GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Polysacc_synt - Polysaccharide biosynthesis protein
Pfam: PF01943 (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: CL0222
Length: 273
Sequences: 16032
Seq/Len: 58.73
HH_delta: 0.263 (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
137_R140_Y1.422233.911
121_L178_L1.331563.662
39_S245_S1.287573.541
205_K209_R1.258183.460
62_R66_E0.938462.581
139_K143_I0.864682.378
64_I134_G0.789092.170
201_K205_K0.771112.121
144_S183_I0.743712.045
31_G34_E0.741392.039
228_D244_Y0.73152.012
148_S180_S0.724291.992
110_I167_W0.715581.968
237_G240_A0.677061.862
124_L181_L0.667451.835
144_S184_S0.653131.796
155_L172_G0.650091.788
76_A200_S0.64461.773
23_I249_R0.642931.768
200_S203_F0.627721.726
68_K73_L0.622161.711
151_L179_V0.619871.705
63_F210_F0.611691.682
63_F66_E0.610971.680
167_W171_L0.607971.672
121_L181_L0.602511.657
25_I157_L0.601731.655
9_F260_S0.595781.638
26_L169_F0.585141.609
113_I117_L0.567841.562
168_G172_G0.563831.551
182_I186_F0.551341.516
158_L162_L0.546461.503
101_F105_P0.533561.467
143_I147_I0.530651.459
93_L97_L0.530311.458
60_I81_V0.529961.457
128_F184_S0.529891.457
157_L161_F0.523911.441
131_L135_L0.520871.432
14_L146_I0.518771.427
85_L127_V0.517811.424
78_F131_L0.515261.417
25_I160_L0.506551.393
73_L76_A0.505031.389
102_F105_P0.493761.358
38_Y42_L0.489271.345
24_P28_R0.485271.334
140_Y187_Y0.482721.327
212_L216_L0.479751.319
11_S145_N0.476121.309
219_L223_L0.470581.294
165_S168_G0.470181.293
154_L158_L0.466931.284
186_F190_R0.464431.277
232_I244_Y0.462431.272
114_L167_W0.461081.268
117_L120_I0.460731.267
114_L118_I0.459541.264
203_F206_E0.446891.229
118_I174_V0.446321.227
156_I169_F0.443951.221
87_I91_I0.442841.218
10_L142_A0.438141.205
40_L233_G0.437471.203
59_A210_F0.436331.200
154_L157_L0.435831.199
59_A63_F0.435731.198
137_R191_K0.432751.190
240_A243_I0.432741.190
25_I156_I0.430191.183
86_L124_L0.428691.179
156_I160_L0.427281.175
233_G241_V0.426741.174
150_L154_L0.424821.168
59_A69_D0.419891.155
111_L115_A0.419531.154
72_E76_A0.417891.149
199_F204_F0.417391.148
144_S187_Y0.416281.145
208_L212_L0.4151.141
101_F104_N0.414411.140
32_P242_G0.413421.137
152_S176_S0.413081.136
63_F73_L0.412811.135
65_A134_G0.412581.135
22_T173_L0.41191.133
156_I172_G0.41091.130
232_I241_V0.408291.123
109_L113_I0.406511.118
93_L120_I0.405961.116
24_P27_A0.403721.110
112_I116_L0.402491.107
152_S173_L0.40231.106
147_I183_I0.401991.105
167_W170_L0.40031.101
22_T152_S0.399551.099
27_A35_Y0.398651.096
20_F24_P0.398381.096
202_K205_K0.396541.090
38_Y166_L0.396531.090
230_L234_Y0.395961.089
133_Q141_I0.393821.083
172_G176_S0.393731.083
73_L203_F0.393671.083
13_I17_L0.38791.067
66_E69_D0.387331.065
65_A68_K0.386971.064
171_L174_V0.386461.063
147_I150_L0.380611.047
39_S242_G0.379231.043
61_V65_A0.376341.035
160_L169_F0.374661.030
32_P239_E0.372461.024
56_L59_A0.372151.023
129_S133_Q0.371751.022
151_L155_L0.37121.021
185_L189_R0.369921.017
65_A69_D0.369441.016
60_I64_I0.368271.013
125_S180_S0.367741.011
107_L110_I0.366471.008
75_S79_S0.363991.001
12_N16_A0.362690.997
