GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UAA - UAA transporter family
Pfam: PF08449 (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: CL0184
Length: 303
Sequences: 16729
Seq/Len: 55.21
HH_delta: 0.746 (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
84_A159_L1.316383.064
269_S275_H1.162052.704
123_S291_G1.116772.599
244_Y248_K1.02022.374
83_A158_L1.01572.364
92_T156_I1.012792.357
80_L161_L0.930442.165
80_L158_L0.895382.084
114_K174_E0.883732.057
103_P163_L0.881872.052
94_I265_S0.878652.045
107_L171_V0.854331.988
37_F200_L0.839831.955
99_S103_P0.836841.948
157_I161_L0.821411.912
117_S120_Q0.817621.903
60_R63_P0.816671.901
108_G114_K0.803451.870
105_M124_V0.781161.818
44_A193_L0.767771.787
88_I156_I0.743941.731
41_A196_L0.742321.728
244_Y247_K0.739291.721
93_Q159_L0.729131.697
104_V255_T0.727891.694
109_V116_Y0.725651.689
123_S294_L0.723221.683
88_I155_G0.715171.664
127_I259_T0.713461.660
118_R122_L0.680641.584
268_L272_I0.679891.582
108_G112_L0.676351.574
62_I65_K0.674721.570
250_S253_T0.672231.564
80_L165_L0.668931.557
123_S295_Y0.643941.499
76_L165_L0.636021.480
48_F189_F0.632711.472
197_P201_I0.628781.463
278_S281_Q0.623231.450
61_K65_K0.622851.450
107_L168_F0.617591.437
264_L268_L0.617211.436
45_L49_I0.616981.436
127_I291_G0.615031.431
167_A171_V0.614951.431
87_Y155_G0.614831.431
44_A196_L0.606821.412
125_L129_I0.601151.399
130_G284_G0.59931.395
90_Y269_S0.597551.391
83_A87_Y0.5961.387
130_G288_V0.592841.380
173_Q243_F0.589981.373
282_W286_V0.585341.362
89_S92_T0.580261.350
83_A86_K0.579541.349
163_L167_A0.57921.348
279_P283_I0.571831.331
87_Y158_L0.570941.329
133_I287_L0.559751.303
222_P226_L0.55911.301
103_P167_A0.556731.296
91_P266_I0.552171.285
133_I280_L0.552071.285
260_L264_L0.55091.282
293_F297_Y0.548591.277
48_F52_S0.548381.276
229_L232_S0.545811.270
236_A239_Q0.544111.266
49_I52_S0.542221.262
71_S194_F0.5381.252
107_L111_I0.537581.251
201_I204_F0.535771.247
37_F196_L0.535651.247
69_I172_Y0.534991.245
112_L171_V0.534941.245
107_L167_A0.533181.241
107_L164_L0.526651.226
110_L113_G0.525851.224
227_Y230_L0.525821.224
121_Y125_L0.523161.218
37_F41_A0.516411.202
85_L93_Q0.515411.199
134_F284_G0.513871.196
95_V285_I0.510811.189
198_F201_I0.508011.182
130_G291_G0.506881.180
109_V115_R0.50531.176
103_P164_L0.501391.167
159_L163_L0.490581.142
286_V290_A0.487831.135
49_I53_L0.483371.125
231_F236_A0.481721.121
235_G238_G0.481591.121
60_R64_L0.479631.116
104_V170_G0.479261.115
174_E178_K0.479181.115
104_V251_A0.475741.107
183_S186_E0.47511.106
174_E251_A0.474991.105
88_I92_T0.472811.100
260_L263_F0.472171.099
81_S85_L0.471861.098
238_G242_I0.469361.092
277_L282_W0.466421.085
102_I127_I0.466211.085
61_K64_L0.462441.076
246_I250_S0.457971.066
201_I205_L0.455591.060
96_F163_L0.451091.050
155_G159_L0.450531.048
245_L254_T0.45041.048
43_N192_N0.450131.048
44_A48_F0.448731.044
