GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RhaT - L-rhamnose-proton symport protein (RhaT)
Pfam: PF06379 (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: 344
Sequences: 12949
Seq/Len: 37.64
HH_delta: 0.809 (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
93_A178_A1.227883.395
11_F278_M1.026492.838
140_G334_S0.975362.697
20_G302_F0.920872.546
278_M282_K0.91852.539
89_T180_L0.912442.523
92_L177_I0.882712.440
307_G312_E0.877092.425
12_H279_G0.832432.301
26_F91_G0.775012.143
101_L175_L0.770752.131
114_G292_W0.765662.117
20_G306_W0.765512.116
278_M281_S0.75562.089
113_F182_G0.752242.080
118_P131_T0.749122.071
17_F302_F0.74472.059
176_I180_L0.72111.994
119_P133_S0.711511.967
27_K312_E0.707041.955
89_T177_I0.66281.832
102_G178_A0.657881.819
321_I324_L0.656561.815
322_R326_L0.656141.814
134_G137_V0.651761.802
115_T141_V0.650311.798
263_A266_G0.649481.796
25_P264_L0.647571.790
97_L174_G0.622981.722
135_Q139_L0.614061.698
266_G270_Y0.596871.650
256_L260_L0.594661.644
150_I330_V0.578581.600
142_A146_I0.567741.570
109_L113_F0.56431.560
151_C327_G0.564151.560
85_I184_M0.563551.558
325_V329_A0.562151.554
117_I187_C0.561841.553
89_T184_M0.559811.548
140_G338_V0.553581.530
10_I14_I0.552821.528
144_C296_M0.55221.527
11_F275_F0.550271.521
117_I121_F0.547371.513
15_G279_G0.540631.495
96_Y173_K0.538481.489
97_L175_L0.536731.484
113_F183_V0.532551.472
92_L96_Y0.532441.472
33_S36_S0.530211.466
261_F264_L0.5211.440
329_A333_L0.518751.434
74_F78_L0.515791.426
150_I323_V0.515271.425
24_V306_W0.514951.424
15_G19_S0.514591.423
138_L142_A0.512211.416
306_W309_I0.511961.415
136_I337_I0.506231.400
147_G331_L0.501911.388
70_A74_F0.500531.384
97_L101_L0.499921.382
308_L320_T0.499261.380
284_G290_S0.490471.356
302_F306_W0.489581.354
113_F186_A0.486721.346
320_T325_V0.486011.344
172_K176_I0.484671.340
82_L187_C0.483481.337
226_I230_I0.482971.335
15_G275_F0.478561.323
18_A275_F0.471321.303
90_F94_M0.470151.300
114_G118_P0.468521.295
104_S303_S0.467481.292
99_V310_L0.467271.292
280_E284_G0.466891.291
119_P132_P0.453581.254
311_K319_K0.451811.249
144_C334_S0.450311.245
16_G302_F0.446471.234
131_T137_V0.445721.232
71_S74_F0.440931.219
19_S272_Q0.436281.206
135_Q138_L0.433621.199
98_G101_L0.430811.191
21_S306_W0.430521.190
100_S304_N0.428531.185
108_G111_A0.425071.175
92_L95_R0.424731.174
19_S276_Y0.422061.167
24_V309_I0.416791.152
182_G186_A0.414451.146
9_I294_I0.409711.133
134_G138_L0.407731.127
8_G282_K0.407021.125
256_L259_Y0.406351.123
183_V187_C0.404081.117
112_V144_C0.403531.116
117_I120_I0.402921.114
264_L267_V0.397631.099
297_A302_F0.397481.099
14_I275_F0.397031.098
96_Y174_G0.395111.092
96_Y177_I0.392621.085
99_V307_G0.390451.079
223_G227_T0.389871.078
94_M102_G0.379561.049
300_V328_I0.378921.048
70_A73_L0.37721.043
283_L291_S0.374641.036
117_I183_V0.372761.031
283_L290_S0.371951.028
8_G283_L0.371811.028
21_S264_L0.371241.026
26_F94_M0.370731.025
257_K260_L0.368051.018
147_G334_S0.367731.017
146_I150_I0.367561.016
