GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glycos_transf_4 - Glycosyl transferase family 4
Pfam: PF00953 (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. )
Length: 159
Sequences: 3165
Seq/Len: 19.91
HH_delta: 0.93 (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
24_S27_L0.794983.176
117_C154_L0.726622.902
10_L35_A0.66932.673
102_A118_L0.650732.599
8_L146_F0.628782.512
116_L150_L0.518552.071
7_A149_F0.505962.021
91_A124_L0.50372.012
95_I121_A0.492371.967
21_K24_S0.463611.852
99_L121_A0.443651.772
28_R145_L0.440311.759
33_L70_V0.432171.726
17_L21_K0.415741.661
14_I31_L0.413451.652
16_L20_L0.411821.645
91_A128_L0.411211.643
73_I152_A0.410461.640
39_L153_V0.401631.604
80_F94_S0.400181.599
72_W76_F0.396731.585
102_A117_C0.396041.582
28_R32_Q0.394191.575
91_A95_I0.391641.564
63_W67_I0.385491.540
87_D134_P0.384051.534
120_L150_L0.382111.526
94_S98_L0.371441.484
29_L32_Q0.366011.462
33_L37_L0.3631.450
7_A39_L0.358551.432
11_I149_F0.352561.408
120_L147_L0.345281.379
98_L151_L0.340921.362
83_M93_V0.33751.348
73_I153_V0.336791.345
81_N141_D0.336721.345
119_A122_G0.333861.334
69_T156_I0.331541.324
6_L10_L0.330441.320
64_L67_I0.328891.314
12_G142_S0.328871.314
37_L41_F0.322541.288
94_S147_L0.320681.281
40_V70_V0.31431.255
28_R31_L0.309421.236
91_A139_M0.308321.232
40_V66_I0.306921.226
138_F141_D0.305211.219
4_L113_L0.303721.213
7_A153_V0.303381.212
98_L124_L0.301781.205
128_L132_F0.297051.187
7_A35_A0.296911.186
13_L17_L0.293581.173
124_L147_L0.291691.165
98_L120_L0.29161.165
106_Y114_A0.286611.145
40_V69_T0.284611.137
122_G126_G0.283181.131
80_F90_A0.281851.126
8_L150_L0.280321.120
78_N81_N0.275821.102
75_G79_A0.275121.099
28_R82_F0.273951.094
32_Q77_I0.272691.089
36_A74_V0.270911.082
97_A151_L0.269341.076
98_L121_A0.268751.074
77_I149_F0.267241.067
32_Q78_N0.26441.056
98_L117_C0.262841.050
14_I35_A0.262791.050
24_S28_R0.261881.046
102_A114_A0.257831.030
15_G145_L0.257431.028
49_L52_P0.255341.020
95_I125_L0.25441.016
105_A114_A0.254241.016
16_L142_S0.252781.010
36_A73_I0.250281.000
91_A127_F0.249740.998
12_G146_F0.248650.993
39_L73_I0.247350.988
61_G64_L0.24720.987
36_A70_V0.247140.987
84_D139_M0.246380.984
6_L38_L0.245710.981
72_W155_A0.245110.979
51_I54_G0.244870.978
76_F155_A0.241640.965
26_R30_L0.238470.953
89_L92_G0.236510.945
77_I145_L0.236010.943
84_D143_G0.234650.937
116_L154_L0.234330.936
84_D90_A0.233910.934
127_F139_M0.232280.928
92_G96_I0.231790.926
99_L103_V0.229470.917
146_F150_L0.228250.912
101_L155_A0.227420.908
28_R77_I0.226340.904
65_A69_T0.22570.902
3_L42_L0.222850.890
105_A113_L0.219620.877
11_I146_F0.219560.877
80_F97_A0.218510.873
102_A106_Y0.21770.870
9_L13_L0.217160.867
71_L75_G0.216910.866
90_A147_L0.216910.866
87_D139_M0.21690.866
59_N64_L0.215460.861
8_L116_L0.213790.854
29_L33_L0.212770.850