250_S254_T0.443861.033
88_I159_L0.443451.032
68_A194_F0.442161.029
174_E250_S0.442011.029
104_V167_A0.439981.024
189_F193_L0.439931.024
117_S121_Y0.438681.021
226_L229_L0.432131.006
256_I295_Y0.430581.002
88_I93_Q0.429741.000
225_L229_L0.428270.997
119_R294_L0.427250.994
116_Y121_Y0.426460.992
277_L281_Q0.42560.990
118_R121_Y0.424370.988
105_M116_Y0.424120.987
239_Q242_I0.421540.981
95_V132_A0.419680.977
65_K69_I0.417960.973
221_H225_L0.415390.967
249_F254_T0.414680.965
232_S236_A0.41420.964
96_F159_L0.413830.963
90_Y273_F0.413280.962
78_S81_S0.412410.960
96_F160_L0.411680.958
195_S199_L0.410650.956
42_F46_F0.410290.955
223_S226_L0.405530.944
285_I289_F0.4050.943
129_I133_I0.404840.942
84_A93_Q0.401580.935
114_K120_Q0.401510.934
77_A169_T0.399460.930
126_L291_G0.397150.924
226_L230_L0.396970.924
39_Q235_G0.396020.922
44_A189_F0.394760.919
202_L205_L0.394320.918
90_Y94_I0.393270.915
36_T82_N0.393260.915
196_L200_L0.393160.915
107_L110_L0.392980.915
74_F169_T0.391960.912
73_L168_F0.388690.905
50_L53_L0.388540.904
33_L79_V0.388210.903
246_I254_T0.38760.902
66_K70_L0.384840.896
270_V277_L0.383830.893
34_F38_V0.383630.893
221_H224_V0.383540.893
194_F197_P0.383480.892
234_T238_G0.382030.889
231_F234_T0.380570.886
235_G239_Q0.379480.883
236_A240_F0.379430.883
37_F203_L0.378050.880
263_F285_I0.377680.879
99_S131_V0.376170.875
73_L172_Y0.373650.870
222_P225_L0.372810.868
64_L68_A0.372750.867
71_S75_F0.370020.861
131_V135_T0.369880.861
65_K68_A0.368720.858
158_L161_L0.368360.857
71_S74_F0.368260.857
132_A136_L0.368080.857
62_I66_K0.36720.855
106_I124_V0.362340.843
104_V171_V0.361580.841
122_L126_L0.361370.841
194_F198_F0.361150.840
156_I160_L0.359230.836
95_V135_T0.358540.834
38_V42_F0.357790.833
133_I284_G0.356180.829
75_F198_F0.355990.828
39_Q43_N0.354710.826
193_L197_P0.354520.825
95_V134_F0.354510.825
266_I277_L0.353630.823
283_I287_L0.352510.820
73_L165_L0.351670.818
41_A200_L0.351320.818
106_I110_L0.350520.816
164_L168_F0.349660.814
255_T258_T0.349610.814
249_F253_T0.3490.812
198_F202_L0.347710.809
168_F172_Y0.347530.809
63_P66_K0.347480.809
33_L202_L0.346640.807
123_S127_I0.346370.806
279_P282_W0.345860.805
268_L271_I0.345660.804
77_A81_S0.345350.804
269_S273_F0.344570.802
36_T199_L0.343490.799
241_F244_Y0.34330.799
173_Q246_I0.343210.799
278_S282_W0.343160.799
98_S101_P0.342740.798
66_K172_Y0.340660.793
229_L233_L0.340310.792
266_I270_V0.340310.792
74_F78_S0.339780.791
42_F232_S0.337740.786
187_L191_T0.337320.785
133_I283_I0.336930.784
223_S227_Y0.336580.783
41_A45_L0.335960.782
64_L67_Y0.333840.777
188_M192_N0.333190.775
114_K252_L0.333150.775
220_A224_V0.333030.775
234_T237_L0.331890.772
283_I286_V0.331540.772
82_N86_K0.331030.770
90_Y275_H0.331030.770
84_A88_I0.330960.770
50_L54_F0.330550.769
104_V108_G0.329770.767
40_F195_S0.327610.762
109_V113_G0.327380.762
175_K178_K0.32660.760
267_L271_I0.324930.756