208_L211_G0.361530.994
183_I186_F0.360850.992
176_S180_S0.359320.988
62_R65_A0.358640.986
76_A80_S0.358210.985
55_G211_G0.358050.985
136_Q268_R0.35760.983
84_L204_F0.356490.980
157_L160_L0.355750.978
91_I94_L0.355740.978
63_F206_E0.355150.977
96_L100_S0.35510.977
158_L161_F0.355020.976
80_S204_F0.354520.975
155_L159_L0.353120.971
209_R213_P0.352790.970
34_E37_I0.352530.969
137_R141_I0.351680.967
128_F185_L0.351520.967
94_L97_L0.351350.966
27_A246_V0.351280.966
94_L98_I0.35030.963
128_F181_L0.350070.963
36_G242_G0.348590.959
227_I231_I0.348320.958
67_Y73_L0.347210.955
151_L176_S0.346930.954
59_A65_A0.344940.949
79_S196_F0.34430.947
178_L182_I0.34430.947
40_L43_S0.344080.946
194_P197_S0.34370.945
159_L162_L0.343680.945
59_A62_R0.342690.942
23_I35_Y0.342670.942
46_S50_I0.342560.942
132_L188_L0.342540.942
128_F188_L0.339510.934
112_I115_A0.339470.934
226_Q229_R0.339220.933
130_G133_Q0.338770.932
244_Y248_Y0.337480.928
133_Q138_F0.335490.923
114_L170_L0.335050.921
114_L171_L0.335010.921
92_F96_L0.334660.920
17_L21_I0.333930.918
114_L117_L0.332990.916
212_L215_F0.332780.915
63_F67_Y0.330940.910
147_I151_L0.330740.910
32_P243_I0.330350.908
105_P108_S0.330170.908
152_S172_G0.330170.908
68_K135_L0.330050.908
171_L175_I0.329630.906
97_L113_I0.329510.906
186_F189_R0.328580.904
77_Y203_F0.327480.901
222_W226_Q0.327070.899
210_F214_L0.326540.898
111_L118_I0.326170.897
96_L99_A0.324630.893
33_E107_L0.324540.892
239_E243_I0.323890.891
155_L175_I0.32360.890
242_G246_V0.323110.889
53_D57_S0.32290.888
93_L96_L0.321790.885
152_S156_I0.321160.883
249_R253_A0.320990.883
206_E209_R0.319790.879
83_F87_I0.319710.879
86_L90_L0.319690.879
156_I159_L0.319430.878
80_S84_L0.319260.878
138_F264_V0.318930.877
42_L46_S0.318840.877
74_R78_F0.318630.876
187_Y191_K0.318620.876
224_Y227_I0.318370.876
229_R233_G0.316750.871
229_R241_V0.314160.864
183_I187_Y0.313130.861
146_I150_L0.312730.860
112_I118_I0.311570.857
116_L119_L0.311520.857
76_A203_F0.311370.856
74_R77_Y0.310440.854
73_L77_Y0.310390.854
61_V134_G0.310360.853
106_S109_L0.310170.853
26_L38_Y0.30850.848
209_R212_L0.308380.848
63_F68_K0.308290.848
74_R135_L0.307790.846
104_N107_L0.307180.845
111_L117_L0.305750.841
144_S180_S0.305370.840
8_L263_T0.305280.840
61_V130_G0.305250.839
174_V177_S0.303680.835
43_S229_R0.303230.834
260_S264_V0.302070.831
113_I116_L0.300810.827
226_Q230_L0.300570.827
36_G39_S0.30050.826
76_A79_S0.30030.826
164_S171_L0.299930.825
227_I230_L0.299110.823
36_G241_V0.298970.822
8_L12_N0.298440.821
53_D123_S0.29830.820
196_F199_F0.298140.820
228_D248_Y0.298010.820
132_L140_Y0.297530.818
228_D231_I0.297210.817
249_R252_S0.296430.815
62_R210_F0.296190.815
64_I69_D0.294930.811
60_I130_G0.294620.810
248_Y251_A0.293940.808
190_R193_R0.293460.807
100_S113_I0.293330.807
125_S181_L0.29290.805
143_I146_I0.292610.805
201_K204_F0.291410.801
8_L138_F0.291270.801
63_F77_Y0.291090.801
43_S245_S0.290410.799
110_I114_L0.28860.794
40_L241_V0.288310.793
18_I22_T0.288140.792
85_L88_F0.287070.789
137_R187_Y0.286970.789
121_L174_V0.286620.788
130_G134_G0.286060.787
55_G65_A0.285140.784
