GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BPD_transp_2 - Branched-chain amino acid transport system permease component
Pfam: PF02653 (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: CL0142
Length: 267
Sequences: 14280
Seq/Len: 53.48
HH_delta: 0.872 (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
62_I187_A1.665513.882
66_A183_A1.534833.578
66_A187_A1.210512.822
164_P178_R1.190292.775
42_A64_V1.157842.699
69_G186_G1.11572.601
173_N176_R1.082412.523
70_L183_A1.061492.474
157_L181_A1.038592.421
13_A137_A1.000112.331
65_G190_G0.983142.292
20_S230_A0.972842.268
78_R175_K0.966082.252
65_G186_G0.951512.218
46_L60_L0.922842.151
153_L180_I0.906222.112
146_F150_R0.898512.094
147_L153_L0.895582.088
176_R180_I0.886792.067
62_I191_L0.877822.046
214_D241_E0.860342.005
143_L147_L0.853531.990
160_V177_V0.850521.983
15_L215_A0.819861.911
70_L179_L0.817321.905
53_P56_L0.776881.811
156_A177_V0.768261.791
145_W149_K0.754981.760
142_V146_F0.729571.701
72_L90_L0.726491.693
159_A167_A0.708221.651
58_L194_A0.707031.648
172_I177_V0.705631.645
22_V185_S0.703481.640
74_L78_R0.701311.635
9_G238_G0.690541.610
73_G179_L0.68911.606
152_R156_A0.683881.594
153_L157_L0.667091.555
16_A230_A0.661281.541
55_W59_P0.656181.530
164_P168_R0.653871.524
43_A194_A0.650561.516
13_A234_A0.64691.508
165_E168_R0.644291.502
93_I96_G0.642771.498
37_G98_V0.64011.492
141_A231_I0.634791.480
21_L144_L0.631111.471
38_L68_I0.630311.469
9_G235_L0.62831.465
222_G229_G0.627861.464
14_L192_A0.62351.453
15_L36_A0.620031.445
25_T181_A0.620011.445
21_L181_A0.612821.429
156_A172_I0.60711.415
34_G95_V0.599911.398
160_V174_V0.596131.390
36_A196_Y0.592181.380
63_L66_A0.590771.377
122_F125_L0.590211.376
62_I194_A0.590161.376
179_L183_A0.587941.371
24_I158_R0.58351.360
222_G233_G0.579061.350
57_A61_A0.575441.341
18_G188_L0.570271.329
226_S229_G0.569411.327
24_I225_G0.569151.327
180_I184_I0.567471.323
52_P60_L0.565111.317
59_P63_L0.564671.316
183_A187_A0.563881.314
180_I183_A0.558691.302
90_L94_L0.557961.301
43_A61_A0.555431.295
139_L143_L0.553291.290
193_G197_A0.55311.289
156_A167_A0.55111.285
27_V182_F0.550071.282
78_R179_L0.546771.275
214_D259_I0.54071.260
19_L219_A0.52491.224
17_L144_L0.522161.217
167_A172_I0.518391.208
157_L177_V0.517641.207
66_A190_G0.512021.194
63_L67_L0.510741.191
168_R175_K0.509061.187
13_A231_I0.509031.187
61_A65_G0.507951.184
27_V83_Y0.507831.184
68_I94_L0.506941.182
32_H189_A0.504971.177
14_L195_L0.499961.165
218_A233_G0.495511.155
52_P56_L0.49341.150
74_L179_L0.493111.149
254_W257_I0.492181.147
56_L59_P0.490881.144
41_Y205_P0.48891.140
186_G190_G0.48741.136
160_V167_A0.485651.132
77_A175_K0.483051.126
16_A219_A0.481381.122
80_R164_P0.480571.120
42_A46_L0.475751.109
46_L50_F0.47471.107
135_L139_L0.473081.103
19_L32_H0.467141.089
16_A218_A0.462611.078
47_S57_A0.460891.074
9_G234_A0.459721.072
144_L184_I0.448751.046
98_V102_I0.447451.043
21_L148_L0.446981.042
5_I239_L0.445741.039
27_V178_R0.445291.038
40_A207_F0.444381.036
19_L215_A0.4431.033
67_L70_L0.442551.032
30_L216_F0.44211.031
29_N32_H0.440741.027
138_L142_V0.440691.027
149_K158_R0.437291.019
