_L359_K0.183270.886
158_L267_A0.183070.885
246_G250_S0.181750.878
167_I171_Q0.181490.877
181_P185_G0.180230.871
192_T195_A0.179940.870
166_P174_S0.179880.869
69_A351_L0.179870.869
301_Y305_L0.179190.866
172_A175_G0.178840.864
249_S253_F0.17870.864
256_D262_L0.178560.863
87_S341_L0.178380.862
134_L306_F0.177630.858
259_G262_L0.177220.857
342_M349_I0.176910.855
232_G239_Y0.176790.854
299_A313_V0.176660.854
67_D70_S0.17640.853
129_T292_I0.176340.852
249_S270_L0.176270.852
249_S266_I0.176170.851
283_V287_C0.176150.851
208_A224_T0.1760.851
205_I293_G0.175960.850
121_F124_I0.175750.849
318_F322_S0.175670.849
175_G178_A0.175420.848
231_A238_I0.175270.847
216_D222_K0.174460.843
137_S141_D0.174380.843
106_I110_F0.17430.842
30_Q33_G0.174170.842
61_S207_N0.173910.841
274_A278_L0.173720.840
64_G67_D0.173550.839
161_K164_F0.17320.837
298_C318_F0.173160.837
219_E226_K0.172690.835
338_V342_M0.172640.834
87_S93_A0.171310.828
143_I292_I0.17130.828
167_I173_P0.171230.828
55_V59_A0.171140.827
129_T288_L0.170840.826
180_N183_F0.170830.826
117_S121_F0.170610.825
70_S78_L0.170580.824
77_A81_T0.170430.824
341_L344_I0.170340.823
345_Y352_I0.170310.823
158_L266_I0.169910.821
155_L286_A0.169840.821
46_T197_A0.169820.821
158_L162_G0.169820.821
85_Y88_I0.169390.819
162_G249_S0.169360.819
15_M19_A0.168840.816
16_F232_G0.168310.813
125_F129_T0.16810.812
74_P78_L0.1680.812
171_Q179_S0.167850.811
86_L91_L0.167110.808
334_I341_L0.167080.808
111_P115_N0.166970.807
338_V345_Y0.166950.807
341_L345_Y0.166780.806
12_L15_M0.166320.804
302_F317_I0.166280.804
85_Y89_G0.166180.803
330_L337_S0.166170.803
245_L248_T0.165130.798
51_P226_K0.165120.798
246_G249_S0.165120.798
334_I337_S0.164980.797
168_G172_A0.164880.797
177_Y182_F0.164590.795
124_I127_A0.16450.795
88_I92_F0.164320.794
340_I345_Y0.16420.794
225_I228_G0.16320.789
98_A101_S0.162920.787
264_S283_V0.162670.786
147_L285_L0.162650.786
126_F322_S0.1620.783
75_K78_L0.161760.782
166_P170_P0.161560.781
47_G51_P0.161510.781
309_I312_K0.161380.780
80_F84_I0.161190.779
268_N273_S0.161080.779
171_Q174_S0.160870.777
267_A274_A0.160730.777
89_G318_F0.160720.777
51_P54_G0.160480.776
135_N138_K0.160090.774
213_G310_S0.160070.774
102_F283_V0.159830.772
332_Q339_P0.159820.772
339_P345_Y0.15970.772
185_G328_L0.159430.771
133_S314_W0.159290.770
124_I131_L0.159070.769
191_Q195_A0.158820.768
299_A314_W0.158650.767
41_I181_P0.158320.765
165_S169_P0.157460.761
162_G267_A0.15740.761
347_V350_V0.157230.760
281_I285_L0.157150.760
344_I348_A0.156810.758
80_F344_I0.156690.757
189_G196_L0.156640.757
51_P55_V0.156540.757
111_P116_I0.156480.756
298_C311_Y0.156440.756
57_A61_S0.156320.755
317_I320_I0.155980.754
13_F19_A0.155820.753
103_E110_F0.155640.752
125_F288_L0.15560.752
42_G46_T0.154670.748
222_K225_I0.154560.747
115_N118_L0.154550.747
245_L250_S0.154480.747
350_V356_L0.154270.746
86_L90_P0.154220.745
11_A228_G0.15410.745
15_M20_G0.153970.744
151_L290_T0.153410.741
14_A60_K0.153280.741
253_F269_H0.153210.740
