GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_transf_28 - Glycosyltransferase family 28 N-terminal domain
Pfam: PF03033 (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: 139
Sequences: 8151
Seq/Len: 58.64
HH_delta: 0.279 (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
30_R49_V0.994623.108
21_A24_R0.982573.071
3_I19_A0.981713.068
21_A25_R0.898142.807
106_A124_G0.74922.341
89_P119_Q0.693792.168
38_R42_E0.614451.920
28_E47_E0.61141.911
10_G14_P0.595931.862
11_H107_A0.58611.832
9_R13_Y0.565051.766
80_A84_L0.544041.700
104_I117_A0.53451.670
84_L112_A0.516741.615
117_A124_G0.509281.592
106_A113_A0.503221.573
3_I15_F0.490831.534
92_V107_A0.472781.478
105_I109_L0.465121.454
19_A46_L0.452811.415
22_L27_H0.444781.390
33_T37_F0.441811.381
104_I122_I0.440551.377
23_R46_L0.439391.373
20_R23_R0.439311.373
23_R29_V0.437661.368
16_L20_R0.435591.361
40_R43_A0.429671.343
17_A21_A0.427151.335
38_R48_F0.426771.334
20_R46_L0.423651.324
80_A112_A0.420241.313
2_L32_A0.417311.304
35_P50_P0.406991.272
3_I22_L0.403321.260
30_R47_E0.394651.233
79_E82_R0.393041.228
114_A124_G0.392631.227
10_G16_L0.386821.209
2_L84_L0.386541.208
108_P126_A0.379561.186
3_I105_I0.374361.170
81_M85_A0.371791.162
15_F31_L0.369741.155
103_V125_V0.367291.148
108_P111_F0.364021.138
22_L26_G0.363251.135
93_V119_Q0.361831.131
84_L87_F0.361071.128
116_V120_L0.360681.127
30_R101_D0.360611.127
65_A68_R0.356721.115
27_H102_D0.355321.110
7_G11_H0.353471.105
78_E82_R0.350571.096
5_T15_F0.342151.069
39_E42_E0.339181.060
90_D94_A0.339141.060
36_D40_R0.334761.046
12_V37_F0.334321.045
17_A20_R0.332831.040
64_L68_R0.332111.038
82_R86_R0.330081.032
30_R87_F0.328411.026
22_L29_V0.324841.015
63_P66_N0.32451.014
93_V97_G0.323621.011
52_P79_E0.323081.010
93_V96_G0.322241.007
27_H30_R0.319610.999
35_P39_E0.315720.987
114_A118_E0.313480.980
113_A124_G0.311950.975
94_A97_G0.311510.974
66_N69_R0.309990.969
37_F40_R0.309840.968
81_M109_L0.305020.953
85_A110_A0.300880.940
94_A98_Y0.300410.939
15_F127_N0.296250.926
118_E124_G0.290460.908
30_R99_V0.290140.907
10_G13_Y0.289740.905
33_T48_F0.289390.904
8_T11_H0.286760.896
20_R44_A0.284630.890
14_P17_A0.284440.889
60_S63_P0.282980.884
29_V46_L0.282670.883
107_A129_L0.278810.871
82_R85_A0.278380.870
90_D93_V0.275460.861
87_F90_D0.275380.861
33_T38_R0.275250.860
12_V15_F0.273190.854
89_P96_G0.271430.848
102_D105_I0.269620.843
108_P128_R0.269450.842
106_A114_A0.266530.833
60_S65_A0.261980.819
38_R41_V0.261790.818
63_P67_L0.260690.815
13_Y17_A0.259650.811
2_L30_R0.259620.811
78_E81_M0.258950.809
49_V94_A0.25870.808
73_L76_G0.258610.808
26_G29_V0.257480.805
85_A89_P0.255030.797
47_E50_P0.254670.796
83_I86_R0.253790.793
42_E45_G0.251150.785
56_R60_S0.251120.785
99_V102_D0.250190.782
8_T107_A0.248550.777
81_M110_A0.247920.775
91_L96_G0.247490.773
79_E83_I0.247230.773
53_G56_R0.245340.767
6_G126_A0.244690.765
101_D126_A0.244090.763
18_L27_H0.243350.761
104_I114_A0.241140.754
86_R90_D0.237950.744
31_L46_L0.237360.742
94_A100_A0.237040.741
35_P38_R0.233750.731
97_G100_A0.233660.730
18_L22_L0.232420.726
125_V128_R0.232150.726
63_P68_R0.229050.716
93_V120_L0.22890.715
31_L106_A0.227590.711
11_H14_P0.227010.709
117_A122_I0.225640.705
11_H105_I0.225570.705
2_L31_L0.224810.703
51_I54_D0.224760.702
78_E109_L0.224290.701
9_R15_F0.2240.700
93_V116_V0.22350.698
34_P37_F0.222820.696
108_P114_A0.221820.693
12_V16_L0.221270.692
91_L94_A0.220990.691
8_T14_P0.220820.690
23_R26_G0.220550.689
31_L41_V0.220340.689
83_I87_F0.220190.688
23_R116_V0.219310.685
67_L70_L0.218850.684
12_V41_V0.216920.678
9_R37_F0.215040.672
23_R28_E0.214890.672
34_P52_P0.212390.664
4_A113_A0.211620.661
15_F108_P0.211540.661
81_M86_R0.210940.659
84_L89_P0.210860.659
20_R24_R0.21010.657
12_V19_A0.20970.655
41_V44_A0.209620.655
36_D39_E0.209240.654
33_T36_D0.20840.651
70_L73_L0.208180.651
47_E99_V0.206820.646
35_P52_P0.206560.646
15_F107_A0.205450.642
39_E43_A0.205170.641
77_L80_A0.204060.638
89_P92_V0.203110.635
5_T31_L0.201960.631
85_A119_Q0.201780.631
7_G14_P0.20110.628
14_P127_N0.200960.628
3_I18_L0.200690.627
59_R63_P0.200020.625
12_V31_L0.199580.624
56_R63_P0.199390.623
58_P67_L0.199380.623
13_Y40_R0.198030.619
19_A31_L0.197710.618
89_P93_V0.19690.615
104_I124_G0.196310.614
84_L92_V0.196210.613
12_V33_T0.195590.611
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
2pq6A0.956899.60.279
2vchA0.942499.60.312
3hbfA0.956899.60.312
4amgA0.992899.60.315
2acvA0.935399.50.328
2iyaA0.949699.50.332
2c1xA0.935399.50.357
1iirA0.928199.50.359
3rscA0.956899.50.365
3ia7A0.956899.50.365

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