37_L70_V0.212550.849
126_G130_F0.212550.849
36_A40_V0.211880.846
95_I124_L0.211510.845
125_L129_I0.210330.840
23_L31_L0.210280.840
28_R141_D0.209940.839
117_C150_L0.209330.836
96_I100_A0.208340.832
81_N138_F0.207970.831
68_L72_W0.207960.831
84_D144_S0.20690.826
32_Q145_L0.206480.825
132_F136_K0.206350.824
59_N63_W0.206170.824
27_L30_L0.205570.821
17_L23_L0.204220.816
4_L150_L0.203710.814
94_S124_L0.203080.811
90_A139_M0.202460.809
12_G16_L0.202130.807
11_I14_I0.19940.796
33_L74_V0.197320.788
101_L117_C0.195510.781
129_I132_F0.19390.775
83_M89_L0.193750.774
140_G143_G0.193730.774
69_T73_I0.193690.774
32_Q74_V0.192890.770
102_A121_A0.192340.768
94_S151_L0.192090.767
84_D141_D0.19190.767
18_D87_D0.191780.766
102_A105_A0.191740.766
29_L74_V0.191290.764
139_M144_S0.190310.760
61_G67_I0.189870.758
139_M143_G0.188110.751
49_L54_G0.187210.748
51_I56_G0.187050.747
37_L66_I0.186520.745
15_G142_S0.185210.740
140_G148_G0.184550.737
48_S59_N0.18420.736
130_F136_K0.183820.734
129_I136_K0.18360.733
45_G65_A0.183550.733
4_L153_V0.183260.732
47_T51_I0.182520.729
10_L14_I0.182180.728
90_A127_F0.181280.724
78_N141_D0.180820.722
36_A49_L0.180610.721
47_T107_L0.180530.721
41_F66_I0.178340.712
28_R142_S0.178220.712
11_I31_L0.178070.711
38_L42_L0.177860.710
17_L20_L0.177790.710
11_I36_A0.177720.710
32_Q144_S0.177070.707
39_L43_G0.1770.707
14_I145_L0.175390.701
131_N138_F0.17440.697
18_D135_A0.174230.696
70_V97_A0.174110.695
76_F152_A0.173810.694
11_I77_I0.173770.694
72_W152_A0.173430.693
127_F143_G0.173160.692
118_L122_G0.172920.691
121_A124_L0.170970.683
110_N113_L0.169650.678
11_I35_A0.169470.677
84_D87_D0.169260.676
10_L31_L0.168840.674
101_L104_I0.168390.673
80_F86_I0.168220.672
87_D135_A0.167660.670
39_L136_K0.16750.669
126_G129_I0.167390.669
29_L70_V0.167290.668
113_L157_L0.167090.667
80_F151_L0.165880.663
92_G95_I0.165630.662
25_P82_F0.165230.660
18_D145_L0.164640.658
4_L8_L0.163840.654
82_F145_L0.162640.650
70_V74_V0.162590.649
47_T59_N0.162340.648
74_V78_N0.162040.647
21_K27_L0.161370.645
11_I32_Q0.160360.641
32_Q139_M0.160250.640
86_I89_L0.159230.636
84_D127_F0.158870.635
87_D145_L0.158510.633
115_I119_A0.156750.626
95_I99_L0.156070.623
135_A144_S0.155210.620
73_I100_A0.155190.620
149_F153_V0.154720.618
87_D131_N0.154610.618
85_G138_F0.154050.615
30_L41_F0.153690.614
67_I70_V0.153410.613
93_V97_A0.152760.610
143_G147_L0.15220.608
57_I109_G0.152110.608
18_D81_N0.15190.607
98_L150_L0.151570.605
90_A98_L0.150650.602
22_G101_L0.149470.597
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
2ls4A0.163515.60.93
4h44B0.36482.30.951
1vf5B0.38992.10.952
1xrdA0.32081.50.956
1orqC0.35221.30.957
1btqA0.10691.20.959
3s79A0.42770.70.963
3ldcA0.33330.60.966
1pp9C0.49060.50.967
3hfeA0.12580.50.967
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