228_L232_L0.436371.017
131_I135_L0.434681.013
83_Y182_F0.43351.011
88_L91_F0.428230.998
241_E259_I0.427790.997
153_L177_V0.427080.996
145_W150_R0.426550.994
39_G193_G0.425080.991
190_G194_A0.425010.991
46_L57_A0.421820.983
69_G183_A0.414890.967
62_I190_G0.414830.967
43_A198_P0.414330.966
115_S119_F0.411110.958
67_L71_L0.409690.955
25_T157_L0.409050.954
118_L122_F0.408920.953
61_A194_A0.408720.953
244_V248_L0.407740.950
217_A263_L0.407070.949
187_A191_L0.406950.949
185_S189_A0.403930.942
74_L79_L0.403790.941
42_A60_L0.403140.940
90_L93_I0.402940.939
16_A234_A0.402020.937
140_V188_L0.400080.933
18_G32_H0.39930.931
141_A188_L0.39930.931
189_A193_G0.398810.930
112_I115_S0.395760.923
45_L49_A0.395310.921
62_I66_A0.394950.921
5_I238_G0.394850.920
17_L140_V0.394570.920
155_R158_R0.392830.916
73_G78_R0.39180.913
33_G212_G0.391750.913
41_Y98_V0.391210.912
35_F72_L0.390560.910
164_P174_V0.387490.903
242_T245_S0.386780.902
72_L86_I0.385590.899
184_I188_L0.384670.897
177_V180_I0.384670.897
224_A230_A0.384240.896
137_A141_A0.382070.891
21_L184_I0.380540.887
163_N166_A0.380270.886
95_V212_G0.379780.885
46_L49_A0.37710.879
77_A87_T0.376330.877
166_A170_L0.375820.876
261_L265_L0.374390.873
15_L192_A0.374330.873
133_I195_L0.373850.871
153_L184_I0.372190.868
168_R174_V0.371370.866
211_I214_D0.370820.864
36_A211_I0.370340.863
187_A190_G0.369250.861
33_G210_G0.369230.861
65_G69_G0.367970.858
20_S225_G0.367840.857
8_Q12_Y0.367690.857
20_S224_A0.367010.856
23_Y219_A0.366570.854
89_L92_F0.366570.854
22_V29_N0.365420.852
15_L18_G0.365070.851
46_L52_P0.362960.846
40_A197_A0.362790.846
15_L32_H0.361740.843
38_L42_A0.360890.841
76_V86_I0.359840.839
174_V178_R0.359630.838
11_I192_A0.359360.838
88_L92_F0.358660.836
147_L150_R0.358060.835
89_L93_I0.356050.830
9_G13_A0.355770.829
226_S230_A0.355350.828
40_A203_V0.353720.825
102_I105_I0.352520.822
142_V145_W0.352460.822
20_S219_A0.351970.820
235_L239_L0.351770.820
56_L60_L0.351170.819
13_A141_A0.350840.818
93_I97_L0.350670.817
218_A222_G0.349390.814
59_P62_I0.348980.813
35_F65_G0.348680.813
81_G86_I0.348490.812
36_A192_A0.347930.811
176_R179_L0.347240.809
132_Y135_L0.344840.804
160_V181_A0.34380.801
148_L157_L0.342280.798
218_A234_A0.341230.795
39_G61_A0.340990.795
23_Y216_F0.340710.794
92_F95_V0.339270.791
96_G99_L0.339240.791
75_L86_I0.338640.789
253_E256_Q0.336370.784
147_L151_T0.336190.784
143_L146_F0.335650.782
237_I259_I0.335410.782
73_G77_A0.333250.777
58_L62_I0.333180.777
71_L75_L0.332960.776
34_G91_F0.332870.776
87_T91_F0.332750.776
18_G189_A0.331380.772
10_A134_F0.330810.771
25_T160_V0.328860.767
24_I149_K0.328530.766
217_A259_I0.328510.766
45_L102_I0.328110.765
71_L90_L0.326830.762
76_V83_Y0.326280.761
175_K179_L0.326260.761
119_F122_F0.32530.758
140_V144_L0.324770.757
14_L137_A0.324070.755
23_Y224_A0.323610.754
89_L264_L0.323040.753
18_G185_S0.322260.751
75_L81_G0.320140.746
76_V182_F0.319990.746
35_F68_I0.31860.743
44_A203_V0.317660.740
219_A224_A0.317010.739
120_F123_G0.315530.736
21_L149_K0.314960.734
89_L96_G0.314190.732
31_G72_L0.314150.732
240_I262_I0.313310.730
5_I242_T0.3130.730
