GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_transf_9 - Glycosyltransferase family 9 (heptosyltransferase)
Pfam: PF01075 (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: 247
Sequences: 6832
Seq/Len: 27.66
HH_delta: 0.204 (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
151_K155_D1.093184.085
110_I184_A0.875783.272
139_R167_N0.831793.108
109_G184_A0.7352.746
187_V198_A0.685962.563
106_P139_R0.680932.544
195_M207_A0.598562.236
144_G170_G0.519791.942
187_V203_T0.516051.928
132_R136_R0.505351.888
5_I9_R0.501731.875
5_I32_S0.497951.861
9_R32_S0.492051.838
131_E135_E0.490511.833
27_L31_L0.4841.808
18_D25_S0.48261.803
155_D159_A0.479841.793
97_R183_R0.479561.792
16_V29_A0.474751.774
128_E157_I0.473761.770
177_L194_P0.463451.732
126_W190_N0.457291.709
133_L138_Y0.453111.693
132_R135_E0.449471.679
145_G151_K0.442911.655
184_A203_T0.434521.624
122_P125_K0.428531.601
134_K165_V0.427031.596
121_W125_K0.426951.595
176_E179_A0.426561.594
105_K139_R0.423391.582
130_I140_V0.416471.556
6_K10_K0.408421.526
5_I31_L0.407811.524
152_E156_Q0.40671.520
107_Y185_D0.398921.491
106_P185_D0.393851.472
131_E161_L0.388121.450
127_A160_G0.387881.449
123_A156_Q0.381381.425
189_G195_M0.376141.405
152_E155_D0.376111.405
128_E131_E0.372021.390
94_A98_E0.370841.386
7_K11_E0.369951.382
110_I130_I0.365551.366
95_A176_E0.365421.365
120_R190_N0.360871.348
148_E153_I0.359011.341
95_A99_L0.356941.334
99_L176_E0.352461.317
181_I203_T0.351331.313
158_A168_L0.351131.312
108_I186_L0.350191.308
107_Y139_R0.343361.283
157_I161_L0.342781.281
103_K106_P0.342011.278
107_Y183_R0.341531.276
156_Q159_A0.341271.275
109_G181_I0.336921.259
92_E175_R0.333451.246
65_D68_L0.332791.243
186_L206_V0.332711.243
109_G143_L0.332441.242
30_R37_R0.332431.242
127_A130_I0.329451.231
115_S142_L0.327711.224
179_A182_S0.326281.219
111_N121_W0.32541.216
174_L180_L0.325011.214
108_I141_V0.32261.205
111_N143_L0.317761.187
8_L32_S0.317011.184
141_V180_L0.316541.183
178_A197_L0.316151.181
122_P192_T0.312911.169
154_A158_A0.312611.168
93_E182_S0.312161.166
107_Y184_A0.311681.165
107_Y138_Y0.309941.158
125_K128_E0.309871.158
143_L177_L0.308711.153
96_A99_L0.305851.143
18_D26_A0.304851.139
181_I201_L0.303331.133
154_A169_A0.302741.131
109_G186_L0.30021.122
89_S92_E0.297331.111
156_Q160_G0.294951.102
143_L169_A0.289881.083
95_A98_E0.289021.080
102_S105_K0.28771.075
126_W130_I0.286961.072
198_A205_T0.283931.061
68_L72_S0.281261.051
108_I140_V0.280041.046
96_A180_L0.279811.045
69_S72_S0.279751.045
121_W126_W0.27891.042
90_E94_A0.27541.029
129_L132_R0.268491.003
36_I53_R0.267881.001
69_S73_E0.26761.000
138_Y185_D0.262320.980
34_A37_R0.262270.980
126_W140_V0.262120.979
167_N170_G0.259770.971
71_L77_I0.257570.962
28_L32_S0.256240.957
118_S193_G0.255660.955
191_D197_L0.250990.938
120_R192_T0.249890.934
52_N56_D0.249510.932
142_L154_A0.248880.930
18_D21_G0.248370.928
93_E97_R0.247780.926
55_V58_P0.247410.924
123_A127_A0.247240.924
62_H65_D0.24670.922
114_A119_K0.246680.922
114_A118_S0.245440.917
199_A205_T0.243970.912
92_E95_A0.242660.907
8_L34_A0.241610.903
195_M205_T0.239870.896
61_K64_V0.239680.896
154_A157_I0.239050.893
131_E134_K0.238720.892
96_A183_R0.238490.891
131_E160_G0.238060.889
4_L8_L0.238050.889
177_L181_I0.237960.889
126_W129_L0.237910.889
128_E132_R0.237850.889
119_K191_D0.234270.875
131_E162_Q0.233380.872
29_A37_R0.232650.869
106_P138_Y0.232220.868
7_K10_K0.232070.867
90_E93_E0.231190.864
155_D167_N0.229490.857
30_R33_G0.228680.854
106_P137_G0.227370.850
188_I206_V0.226570.847
153_I157_I0.226530.846
61_K69_S0.226380.846
182_S203_T0.225270.842