85_L123_S0.28510.784
91_I95_I0.284550.783
41_A112_I0.284310.782
37_I40_L0.284150.781
28_R161_F0.283890.781
252_S255_S0.283470.780
144_S148_S0.283070.778
8_L264_V0.282790.778
148_S152_S0.282440.777
22_T153_L0.281550.774
241_V245_S0.281250.773
120_I123_S0.28080.772
11_S142_A0.280570.772
140_Y143_I0.280520.771
35_Y246_V0.280420.771
115_A118_I0.279270.768
72_E75_S0.279230.768
230_L233_G0.278880.767
59_A68_K0.27820.765
245_S249_R0.277990.764
95_I98_I0.277920.764
33_E238_P0.276950.762
60_I77_Y0.27680.761
66_E206_E0.275540.758
108_S112_I0.274890.756
116_L120_I0.274870.756
179_V183_I0.27430.754
34_E166_L0.273890.753
38_Y169_F0.273550.752
203_F207_I0.273540.752
30_L35_Y0.273420.752
30_L34_E0.271990.748
25_I161_F0.271310.746
255_S258_L0.27090.745
62_R69_D0.270210.743
129_S145_N0.269780.742
78_F82_L0.269370.741
122_S177_S0.2690.740
97_L100_S0.268560.739
125_S184_S0.267920.737
174_V178_L0.267460.736
22_T156_I0.267440.735
248_Y252_S0.267150.735
251_A254_I0.267070.734
37_I107_L0.266820.734
23_I26_L0.266350.732
202_K206_E0.266260.732
18_I21_I0.265220.729
96_L116_L0.264660.728
35_Y39_S0.264390.727
64_I135_L0.264060.726
129_S141_I0.263870.726
29_Y161_F0.263630.725
231_I235_F0.263540.725
33_E37_I0.262810.723
23_I27_A0.26260.722
214_L217_S0.262550.722
155_L158_L0.262290.721
265_L269_L0.26190.720
221_S225_S0.261870.720
64_I74_R0.26170.720
109_L112_I0.261690.720
56_L81_V0.261130.718
33_E36_G0.261020.718
180_S184_S0.260690.717
126_S129_S0.258590.711
32_P35_Y0.258530.711
62_R67_Y0.257640.709
29_Y160_L0.257450.708
127_V130_G0.255780.703
17_L20_F0.255120.702
21_I24_P0.254180.699
21_I153_L0.254160.699
111_L114_L0.254140.699
162_L165_S0.253340.697
101_F108_S0.253330.697
254_I258_L0.253130.696
81_V207_I0.25220.694
189_R192_L0.251840.693
54_L57_S0.251650.692
216_L219_L0.251540.692
159_L175_I0.251260.691
184_S187_Y0.251060.690
77_Y81_V0.250120.688
115_A119_L0.249990.687
189_R193_R0.249920.687
125_S177_S0.249650.687
148_S176_S0.249410.686
18_I153_L0.248830.684
11_S14_L0.24790.682
79_S83_F0.247770.681
14_L18_I0.247720.681
129_S144_S0.246980.679
25_I29_Y0.246930.679
208_L213_P0.246820.679
173_L177_S0.246130.677
195_R198_F0.24570.676
106_S110_I0.245580.675
239_E242_G0.245430.675
202_K209_R0.245320.675
132_L184_S0.245160.674
175_I179_V0.244860.673
204_F208_L0.244480.672
14_L150_L0.244260.672
45_V115_A0.243830.671
46_S49_S0.243180.669
15_S18_I0.243110.669
140_Y183_I0.241960.665
67_Y203_F0.241880.665
61_V266_F0.241680.665
107_L238_P0.24110.663
89_S93_L0.240910.663
121_L125_S0.240740.662
245_S248_Y0.240730.662
220_L224_Y0.240530.661
62_R68_K0.240110.660
79_S197_S0.239030.657
176_S179_V0.238640.656
80_S199_F0.238640.656
56_L60_I0.238580.656
216_L220_L0.238440.656
82_L85_L0.237980.654
82_L128_F0.237740.654
137_R143_I0.237310.653
259_S262_S0.237280.653
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
3w4tA0.992799.90.263
3mktA0.98999.90.273
4humA0.98999.80.393
3w4tA0.7473990.628
3mktA0.743698.90.641
4humA0.747398.50.692
3zuxA0.717916.10.92
2gfpA0.882810.90.926
1pw4A0.69235.30.935
3l1lA0.6965.20.935

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