35_F189_A0.31290.729
29_N185_S0.312670.729
25_T178_R0.311520.726
42_A45_L0.310030.723
146_F149_K0.308660.720
12_Y241_E0.307290.716
14_L191_L0.307250.716
107_G111_G0.306380.714
214_D256_Q0.305180.711
144_L188_L0.302920.706
14_L140_V0.302840.706
210_G214_D0.30180.704
75_L79_L0.299150.697
117_P120_F0.297950.695
175_K178_R0.29770.694
230_A234_A0.295780.689
221_I266_V0.29490.687
158_R225_G0.293340.684
134_F138_L0.293080.683
100_I254_W0.293060.683
5_I9_G0.291530.680
39_G189_A0.290930.678
197_A207_F0.29070.678
230_A233_G0.290660.678
262_I266_V0.290480.677
146_F227_P0.290170.676
38_L94_L0.289430.675
17_L230_A0.288690.673
38_L64_V0.288530.673
4_N242_T0.288520.673
36_A208_G0.287980.671
21_L147_L0.287660.671
220_V223_G0.287630.670
11_I199_Y0.287350.670
6_L10_A0.285580.666
125_L128_F0.284890.664
39_G64_V0.284820.664
32_H185_S0.2840.662
41_Y102_I0.283410.661
45_L101_L0.283130.660
140_V191_L0.282280.658
160_V178_R0.281870.657
85_I88_L0.280890.655
222_G230_A0.280760.654
229_G233_G0.280750.654
234_A238_G0.280210.653
242_T247_Y0.280040.653
43_A193_G0.27960.652
104_G107_G0.2790.650
85_I89_L0.278410.649
113_S116_P0.276980.646
3_F7_V0.275930.643
77_A179_L0.275920.643
43_A47_S0.275780.643
97_L100_I0.275320.642
167_A174_V0.274970.641
196_Y200_Y0.274890.641
7_V199_Y0.27350.638
11_I196_Y0.272280.635
119_F123_G0.272110.634
35_F94_L0.270320.630
127_P130_Q0.269370.628
20_S24_I0.267920.625
35_F186_G0.267170.623
108_G111_G0.266830.622
70_L74_L0.266520.621
37_G95_V0.26650.621
127_P135_L0.266380.621
35_F39_G0.266190.621
256_Q259_I0.266030.620
38_L65_G0.265090.618
26_G164_P0.265010.618
33_G208_G0.264740.617
27_V164_P0.264470.616
39_G65_G0.264260.616
10_A137_A0.264220.616
80_R175_K0.2640.615
233_G236_L0.262410.612
8_Q242_T0.262210.611
20_S226_S0.261690.610
52_P57_A0.261610.610
22_V27_V0.259870.606
65_G187_A0.25960.605
236_L240_I0.259470.605
125_L132_Y0.258650.603
220_V224_A0.258440.602
12_Y234_A0.258230.602
23_Y28_I0.258030.601
20_S227_P0.256360.598
114_G117_P0.25590.597
126_I131_I0.255780.596
238_G242_T0.253190.590
128_F135_L0.25250.589
158_R161_G0.252250.588
147_L180_I0.252030.587
118_L121_F0.25190.587
137_A231_I0.250220.583
46_L64_V0.250110.583
4_N8_Q0.249610.582
18_G22_V0.249560.582
22_V182_F0.24930.581
86_I89_L0.249060.581
228_L231_I0.248650.580
12_Y218_A0.24810.578
209_F212_G0.247940.578
229_G234_A0.2470.576
184_I187_A0.246620.575
132_Y136_V0.245610.573
37_G208_G0.245340.572
98_V101_L0.244580.570
39_G194_A0.243510.568
94_L98_V0.243430.567
141_A144_L0.243180.567
103_S107_G0.242830.566
227_P230_A0.242430.565
89_L95_V0.242190.565
17_L145_W0.241880.564
54_W57_A0.241580.563
91_F95_V0.241460.563
242_T246_S0.240880.562
218_A230_A0.24040.560
167_A173_N0.240230.560
6_L9_G0.23990.559
12_Y214_D0.239510.558
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
2nq2A0.925196.30.872
4g1uA0.936395.60.88
2qi9A0.921393.40.894
1u7gA0.55814.60.956
3dh4A0.5884.30.957
2xq2A0.71163.70.958
2zy9A0.34463.70.958
2b2hA0.65923.40.959
1iijA0.13112.50.962
2ksfA0.34462.30.962
If you are interested in a protein containing this domain,
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