GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_trans_4_3 - Gkycosyl transferase family 4 group
Pfam: PF12000 (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: 171
Sequences: 6485
Seq/Len: 37.92
HH_delta: 0.346 (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
7_V24_V1.589084.919
138_A159_S1.441884.463
7_V65_F1.072763.321
93_G136_A1.043983.231
71_I94_Y1.027183.179
7_V67_P0.990093.065
7_V22_R0.985773.051
147_R151_P0.974913.018
147_R160_V0.779172.412
142_P163_D0.771132.387
140_I161_I0.74282.299
148_S152_A0.73262.268
147_R158_I0.708682.194
144_R147_R0.708332.192
141_S158_I0.676022.092
144_R148_S0.669662.073
72_A93_G0.658452.038
5_E22_R0.632871.959
72_A91_L0.599281.855
4_H68_D0.556391.722
73_H94_Y0.554711.717
141_S147_R0.540521.673
144_R160_V0.540311.672
142_P146_Q0.503041.557
83_K91_L0.480131.486
83_K137_D0.478321.481
91_L136_A0.46791.448
90_P137_D0.462761.432
141_S146_Q0.451881.399
148_S151_P0.44921.390
70_I83_K0.446181.381
10_T23_V0.437641.355
82_L86_F0.435451.348
151_P155_R0.434061.344
86_F89_A0.432341.338
81_F85_V0.431981.337
73_H100_R0.422291.307
92_I140_I0.422141.307
141_S150_F0.415211.285
94_Y100_R0.405921.256
70_I89_A0.398331.233
92_I138_A0.395981.226
136_A139_G0.383451.187
95_F139_G0.375061.161
127_A131_L0.36111.118
56_A59_Q0.349431.082
71_I92_I0.346941.074
57_A61_R0.34681.073
127_A130_L0.344191.065
129_N133_L0.340611.054
69_V92_I0.334291.035
143_T146_Q0.331911.027
123_R127_A0.331541.026
8_F23_V0.329951.021
3_G6_V0.32611.009
81_F131_L0.324581.005
84_D137_D0.318740.987
84_D88_D0.318630.986
142_P162_H0.318330.985
150_F158_I0.317170.982
151_P157_K0.311740.965
9_L24_V0.311560.964
151_P154_F0.311480.964
95_F150_F0.311060.963
73_H142_P0.30480.943
94_Y142_P0.303560.940
54_A58_R0.30240.936
101_A106_V0.301110.932
75_G78_E0.299830.928
73_H163_D0.298930.925
59_Q64_G0.294760.912
149_Q152_A0.294050.910
78_E129_N0.29370.909
146_Q150_F0.28870.894
74_P77_G0.285510.884
75_G80_L0.279960.867
143_T163_D0.27850.862
102_S105_D0.278280.861
149_Q153_E0.276240.855
121_R125_R0.273090.845
56_A61_R0.272280.843
22_R65_F0.271480.840
145_W149_Q0.270510.837
94_Y164_G0.266550.825
84_D135_Q0.265860.823
130_L134_E0.263320.815
145_W148_S0.263190.815
75_G95_F0.261320.809
95_F146_Q0.260040.805
9_L67_P0.259910.804
10_T25_R0.25990.804
5_E68_D0.258690.801
125_R129_N0.257290.796
141_S160_V0.254830.789
17_I20_G0.253890.786
81_F84_D0.253160.784
67_P89_A0.252870.783
123_R126_N0.251560.779
54_A85_V0.247570.766
75_G146_Q0.246490.763
67_P70_I0.245240.759
120_A123_R0.24390.755
151_P158_I0.241850.749
18_P21_V0.240240.744
28_P31_G0.23980.742
131_L135_Q0.239640.742
124_M128_H0.23920.740
58_R85_V0.236060.731
91_L94_Y0.235440.729
52_A56_A0.231970.718
9_L26_Y0.231390.716
17_I21_V0.230970.715
74_P82_L0.230830.714
94_Y163_D0.228930.709
53_V57_A0.227830.705
126_N129_N0.22750.704
4_H7_V0.226290.700
11_E28_P0.225040.697
77_G101_A0.224570.695
126_N130_L0.22450.695
94_Y140_I0.221580.686
147_R155_R0.220410.682
94_Y161_I0.220170.681
155_R158_I0.219910.681
66_V89_A0.219050.678
100_R142_P0.217920.675
122_L125_R0.217050.672
95_F164_G0.215810.668
151_P156_S0.214180.663
13_K16_P0.214170.663
10_T13_K0.212560.658
17_I22_R0.21210.657
58_R61_R0.211670.655
51_Q55_R0.211290.654
5_E67_P0.210190.651
6_V10_T0.20940.648
129_N132_A0.209250.648
95_F100_R0.205650.637
84_D89_A0.205580.636
146_Q149_Q0.204190.632
95_F133_L0.204160.632
143_T162_H0.204040.632
144_R162_H0.203840.631
91_L137_D0.202810.628
68_D90_P0.202660.627
71_I74_P0.200810.622
73_H146_Q0.200370.620
129_N154_F0.200210.620
106_V122_L0.199290.617
56_A60_L0.197770.612
73_H164_G0.195360.605
12_R15_P0.19420.601
132_A135_Q0.193890.600
95_F142_P0.193580.599
85_V88_D0.191730.593
91_L135_Q0.191370.592
74_P146_Q0.191190.592
85_V89_A0.190640.590
53_V61_R0.190630.590
72_A78_E0.189150.585
142_P145_W0.188640.584
28_P132_A0.188340.583
83_K86_F0.187340.580
24_V64_G0.186780.578
77_G80_L0.186390.577
148_S155_R0.185870.575
66_V88_D0.185550.574
100_R105_D0.185290.574
14_R131_L0.18490.572
6_V21_V0.18460.571
71_I100_R0.183890.569
6_V22_R0.183530.568
74_P78_E0.182710.566
159_S162_H0.181550.562
138_A157_K0.181070.560
19_P22_R0.181010.560
18_P23_V0.18050.559
133_L139_G0.18050.559
145_W162_H0.180450.559
73_H76_W0.180190.558
133_L150_F0.179970.557
78_E93_G0.179770.556
131_L134_E0.179670.556
93_G139_G0.178230.552
52_A55_R0.177990.551
76_W163_D0.177570.550
16_P22_R0.177250.549
11_E74_P0.176670.547
77_G142_P0.176460.546
51_Q54_A0.175120.542
64_G148_S0.17460.540
74_P102_S0.173720.538
105_D145_W0.173470.537
54_A61_R0.171980.532
4_H21_V0.171550.531
88_D168_D0.171060.529
55_R59_Q0.170950.529
17_I152_A0.170930.529
134_E157_K0.170690.528
146_Q160_V0.170410.527
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
3froA0.970899.50.346
3s28A0.92499.50.373
2r60A0.947499.50.38
1rzuA0.988399.40.41
2qzsA0.976699.40.413
3c48A0.900699.30.428
2jjmA0.842199.30.442
2iw1A0.818799.20.47
3okpA0.795399.10.487
2gekA0.812999.10.489

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