35_E39_L0.366481.013
133_S138_L0.365111.009
140_G337_I0.364041.006
93_A102_G0.363251.004
117_I186_A0.362241.001
72_T206_G0.359220.993
16_G20_G0.359060.993
47_L50_P0.35880.992
80_G223_G0.356670.986
308_L319_K0.355290.982
28_K261_F0.354550.980
320_T324_L0.354030.979
147_G327_G0.349770.967
174_G178_A0.347970.962
18_A272_Q0.347040.959
9_I283_L0.346970.959
121_F187_C0.346850.959
304_N328_I0.345850.956
305_V308_L0.34560.955
149_A153_K0.344950.954
72_T76_T0.343720.950
173_K176_I0.34320.949
83_W273_F0.341380.944
16_G297_A0.340930.943
113_F179_V0.336410.930
284_G291_S0.335460.927
260_L264_L0.335280.927
71_S75_W0.334370.924
18_A268_L0.334370.924
116_L141_V0.334260.924
264_L268_L0.333570.922
178_A182_G0.332640.920
263_A267_V0.33180.917
173_K177_I0.331280.916
83_W87_G0.330770.914
322_R325_V0.329580.911
32_W36_S0.328860.909
13_A16_G0.328560.908
280_E291_S0.326510.903
224_G228_N0.326470.903
115_T133_S0.325280.899
74_F77_F0.323920.896
82_L184_M0.323020.893
139_L143_V0.322530.892
27_K31_G0.321250.888
24_V307_G0.321220.888
55_L58_I0.321010.887
172_K175_L0.32070.887
13_A297_A0.319880.884
146_I330_V0.317120.877
12_H294_I0.316160.874
108_G148_I0.315680.873
77_F223_G0.315360.872
328_I332_I0.314710.870
307_G310_L0.313940.868
143_V337_I0.311670.862
150_I326_L0.311410.861
99_V312_E0.309490.856
222_W226_I0.309090.855
279_G291_S0.308230.852
326_L330_V0.308180.852
271_S275_F0.306580.848
227_T231_Y0.305430.844
225_F229_L0.304490.842
227_T230_I0.30390.840
97_L100_S0.302590.837
36_S39_L0.302030.835
321_I325_V0.301620.834
83_W86_G0.300810.832
296_M335_V0.300560.831
77_F81_V0.299490.828
265_A268_L0.298860.826
260_L263_A0.296590.820
257_K261_F0.296430.820
115_T119_P0.295970.818
275_F278_M0.295940.818
89_T181_S0.29590.818
54_A58_I0.295540.817
86_G184_M0.294580.814
324_L328_I0.294420.814
116_L119_P0.292360.808
24_V99_V0.291810.807
153_K321_I0.29090.804
136_I139_L0.290780.804
268_L271_S0.290350.803
218_V222_W0.290140.802
75_W79_F0.289960.802
73_L76_T0.288250.797
8_G279_G0.287630.795
132_P135_Q0.287440.795
23_Y90_F0.287160.794
118_P121_F0.286720.793
185_S276_Y0.285470.789
279_G283_L0.284860.788
13_A302_F0.283280.783
131_T289_F0.28280.782
85_I89_T0.282210.780
219_V222_W0.281830.779
261_F265_A0.281590.778
112_V145_L0.281570.778
304_N308_L0.281440.778
222_W225_F0.281140.777
106_A178_A0.280140.774
274_F278_M0.279890.774
275_F279_G0.279480.773
290_S293_A0.279140.772
148_I152_G0.27870.771
143_V333_L0.277860.768
20_G303_S0.27730.767
97_L178_A0.276520.764
104_S108_G0.276270.764
297_A300_V0.276070.763
143_V334_S0.275560.762
116_L120_I0.274080.758
18_A271_S0.273920.757
96_Y171_F0.273460.756
9_I290_S0.273040.755
28_K310_L0.272550.754
24_V303_S0.272160.752
90_F102_G0.272150.752
25_P261_F0.27160.751
33_S39_L0.271260.750
111_A114_G0.270850.749
177_I180_L0.269840.746
105_I328_I0.26880.743
80_G84_G0.268360.742
73_L77_F0.26730.739
16_G298_L0.266230.736
134_G139_L0.265870.735
30_K95_R0.265790.735
104_S307_G0.265780.735
24_V27_K0.264940.732
