GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glycos_transf_N - 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase)
Pfam: PF04413 (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: CL0113
Length: 186
Sequences: 5516
Seq/Len: 29.66
HH_delta: 0.525 (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
152_R175_H1.15784.062
92_D117_R1.087633.815
161_A165_R0.999913.508
43_R46_K0.856913.006
161_A176_V0.75642.653
162_E166_K0.746152.618
158_E162_E0.723822.539
122_V154_L0.697462.447
99_L114_A0.623112.186
155_A174_V0.617872.168
98_L122_V0.61652.163
43_R47_Q0.593692.083
88_R117_R0.593672.083
120_P151_D0.570992.003
25_W91_L0.555231.948
90_F94_W0.550171.930
101_W121_V0.542811.904
100_I122_V0.531881.866
54_L94_W0.529191.856
162_E165_R0.527451.850
25_W54_L0.492721.728
24_I98_L0.488511.714
158_E161_A0.485411.703
155_A161_A0.484511.700
123_L150_F0.46811.642
157_S160_D0.459891.613
26_I41_I0.444081.558
141_F144_R0.432021.516
89_R93_H0.415921.459
115_K151_D0.415211.457
48_R51_L0.412951.449
109_N147_L0.409721.437
88_R92_D0.400681.406
161_A174_V0.395991.389
148_S153_I0.387221.358
115_K149_R0.383451.345
91_L114_A0.371261.302
158_E176_V0.369241.295
40_L100_I0.367771.290
42_K46_K0.3661.284
81_L85_W0.363921.277
150_F153_I0.360831.266
122_V152_R0.360811.266
38_R42_K0.359461.261
26_I100_I0.352961.238
82_D86_A0.352061.235
98_L120_P0.349651.227
41_I45_R0.349291.225
88_R113_E0.346121.214
45_R73_R0.344931.210
37_A104_T0.343531.205
154_L177_T0.342081.200
67_R71_P0.331211.162
83_F86_A0.326191.144
85_W89_R0.323541.135
25_W96_P0.322741.132
25_W90_F0.318171.116
153_I164_F0.318151.116
99_L121_V0.314921.105
135_R142_L0.313121.098
159_A162_E0.304611.069
39_P42_K0.304381.068
155_A164_F0.301381.057
64_E68_K0.300731.055
85_W88_R0.297861.045
42_K45_R0.296481.040
125_N179_N0.295551.037
44_L51_L0.286261.004
40_L180_L0.28541.001
25_W94_W0.284490.998
135_R151_D0.284140.997
26_I44_L0.28410.997
86_A89_R0.283760.995
153_I169_A0.28190.989
27_H87_V0.281470.987
47_Q50_D0.277320.973
121_V150_F0.275450.966
158_E165_R0.275230.966
41_I53_I0.27360.960
163_R166_K0.271510.952
100_I124_V0.265930.933
145_P148_S0.265020.930
82_D85_W0.263620.925
134_R179_N0.261780.918
85_W92_D0.260970.915
110_L146_L0.260730.915
36_A156_Q0.25950.910
65_M68_K0.258090.905
98_L152_R0.256050.898
138_R142_L0.252640.886
52_R97_D0.251160.881
126_A155_A0.250890.880
132_S164_F0.249940.877
89_R92_D0.249220.874
91_L117_R0.249080.874
101_W123_L0.244040.856
45_R52_R0.243720.855
113_E117_R0.240280.843
165_R170_P0.237560.833
36_A125_N0.236620.830
57_T76_V0.236390.829
60_P64_E0.234380.822
155_A176_V0.233780.820
83_F87_V0.233710.820
37_A100_I0.228530.802
114_A121_V0.226930.796
36_A104_T0.226380.794
125_N128_L0.226050.793
39_P43_R0.225430.791
170_P174_V0.225070.790
91_L99_L0.224620.788
165_R174_V0.224450.787
99_L119_I0.223780.785
