GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Nuc_sug_transp - Nucleotide-sugar transporter
Pfam: PF04142 (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: 244
Sequences: 20342
Seq/Len: 83.37
HH_delta: 0.71 (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
37_A119_V1.522773.027
225_S231_F1.381992.747
45_T116_L1.313052.610
33_L121_A1.210852.407
36_V118_A1.181812.349
33_L118_A1.179442.344
56_F123_A1.146412.279
200_F204_Y1.131592.249
47_Q221_T1.084172.155
61_S67_R1.000081.988
67_R134_E0.983081.954
58_A77_L0.969861.928
117_L121_A0.931141.851
52_S56_F0.926331.841
70_S73_Q0.914321.817
234_S237_F0.909121.807
62_V69_L0.878321.746
60_F131_V0.867181.724
33_L125_L0.847171.684
36_V40_Y0.842461.675
200_F203_K0.835961.662
157_L161_L0.827581.645
46_F119_V0.826431.643
206_D209_V0.808751.608
41_L115_G0.808081.606
71_R75_L0.805661.601
224_L228_L0.790731.572
29_I125_L0.79051.571
235_L239_L0.779751.550
43_P225_S0.777571.546
220_L224_L0.772561.536
61_S65_L0.771331.533
41_L116_L0.768071.527
40_Y114_L0.762541.516
38_L46_F0.75461.500
56_F124_F0.745041.481
57_T211_G0.740081.471
113_L117_L0.716811.425
80_L215_A0.715181.422
42_D45_T0.713651.419
134_E138_K0.707861.407
36_V39_S0.700291.392
34_Q38_L0.694251.380
86_L243_L0.692751.377
87_V240_G0.686491.365
78_F82_A0.686051.364
40_Y118_A0.678741.349
56_F127_G0.678311.348
60_F128_F0.673011.338
238_L242_A0.667671.327
44_S222_A0.666951.326
114_L118_A0.665761.323
63_L66_K0.661211.314
18_L22_V0.644761.282
48_V241_A0.642811.278
135_K139_R0.64111.274
62_V68_R0.633111.258
74_W78_F0.632171.257
60_F127_G0.618591.230
86_L236_S0.615811.224
178_H181_S0.613981.220
60_F64_L0.610951.214
233_P238_L0.608061.209
113_L116_L0.608011.209
71_R74_W0.607181.207
41_L45_T0.603051.199
26_L128_F0.599591.192
206_D210_K0.598981.191
22_V132_Y0.598931.191
161_L164_L0.591341.175
158_F161_L0.587451.168
216_V220_L0.585471.164
127_G131_V0.583571.160
70_S74_W0.581851.157
201_V210_K0.579651.152
115_G119_V0.57431.142
83_G240_G0.573021.139
40_Y115_G0.572071.137
43_P229_F0.568051.129
184_V187_V0.567761.129
233_P237_F0.565041.123
52_S84_V0.562851.119
202_L206_D0.559481.112
58_A69_L0.558111.109
195_G198_V0.557951.109
182_W185_W0.556191.106
119_V123_A0.555321.104
114_L117_L0.553941.101
65_L131_V0.553561.100
146_I150_Q0.551151.096
216_V219_V0.551031.095
19_K132_Y0.550721.095
181_S185_W0.54511.084
226_V233_P0.543981.081
18_L21_A0.542831.079
21_A154_F0.540871.075
60_F124_F0.536341.066
57_T130_G0.533581.061
123_A127_G0.53221.058
57_T127_G0.528721.051
191_Q195_G0.528311.050
133_F199_A0.527891.049
67_R73_Q0.526981.047
55_L80_L0.524821.043
134_E207_N0.520821.035
26_L132_Y0.518011.030
147_Q150_Q0.51581.025
162_A166_S0.512761.019
214_T217_S0.508391.011
202_L210_K0.506491.007
219_V241_A0.505131.004
41_L46_F0.504261.002
49_L123_A0.50331.000
51_Q54_I0.497820.990
128_F132_Y0.495040.984
191_Q194_G0.493110.980
49_L119_V0.491510.977
212_F215_A0.490820.976
135_K138_K0.487310.969
24_A154_F0.487110.968
57_T207_N0.486430.967
126_S130_G0.480310.955
43_P47_Q0.479140.952
48_V85_V0.478850.952
59_L77_L0.478080.950
60_F63_L0.477650.949
143_S146_I0.47740.949
37_A46_F0.474360.943
161_L165_L0.474090.942
195_G199_A0.473390.941
48_V88_Q0.472580.939
85_V89_L0.470850.936
27_Y129_A0.469520.933
49_L120_L0.468350.931
19_K136_L0.46670.928
57_T131_V0.466280.927
235_L238_L0.465250.925
225_S229_F0.464560.923
43_P231_F0.463590.921
84_V88_Q0.45370.902
41_L119_V0.452880.900
82_A86_L0.451490.897
69_L74_W0.447980.890
153_L157_L0.447790.890
205_A209_V0.445670.886
185_W189_F0.445380.885
192_A196_L0.445130.885
201_V205_A0.443890.882
196_L200_F0.443110.881
223_V227_L0.44280.880
57_T61_S0.441390.877
148_N151_L0.440750.876
27_Y31_N0.440220.875
224_L227_L0.438030.871