141_V183_R0.225180.841
181_I194_P0.224670.839
25_S29_A0.224660.839
108_I133_L0.224210.838
109_G188_I0.223470.835
120_R126_W0.223290.834
189_G205_T0.222580.832
93_E183_R0.220640.824
83_K87_P0.220450.824
93_E100_L0.220150.823
114_A120_R0.219770.821
112_P177_L0.21920.819
189_G194_P0.218920.818
129_L188_I0.216940.811
140_V166_I0.216180.808
144_G167_N0.214990.803
191_D196_H0.214940.803
96_A100_L0.214710.802
17_I41_G0.214690.802
113_G120_R0.213550.798
15_L38_I0.212340.793
141_V184_A0.21170.791
111_N187_V0.211640.791
50_F57_R0.211270.789
130_I142_L0.210990.788
20_Q42_K0.210440.786
14_D35_K0.209210.782
97_R100_L0.208490.779
22_S25_S0.208110.778
20_Q23_F0.207530.775
174_L196_H0.206690.772
111_N192_T0.205930.769
127_A131_E0.205680.769
49_L52_N0.205630.768
51_Y54_K0.205620.768
109_G180_L0.204860.765
97_R105_K0.204520.764
143_L180_L0.204510.764
61_K65_D0.203570.761
114_A191_D0.203310.760
25_S193_G0.20330.760
108_I185_D0.203190.759
137_G140_V0.202960.758
29_A34_A0.202360.756
155_D158_A0.202160.755
6_K9_R0.202140.755
16_V34_A0.202060.755
3_A7_K0.200910.751
15_L36_I0.200660.750
103_K139_R0.199450.745
18_D24_R0.199160.744
4_L7_K0.197320.737
111_N189_G0.196440.734
29_A36_I0.196070.733
189_G207_A0.195320.730
48_S51_Y0.195140.729
108_I138_Y0.193830.724
126_W188_I0.192470.719
112_P143_L0.192130.718
161_L166_I0.191810.717
20_Q25_S0.191190.714
6_K12_K0.190010.710
158_A162_Q0.189960.710
94_A104_D0.189820.709
23_F27_L0.188870.706
91_E95_A0.187420.700
146_P151_K0.18730.700
26_A36_I0.186820.698
153_I156_Q0.186240.696
190_N208_L0.186190.696
92_E176_E0.185970.695
17_I39_G0.184990.691
88_L91_E0.184910.691
113_G126_W0.184540.690
22_S116_W0.184490.689
50_F54_K0.183510.686
89_S175_R0.182730.683
91_E105_K0.182010.680
19_L39_G0.181660.679
145_G171_K0.18030.674
108_I139_R0.180260.674
143_L174_L0.180260.674
109_G138_Y0.179350.670
108_I188_I0.179170.669
148_E152_E0.179050.669
96_A179_A0.178840.668
22_S195_M0.177950.665
142_L166_I0.177550.663
107_Y186_L0.176910.661
20_Q191_D0.176760.660
180_L183_R0.176140.658
141_V169_A0.175640.656
26_A39_G0.174680.653
100_L183_R0.174460.652
181_I187_V0.174420.652
111_N140_V0.173820.649
144_G168_L0.173470.648
111_N194_P0.172040.643
9_R12_K0.172020.643
121_W129_L0.171980.643
10_K31_L0.171460.641
191_D207_A0.17090.639
97_R102_S0.170880.638
99_L179_A0.169670.634
114_A190_N0.169660.634
111_N190_N0.169540.633
178_A181_I0.16930.633
179_A183_R0.169170.632
102_S108_I0.169080.632
141_V167_N0.168460.629
20_Q116_W0.168450.629
19_L63_M0.168340.629
50_F58_P0.16830.629
109_G177_L0.168260.629
107_Y141_V0.168140.628
98_E101_K0.1680.628
151_K170_G0.167950.628
115_S120_R0.167590.626
63_M66_R0.1670.624
51_Y56_D0.166780.623
93_E179_A0.166740.623
113_G144_G0.165970.620
65_D71_L0.165780.619
8_L13_Y0.16570.619
127_A157_I0.165620.619
50_F53_R0.165080.617
38_I41_G0.16490.616
45_R67_Y0.162560.607
89_S93_E0.162440.607
16_V32_S0.162430.607
113_G190_N0.162350.607
104_D107_Y0.162080.606
33_G36_I0.161050.602
134_K138_Y0.160940.601
40_F64_V0.160910.601
6_K33_G0.160630.600
32_S37_R0.160460.600
198_A203_T0.160430.599
72_S79_Y0.160360.599
145_G148_E0.160110.598
83_K202_G0.159610.596
127_A154_A0.159510.596
42_K118_S0.159060.594
81_S87_P0.158330.592
97_R104_D0.157960.590
142_L168_L0.157910.590
162_Q165_V0.157840.590
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
3tovA0.97571000.204
1pswA0.97981000.222
2gt1A0.96361000.311
3okpA0.971799.60.631
2vsyA0.947499.50.632
3froA0.975799.50.635
2qzsA0.983899.50.637
1rzuA0.983899.50.637
3oy2A0.987999.50.638
2jjmA0.967699.50.638

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