215_K218_K0.153080.740
76_F79_I0.152820.739
174_S178_A0.152770.738
57_A348_A0.152740.738
339_P342_M0.152720.738
182_F189_G0.152690.738
99_A103_E0.152410.737
314_W317_I0.15210.735
132_L143_I0.151540.732
304_E307_P0.15150.732
168_G174_S0.151070.730
169_P174_S0.150850.729
303_S313_V0.150830.729
196_L200_A0.150650.728
218_K222_K0.150630.728
172_A176_A0.150550.728
74_P77_A0.15040.727
335_K339_P0.150360.727
52_L56_I0.149910.725
162_G270_L0.149750.724
58_V222_K0.149370.722
85_Y318_F0.148870.719
282_I286_A0.148580.718
14_A20_G0.148570.718
141_D145_K0.148350.717
320_I323_F0.148330.717
38_P185_G0.148220.716
101_S104_M0.148180.716
185_G327_N0.148030.715
250_S269_H0.147870.715
337_S349_I0.147660.714
150_I285_L0.147520.713
42_G190_Y0.147380.712
107_A118_L0.147230.712
12_L16_F0.147110.711
175_G179_S0.147030.711
302_F312_K0.147020.711
255_D258_N0.146850.710
277_I280_G0.146730.709
134_L309_I0.146720.709
101_S105_G0.14650.708
11_A19_A0.146360.707
220_I227_A0.146330.707
69_A72_V0.146270.707
321_F324_I0.146150.706
244_Y247_A0.14520.702
196_L335_K0.14510.701
87_S340_I0.145090.701
170_P247_A0.144910.700
165_S270_L0.144890.700
211_Q214_Y0.144820.700
255_D259_G0.144820.700
148_T151_L0.144390.698
282_I289_T0.144280.697
213_G305_L0.144260.697
150_I154_L0.144060.696
105_G280_G0.143950.696
73_G81_T0.143920.696
53_L349_I0.143750.695
60_K356_L0.143730.695
161_K267_A0.143610.694
223_Y226_K0.143560.694
338_V344_I0.143270.692
189_G194_D0.14290.691
151_L285_L0.142450.688
290_T293_G0.142280.688
267_A271_F0.142210.687
163_I167_I0.141550.684
20_G350_V0.141270.683
345_Y351_L0.14120.682
166_P169_P0.141070.682
336_I345_Y0.140970.681
76_F347_V0.140240.678
222_K226_K0.140190.678
337_S341_L0.140040.677
254_P257_I0.139920.676
335_K345_Y0.139780.676
312_K316_I0.13920.673
302_F313_V0.139050.672
61_S221_K0.138930.671
11_A18_G0.138840.671
243_A263_L0.138760.671
60_K72_V0.138730.670
329_G332_Q0.138710.670
188_E192_T0.138390.669
258_N328_L0.138350.669
39_A42_G0.13830.668
45_L49_G0.138220.668
15_M293_G0.138170.668
273_S277_I0.138150.668
85_Y92_F0.137750.666
291_A294_L0.137450.664
46_T201_F0.13740.664
156_A238_I0.137390.664
53_L56_I0.137130.663
154_L279_L0.137120.663
330_L349_I0.136970.662
38_P181_P0.13650.660
92_F334_I0.136430.659
140_V144_G0.13630.659
358_D361_I0.136130.658
62_G66_E0.135940.657
332_Q338_V0.135890.657
162_G244_Y0.135840.657
40_M240_G0.135720.656
305_L310_S0.135410.654
118_L123_I0.135360.654
155_L238_I0.135150.653
93_A98_A0.135070.653
66_E77_A0.135040.653
17_F154_L0.1350.652
304_E311_Y0.134760.651
70_S73_G0.134630.651
17_F287_C0.134590.650
351_L357_F0.134580.650
208_A212_K0.134580.650
158_L293_G0.134440.650
352_I358_D0.134320.649
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
4djkA0.94611000.428
3giaA0.92041000.488
3l1lA0.92041000.488
2jlnA0.929798.70.85
2a65A0.974298.40.864
2xq2A0.939197.80.887
3dh4A0.932197.80.888
2wswA0.824431.30.959
1wazA0.10778.80.967
3m73A0.28573.60.972

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