30_Q129_A0.435250.865
35_F39_S0.431820.858
26_L125_L0.430270.855
154_F158_F0.430170.855
41_L44_S0.427820.850
58_A73_Q0.426970.849
169_S172_S0.423920.843
150_Q153_L0.42250.840
187_V192_A0.421930.839
86_L239_L0.421720.838
155_G159_N0.421710.838
239_L243_L0.421380.838
205_A210_K0.418870.833
124_F128_F0.418470.832
64_L128_F0.417850.831
32_N36_V0.416780.828
86_L240_G0.41590.827
52_S123_A0.415560.826
37_A41_L0.415450.826
150_Q154_F0.414430.824
40_Y112_P0.41410.823
184_V188_I0.413680.822
149_M153_L0.413630.822
29_I33_L0.413320.822
181_S184_V0.411940.819
156_I160_L0.411280.818
194_G198_V0.409010.813
112_P116_L0.408740.812
129_A133_F0.408410.812
65_L134_E0.408010.811
148_N152_Y0.404830.805
222_A226_V0.404420.804
130_G211_G0.403670.802
24_A28_A0.402960.801
237_F241_A0.402060.799
236_S239_L0.401590.798
145_W149_M0.399850.795
183_W187_V0.398230.792
58_A62_V0.397750.791
56_F120_L0.396860.789
19_K135_K0.396590.788
69_L73_Q0.396240.788
51_Q84_V0.395050.785
187_V190_L0.392480.780
197_L200_F0.391840.779
190_L195_G0.391810.779
182_W186_I0.391390.778
234_S238_L0.391220.778
185_W190_L0.390230.776
49_L116_L0.390190.776
157_L160_L0.388610.772
68_R72_R0.387840.771
118_A121_A0.386850.769
194_G197_L0.384580.764
33_L122_A0.383040.761
51_Q123_A0.382230.760
30_Q125_L0.381730.759
184_V191_Q0.38170.759
67_R208_I0.380280.756
186_I190_L0.378660.753
17_T20_L0.374730.745
89_L92_S0.373360.742
17_T21_A0.373320.742
154_F157_L0.371940.739
149_M156_I0.371170.738
129_A199_A0.370870.737
226_V232_P0.370750.737
48_V87_V0.370740.737
133_F137_L0.370180.736
59_L63_L0.369780.735
189_F193_I0.367670.731
55_L81_V0.363690.723
75_L79_L0.362880.721
19_K23_P0.362380.720
73_Q77_L0.361740.719
17_T154_F0.360380.716
211_G214_T0.360290.716
47_Q51_Q0.358520.713
81_V85_V0.357670.711
62_V66_K0.357380.710
226_V238_L0.354890.705
223_V226_V0.354380.704
160_L164_L0.352720.701
178_H182_W0.351970.700
208_I212_F0.351620.699
198_V201_V0.350430.697
82_A243_L0.348640.693
238_L241_A0.348460.693
30_Q50_S0.348380.692
23_P133_F0.347090.690
165_L168_G0.346980.690
222_A233_P0.346840.689
72_R75_L0.346480.689
180_Y185_W0.345340.686
134_E206_D0.345150.686
89_L234_S0.344950.686
147_Q151_L0.343380.683
208_I213_A0.341870.680
52_S80_L0.34120.678
34_Q46_F0.340830.677
215_A218_I0.340520.677
22_V25_L0.33950.675
45_T237_F0.337380.671
27_Y30_Q0.337210.670
55_L77_L0.336420.669
34_Q122_A0.33570.667
42_D46_F0.334010.664
61_S64_L0.333280.662
83_G243_L0.332660.661
144_L148_N0.332110.660
67_R207_N0.330840.658
28_A158_F0.330320.657
190_L194_G0.330220.656
52_S55_L0.330020.656
77_L208_I0.32920.654
75_L78_F0.329190.654
160_L163_L0.327470.651
19_K22_V0.327430.651
116_L120_L0.326730.649
81_V215_A0.324960.646
197_L201_V0.324620.645
53_K126_S0.323750.644
180_Y184_V0.323740.644
213_A217_S0.322480.641
34_Q50_S0.322440.641
232_P235_L0.322120.640
37_A115_G0.322080.640
28_A32_N0.321390.639
191_Q199_A0.321090.638
239_L242_A0.317950.632
82_A85_V0.316540.629
65_L135_K0.316480.629
75_L82_A0.315480.627
144_L147_Q0.314790.626
22_V26_L0.314080.624
136_L139_R0.313510.623
227_L230_G0.31250.621
214_T218_I0.312430.621
30_Q34_Q0.311940.620
88_Q116_L0.311820.620
152_Y156_I0.311590.619
183_W186_I0.311310.619
181_S187_V0.311080.618
164_L167_D0.310060.616
222_A241_A0.308120.612
205_A212_F0.307450.611
65_L69_L0.306750.610
179_G182_W0.306350.609
133_F136_L0.306070.608
183_W191_Q0.306010.608
38_L47_Q0.305910.608
196_L199_A0.30580.608
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
2i68A0.487798.30.71
3b5dA0.37798.30.712
2i68A0.381198.30.718
3b5dA0.381197.80.753
3l1lA0.524621.80.916
4he8J0.409812.10.925
1u7gA0.766411.10.926
2wwbB0.21316.50.933
3b9wA0.78286.40.933
3j08A0.30745.60.935
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