51_W55_L0.264660.732
110_C113_F0.263530.729
180_L184_M0.263510.729
53_W57_A0.262860.727
48_I51_W0.262150.725
114_G186_A0.261880.724
276_Y280_E0.26090.721
27_K310_L0.260530.720
304_N307_G0.260350.720
97_L102_G0.260150.719
109_L148_I0.260050.719
293_A296_M0.25820.714
24_V310_L0.257420.712
323_V326_L0.256910.710
137_V284_G0.256390.709
132_P136_I0.255770.707
138_L141_V0.254580.704
171_F175_L0.253340.700
185_S273_F0.253130.700
112_V141_V0.25250.698
28_K309_I0.251950.697
50_P55_L0.251850.696
319_K322_R0.25160.696
270_Y274_F0.251280.695
169_F172_K0.25120.694
147_G330_V0.250880.694
325_V328_I0.250870.694
19_S107_L0.25020.692
293_A338_V0.250180.692
279_G282_K0.249910.691
145_L296_M0.249530.690
81_V227_T0.249240.689
223_G226_I0.248920.688
23_Y107_L0.248150.686
145_L149_A0.246330.681
115_T137_V0.246050.680
29_V261_F0.246010.680
76_T80_G0.245950.680
84_G227_T0.245390.678
22_F269_W0.245230.678
333_L337_I0.244760.677
19_S299_I0.244060.675
16_G294_I0.243240.672
14_I18_A0.242890.672
292_W295_H0.242740.671
262_C266_G0.241570.668
139_L146_I0.240020.664
259_Y263_A0.239350.662
22_F265_A0.238560.660
111_A115_T0.238540.659
265_A269_W0.238520.659
304_N320_T0.237940.658
330_V334_S0.237740.657
220_V225_F0.237030.655
26_F30_K0.23580.652
300_V332_I0.235780.652
300_V331_L0.235470.651
150_I324_L0.235050.650
332_I336_V0.23440.648
297_A335_V0.234360.648
50_P222_W0.234350.648
326_L329_A0.234290.648
236_L240_K0.23380.646
93_A174_G0.23360.646
50_P57_A0.233170.645
319_K324_L0.232250.642
39_L49_V0.231780.641
47_L51_W0.231250.639
93_A97_L0.231050.639
153_K156_S0.230490.637
23_Y298_L0.230330.637
218_V221_L0.229940.636
9_I13_A0.229750.635
118_P289_F0.229750.635
86_G298_L0.229360.634
221_L225_F0.2290.633
106_A182_G0.228290.631
146_I149_A0.227540.629
106_A179_V0.22710.628
296_M331_L0.226440.626
214_L277_G0.226360.626
23_Y307_G0.225750.624
34_W37_Y0.224170.620
106_A109_L0.223640.618
326_L333_L0.223610.618
219_V223_G0.222870.616
100_S104_S0.222620.615
84_G231_Y0.222160.614
105_I148_I0.221670.613
78_L81_V0.221260.612
220_V223_G0.220490.610
133_S137_V0.220050.608
150_I327_G0.219990.608
72_T75_W0.21980.608
12_H283_L0.219730.607
137_V338_V0.218450.604
48_I266_G0.218250.603
98_G102_G0.218060.603
105_I108_G0.217950.603
22_F90_F0.216980.600
49_V57_A0.214220.592
20_G298_L0.213630.591
8_G278_M0.213290.590
308_L325_V0.213170.589
284_G289_F0.212970.589
16_G291_S0.212770.588
109_L144_C0.212730.588
15_G18_A0.212570.588
115_T293_A0.212480.587
220_V224_G0.211930.586
49_V55_L0.211290.584
30_K94_M0.210930.583
50_P54_A0.210850.583
21_S24_V0.210330.581
332_I335_V0.210260.581
86_G272_Q0.209730.580
29_V258_N0.20940.579
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
3b5dA0.319898.30.809
2i68A0.398398.10.82
2i68A0.305298.10.822
3b5dA0.305297.50.849
4he8J0.447731.70.94
2wscI0.11631.70.966
3arcT0.0931.50.967
2lomA0.20061.40.967
3nuhB0.16861.30.968
1q90G0.10761.20.969
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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