142_L146_L0.223360.784
88_R116_R0.222560.781
148_S169_A0.218490.766
26_I40_L0.216970.761
33_E107_W0.216970.761
55_L66_A0.21620.758
57_T60_P0.214360.752
121_V149_R0.213940.751
156_Q160_D0.21360.749
140_P167_L0.213420.749
40_L124_V0.212780.746
104_T109_N0.212380.745
60_P65_M0.211410.742
155_A179_N0.210750.739
156_Q179_N0.210550.739
147_L153_I0.210330.738
140_P143_F0.208420.731
163_R167_L0.208080.730
98_L175_H0.206390.724
143_F147_L0.205980.723
145_P149_R0.205150.720
95_R117_R0.204970.719
155_A160_D0.20420.716
54_L90_F0.203770.715
111_L150_F0.203690.715
33_E41_I0.20320.713
30_S33_E0.201940.708
65_M69_L0.201580.707
52_R94_W0.200640.704
169_A181_K0.200510.703
51_L97_D0.20050.703
79_L82_D0.200320.703
165_R168_G0.200080.702
35_N38_R0.199520.700
24_I44_L0.199510.700
80_P140_P0.199240.699
32_G36_A0.198330.696
144_R147_L0.198320.696
63_R76_V0.197820.694
25_W99_L0.197520.693
33_E105_E0.197340.692
60_P78_Y0.19680.690
74_V77_Q0.196480.689
115_K118_G0.195030.684
144_R149_R0.194970.684
143_F146_L0.194910.684
28_A37_A0.193560.679
79_L114_A0.193380.678
112_R116_R0.192250.674
64_E67_R0.189950.666
123_L126_A0.189380.664
100_I180_L0.18760.658
106_L123_L0.187570.658
37_A41_I0.187190.657
140_P144_R0.186920.656
56_T59_T0.186860.656
87_V91_L0.186630.655
135_R138_R0.185840.652
33_E126_A0.183090.642
84_P88_R0.182690.641
160_D164_F0.182650.641
24_I122_V0.182640.641
28_A34_V0.182380.640
104_T180_L0.182310.640
169_A174_V0.182260.639
154_L175_H0.181970.638
111_L121_V0.181380.636
33_E179_N0.180850.634
48_R52_R0.180380.633
141_F148_S0.179980.631
135_R143_F0.179730.630
90_F93_H0.178950.628
160_D163_R0.178840.627
158_E170_P0.178050.625
55_L63_R0.177990.624
153_I174_V0.177350.622
126_A160_D0.176410.619
31_V105_E0.176230.618
36_A126_A0.176090.618
47_Q51_L0.176060.618
45_R72_D0.1760.617
125_N160_D0.175480.616
33_E178_G0.175330.615
58_T65_M0.174830.613
26_I51_L0.174740.613
49_P70_L0.174120.611
36_A177_T0.173580.609
30_S34_V0.173460.609
63_R67_R0.173440.608
33_E104_T0.172510.605
105_E127_R0.171720.602
32_G128_L0.171390.601
142_L145_P0.171270.601
96_P119_I0.1710.600
177_T180_L0.17020.597
61_T65_M0.169750.595
33_E36_A0.168990.593
80_P108_P0.168910.593
63_R66_A0.168390.591
69_L133_F0.16820.590
97_D100_I0.168180.590
164_F174_V0.167580.588
125_N156_Q0.166780.585
25_W55_L0.166620.585
91_L119_I0.16620.583
36_A123_L0.166030.582
36_A39_P0.165560.581
86_A93_H0.16520.580
133_F166_K0.165120.579
44_L48_R0.165070.579
123_L164_F0.164240.576
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
2xciA0.887199.60.525
1vgvA0.881799.30.591
3okpA0.892599.30.596
2r60A0.91499.30.601
3dzcA0.983999.30.602
2iw1A0.887199.30.607
4fkzA0.892599.20.611
3c48A0.967799.20.611
1v4vA0.908699.20.612
3beoA0.91499.20.615
If you are interested in a protein containing this domain,
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