77_A166_D0.324290.755
59_S62_I0.323780.754
281_Q285_I0.323040.752
230_L233_L0.322410.750
116_Y120_Q0.322390.750
258_T261_R0.321610.748
126_L294_L0.321180.747
68_A71_S0.321030.747
188_M191_T0.320410.746
227_Y231_F0.319770.744
119_R297_Y0.319660.744
102_I124_V0.318850.742
136_L139_S0.318470.741
166_D170_G0.318370.741
63_P67_Y0.317060.738
105_M120_Q0.315980.735
290_A294_L0.313590.730
88_I91_P0.313060.729
101_P259_T0.312380.727
196_L199_L0.312320.727
75_F199_L0.31170.725
280_L283_I0.310490.723
46_F236_A0.310390.722
77_A97_K0.308850.719
96_F156_I0.305990.712
115_R118_R0.305540.711
124_V252_L0.30460.709
52_S55_K0.303840.707
98_S131_V0.303580.707
129_I287_L0.303330.706
94_I98_S0.30310.705
81_S162_S0.302380.704
81_S93_Q0.300670.700
80_L162_S0.299920.698
111_I168_F0.29890.696
42_F45_L0.298490.695
128_T259_T0.298110.694
77_A165_L0.298080.694
79_V83_A0.297260.692
105_M109_V0.297160.692
37_F44_A0.296470.690
34_F37_F0.295010.687
238_G241_F0.294570.686
292_I296_S0.294080.684
169_T173_Q0.293180.682
240_F244_Y0.292240.680
270_V282_W0.292130.680
224_V228_L0.291980.680
190_Y194_F0.291840.679
78_S82_N0.291110.677
267_L270_V0.290120.675
225_L228_L0.289320.673
70_L74_F0.289170.673
120_Q250_S0.288790.672
186_E190_Y0.287810.670
60_R65_K0.287240.668
70_L173_Q0.286930.668
170_G246_I0.285270.664
89_S93_Q0.285170.664
39_Q42_F0.284910.663
224_V227_Y0.283830.661
98_S163_L0.283620.660
192_N195_S0.282760.658
45_L48_F0.28270.658
66_K175_K0.282420.657
84_A155_G0.281940.656
134_F262_K0.281180.654
119_R122_L0.280610.653
102_I128_T0.278440.648
68_A198_F0.278110.647
190_Y193_L0.277690.646
128_T132_A0.2770.645
66_K176_L0.276330.643
46_F232_S0.276260.643
115_R119_R0.276180.643
36_T40_F0.275830.642
51_L54_F0.275830.642
170_G255_T0.275750.642
173_Q177_F0.275440.641
256_I259_T0.274990.640
40_F44_A0.27470.639
160_L164_L0.27470.639
100_K258_T0.274510.639
105_M170_G0.274460.639
64_L194_F0.274390.639
171_V251_A0.274020.638
199_L203_L0.273990.638
185_W188_M0.272370.634
97_K242_I0.271260.631
103_P107_L0.270820.630
270_V276_P0.270710.630
166_D242_I0.270030.628
169_T191_T0.26950.627
99_S163_L0.269110.626
74_F77_A0.268890.626
66_K69_I0.268490.625
97_K261_R0.267490.623
51_L55_K0.267230.622
291_G295_Y0.266920.621
74_F239_Q0.266660.621
193_L196_L0.26640.620
160_L163_L0.265190.617
35_L231_F0.265070.617
51_L189_F0.264020.614
112_L175_K0.263990.614
122_L129_I0.263360.613
177_F187_L0.263180.612
38_V41_A0.261570.609
43_N47_S0.261540.609
259_T292_I0.261090.608
271_I274_G0.261060.608
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
2i68A0.356498.50.746
3b5dA0.346598.30.756
2i68A0.435698.20.766
3b5dA0.356498.10.772
4he8J0.534768.90.905
1u7gA0.772314.30.934
2h3oA0.181512.70.936
4apsA0.73279.10.94
4he8N0.82188.40.941
3hd6A0.91096.20.944
If you are interested in a protein containing this domain,
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